/** * @return * @see net.sourceforge.ondex.core.ONDEXAssociable#getSID() */ public long getSID() { return og.getSID(); }
/** * @param origGraph * the original graph to clone from * @param newGraph * the new graph */ public ONDEXGraphCloner(ONDEXGraph origGraph, ONDEXGraph newGraph) { this.origGraph = origGraph; this.newGraph = newGraph; if (origGraph.equals(newGraph)) { throw new IllegalArgumentException( "Illegal argument graph source and clone are identical"); } else if (origGraph.getSID() == newGraph.getSID()) { throw new IllegalArgumentException( "Illegal argument graph source and clone are of the same name"); } createIndex(); }
.get(origGraph.getSID()); if (targetGraphs == null) { targetGraphs = new HashMap<Long, Map<Integer, Integer>>(); indexedClonedConcepts.put(origGraph.getSID(), targetGraphs); .get(newGraph.getSID()); if (conceptIndex == null) { conceptIndex = new HashMap<Integer, Integer>(); targetGraphs.put(newGraph.getSID(), conceptIndex); targetGraphs = indexedClonedRelations.get(origGraph.getSID()); if (targetGraphs == null) { targetGraphs = new HashMap<Long, Map<Integer, Integer>>(); indexedClonedRelations.put(origGraph.getSID(), targetGraphs); .getSID()); if (relationIndex == null) { relationIndex = new HashMap<Integer, Integer>(); targetGraphs.put(newGraph.getSID(), relationIndex);
/** * Clones a concept from the original graph to the new graph * * @param cid * the id of the concept in the original graph * @return the new Concept in the new graph */ public ONDEXConcept cloneConcept(int cid) { ONDEXConcept concept = origGraph.getConcept(cid); if (concept == null) { throw new NullPointerException(cid + " is not found in orginal Graph " + origGraph.getSID()); } return cloneConcept(concept); }
@Override public void associateGraph(ONDEXGraph g) throws AccessDeniedException { if (sid == -1L || sid == g.getSID()) { sid = sg.getSID(); } else { throw new AccessDeniedException("MetaData is already associated to another graph!"); } }
/** * Propagate event e to the right graph listeners. * * @param e * EventType */ private void fireEventOccurred(EventType e) { ONDEXEventHandler.getEventHandlerForSID(g.getSID()) .fireEventOccurred(e); }
ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent("FASTA file missing :"+file, "parseFastaFile(ONDEXGraph graph, String fileName, WriteFastaFile write)")); return; } else if (!file.canRead()) { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent("FASTA file has no read permissions :"+file, "parseFastaFile(ONDEXGraph graph, String fileName, WriteFastaFile write)")); return;
private void writeSynonym(String synonym, String conceptName, ONDEXConcept c) { String check = (String) ValidatorRegistry.validators.get("cvregex").validate(synonym); if (check != null) { DataSource dataSource = aog.getMetaData().getDataSource(check); if (dataSource == null) { if (!reportedMissingCVs.contains(check)) { ONDEXEventHandler.getEventHandlerForSID(aog.getSID()).fireEventOccurred(new DataSourceMissingEvent("DataSource missing => " + check, "")); reportedMissingCVs.add(check); } } else { if (c.getConceptAccession(synonym, dataSource) == null) { c.createConceptAccession(synonym.toUpperCase(), dataSource, false); } } } else { if (!synonym.equalsIgnoreCase(conceptName)) { c.createConceptName(synonym,false); } } }
/** * setups the filters */ private FileFilter setupFilters(Set<ONDEXConcept> concepts, DataSource targetDataSource) { PDBFileNameFilter filter = new PDBFileNameFilter(); for (ONDEXConcept concept : concepts) { for (ConceptAccession accession : concept.getConceptAccessions()) { if (!accession.getElementOf().equals(targetDataSource)) continue; filter.addFileName(accession.getAccession()); } } ONDEXEventHandler.getEventHandlerForSID(graph.getSID()) .fireEventOccurred( new GeneralOutputEvent("found " + filter.fileNames.size() + " pdb references in current graph", Parser.class.toString())); return filter.fileNames.size() == 0 ? new EntDotZFilter() : filter; }
ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent("Directory does not exits: "+sequenceDir, Parser.getCurrentMethodName())); return null; ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent("Gene sequence data missing: with prefix "+dna_file_prefix+" in directory "+ sequenceDir, Parser.getCurrentMethodName())); }else { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new GeneralOutputEvent("Gene sequence data version: "+fileName.substring(dna_file_prefix.length())+" detected", Parser.getCurrentMethodName()));
ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent("Directory does not exits: "+sequenceDir, Parser.getCurrentMethodName())); return null; ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new DataFileMissingEvent("Protein sequence data missing: with prefix \"TAIR7_pep\" in directory " + sequenceDir, Parser.getCurrentMethodName())); }else { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new GeneralOutputEvent("Protein sequence data version: "+fileName.substring("TAIR7_pep".length())+" detected", Parser.getCurrentMethodName()));
public LuceneEnv getIndex(ONDEXGraph graph, String name) {//pluginInit.makeSimplePlugin().getName() long start = System.currentTimeMillis(); fireEventOccurred(new GeneralOutputEvent("Index required by " + name + " starting index", getCurrentMethodName())); String dir = indexedGraphs.get(graph); if (dir != null && new File(dir).exists()) { LuceneEnv lenv = new LuceneEnv(dir, false); lenv.addONDEXListener(logger); lenv.setONDEXGraph(graph); return lenv; } String graphdir = null; if (Config.ondexDir.endsWith(File.separator)) { graphdir = Config.ondexDir + "index" + File.separator + graph.getName() + File.separator + "index"; } else { graphdir = Config.ondexDir + File.separator + "index" + File.separator + graph.getName() + File.separator + "index"; } dir = graphdir + indexCounter; while (new File(dir).exists()) { dir = graphdir + indexCounter; indexCounter++; } LuceneEnv lenv = new LuceneEnv(dir, true); lenv.addONDEXListener(logger); lenv.setONDEXGraph(graph); LuceneRegistry.sid2luceneEnv.put(graph.getSID(), lenv); indexedGraphs.put(graph, dir); fireEventOccurred(new GeneralOutputEvent("Lucene took " + (System.currentTimeMillis() - start) + " msec.", getCurrentMethodName())); return lenv; }
String[] split = o.split(","); if (split.length != 2) ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new WrongParameterEvent("Invalid input for class types - should be two, comma delimited.", "[Transformer - setONDEXGraph]")); ConceptClass from = graph.getMetaData().getConceptClass(split[0]); if (from == null) { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new WrongParameterEvent("Concept class " + split[0] + " is undefined", "[Transformer - setONDEXGraph]")); from = createCC(graph, split[0]); ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new WrongParameterEvent("Concept class " + split[1] + " is undefined", "[Transformer - setONDEXGraph]")); to = createCC(graph, split[1]); ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new GeneralOutputEvent("Transformer error - graph inconsistency detected(Relatoin number)! Before: " + rCount + " after: " + graph.getRelations().size(), "[Transformer - setONDEXGraph]")); if (cCount != graph.getConcepts().size()) ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new GeneralOutputEvent("Transformer error - graph inconsistency detected(Concepts number)! Before: " + cCount + " after: " + graph.getConcepts().size(), "[Transformer - setONDEXGraph]"));
String[] split = o.toString().split(","); if (split.length != 2) ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new WrongParameterEvent("Invalid input for relation typeset(s) - should be two, comma delimited.", "[Transformer - setONDEXGraph]")); RelationType from = graph.getMetaData().getRelationType(split[0]); if (from == null) ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new WrongParameterEvent("Relation type set " + split[0] + " is undefined", "[Transformer - setONDEXGraph]")); RelationType to = graph.getMetaData().getRelationType(split[1]); if (to == null) ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new WrongParameterEvent("Relation type set " + split[1] + " is undefined", "[Transformer - setONDEXGraph]")); if (to != null && from != null) { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new GeneralOutputEvent("Transformer error - graph inconsistency detected(Relatoin number)! Before: " + rCount + " after: " + graph.getRelations().size(), "[Transformer - setONDEXGraph]")); if (cCount != graph.getConcepts().size()) ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new GeneralOutputEvent("Transformer error - graph inconsistency detected(Concepts number)! Before: " + cCount + " after: " + graph.getConcepts().size(), "[Transformer - setONDEXGraph]")); System.err.println("Skipped duplicates: " + dupes);
/** * searchs for all concepts with given DataSource and adds them to the filter * * @param concepts concepts of perhaps a given cv type * @param targetDataSource which should be seached */ private void setupFilters(Set<ONDEXConcept> concepts, DataSource targetDataSource) throws InvalidPluginArgumentException { accessionFilter = new Filter(); if ((Boolean) super.args .getUniqueValue(ArgumentNames.SEARCH_FOR_PFAM_ACCESSION_ARG)) return; for (ONDEXConcept concept : concepts) { for (ConceptAccession accession : concept.getConceptAccessions()) { // accession equals targetCV if (!accession.getElementOf().equals(targetDataSource)) continue; accessionFilter.addAccession(accession.getAccession()); } } ONDEXEventHandler.getEventHandlerForSID(graph.getSID()) .fireEventOccurred( new GeneralOutputEvent("found " + accessionFilter.accessions.size() + " pfam references in current graph", Parser.class.toString())); }
/** * Setup a new OVTK2Viewer. * * @param aog * ONDEXGraph * @param annotations * XML String * @return OVTK2Viewer */ public static OVTK2Viewer initViewer(ONDEXGraph aog, Map<String, String> annotations) { OVTK2Desktop desktop = OVTK2Desktop.getInstance(); ONDEXEventHandler.getEventHandlerForSID(aog.getSID()).addONDEXONDEXListener(OVTK2Desktop.getDesktopResources().getLogger()); OVTK2Viewer viewer = new OVTK2Viewer(aog, annotations); viewer.addInternalFrameListener(desktop); viewer.addVetoableChangeListener(desktop); // for listening to changes in ModalGraphMouse viewer.addItemListener(OVTK2Desktop.getDesktopResources().getToolBar()); desktop.viewers.add(viewer); return viewer; }
private void setupMetaData() throws InvalidPluginArgumentException { eviType_blast = graph.getMetaData().getEvidenceType(EVIDENCE_BLAST); if (eviType_blast == null) { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new EvidenceTypeMissingEvent( RT_HAS_SIMILAR_SEQUENCE, Mapping.getCurrentMethodName())); ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new AttributeNameMissingEvent( RT_HAS_SIMILAR_SEQUENCE, Mapping.getCurrentMethodName())); ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new AttributeNameMissingEvent( ATT_BITSCORE, Mapping.getCurrentMethodName())); RelationType rt = graph.getMetaData().getRelationType(RT_HAS_SIMILAR_SEQUENCE); if (rt == null) { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new RelationTypeMissingEvent( RT_HAS_SIMILAR_SEQUENCE, Mapping.getCurrentMethodName()));
RelationType rt = graph.getMetaData().getRelationType(is_a); if (rt == null) { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new RelationTypeMissingEvent("Missing:", is_a)); RelationType rt = graph.getMetaData().getRelationType(is_p); if (rt == null) { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new RelationTypeMissingEvent("Missing:", is_p));
ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new EvidenceTypeMissingEvent(MetaData.EVIDENCE_BLAST, Mapping.getCurrentMethodName())); ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new AttributeNameMissingEvent(MetaData.ATT_E_VALUE, Mapping.getCurrentMethodName())); ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new AttributeNameMissingEvent(MetaData.ATT_BITSCORE, Mapping.getCurrentMethodName()));