@Override protected EvidenceType retrieveEvidenceType(String id) { return parent.getEvidenceType(id); }
public EvidenceType safeFetchEvidenceType(String id) { EvidenceType et = metaData.getEvidenceType(id); if (et == null) { et = metaData.getFactory().createEvidenceType(id); } return et; }
protected static EvidenceType createEvidence(ONDEXGraphMetaData meta, String type) throws NullValueException, EmptyStringException{ EvidenceType evidence = meta.getEvidenceType(type); if(evidence == null)evidence = meta.getFactory().createEvidenceType(type); return evidence; }
protected static EvidenceType createEvidence(ONDEXGraphMetaData meta, String type) throws NullValueException, EmptyStringException{ EvidenceType evidence = meta.getEvidenceType(type); if(evidence == null)evidence = meta.getFactory().createEvidenceType(type); return evidence; }
/** * fetches the required metadata or throws a respective runtime * exception if it doesn't exist. * * @param id the id of the metadata object. */ public EvidenceType requireEvidenceType(String id) throws EvidenceTypeMissingException { EvidenceType e = graph.getMetaData().getEvidenceType(id); if (e == null) throw new EvidenceTypeMissingException("Evidence Type " + id + " missing"); else return e; }
/** * fetches the required metadata or throws a respective runtime * exception if it doesn't exist. * * @param id the id of the metadata object. */ public EvidenceType requireEvidenceType(String id) throws EvidenceTypeMissingException { EvidenceType e = graph.getMetaData().getEvidenceType(id); if (e == null) throw new EvidenceTypeMissingException("Evidence Type " + id + " missing"); else return e; }
/** * fetches the required metadata or throws a respective runtime * exception if it doesn't exist. * * @param id the id of the metadata object. */ public EvidenceType requireEvidenceType(String id) throws EvidenceTypeMissingException { EvidenceType e = graph.getMetaData().getEvidenceType(id); if (e == null) throw new EvidenceTypeMissingException("Evidence Type " + id + " missing"); else return e; }
/** * fetches the required metadata or throws a respective runtime * exception if it doesn't exist. * * @param id the id of the metadata object. */ public EvidenceType requireEvidenceType(String id) throws EvidenceTypeMissingException { EvidenceType e = graph.getMetaData().getEvidenceType(id); if (e == null) throw new EvidenceTypeMissingException("Evidence Type " + id + " missing"); else return e; }
/** * Get evidence type * * @param graph * @param type * @return */ public static EvidenceType createEvidence(final ONDEXGraph graph, final String type) { final ONDEXGraphMetaData meta = graph.getMetaData(); EvidenceType evidence = meta.getEvidenceType(type); if (evidence == null) evidence = meta.getFactory().createEvidenceType(type); return evidence; }
/** * Get evidence type * * @param graph * @param type * @return */ public static EvidenceType createEvidence(final ONDEXGraph graph, final String type) { final ONDEXGraphMetaData meta = graph.getMetaData(); EvidenceType evidence = meta.getEvidenceType(type); if (evidence == null) evidence = meta.getFactory().createEvidenceType(type); return evidence; }
private EvidenceType getEvType(ONDEXGraph aog, String str) { EvidenceType ev = aog.getMetaData().getEvidenceType(str); if (ev == null) { ev = aog.getMetaData().getFactory().createEvidenceType(str); } return ev; }
public Blast(String blastDir, String pfamPfad, String tmpDir, String evalue, String bitscore, String hmmThreshold, ONDEXGraph graph, AttributeName seqAtt, ConceptClass conceptType) { super(blastDir, pfamPfad, tmpDir, evalue, bitscore, hmmThreshold, graph, seqAtt, conceptType); this.ccPfam = graph.getMetaData().getConceptClass(MetaData.CC_Pfam); this.dataSourcePfam = graph.getMetaData().getDataSource( MetaData.CV_PFAM); this.blast = graph.getMetaData().getEvidenceType(EV_BLAST); }
public Decypher(String programDir, String pfamPfad, String tmpDir, String evalue, String bitscore, String hmmThreshold, ONDEXGraph graph, AttributeName seqAtt, ConceptClass conceptType) { super(programDir, pfamPfad, tmpDir, evalue, bitscore, hmmThreshold, graph, seqAtt, conceptType); this.hmmer = graph.getMetaData().getEvidenceType(EV_HMMER); this.ccPfam = graph.getMetaData().getConceptClass( MetaData.CC_Pfam); this.dataSourcePfam = graph.getMetaData().getDataSource(MetaData.CV_PFAM); }
private EvidenceType getIMPDEvidenceType() throws InvalidPluginArgumentException{ EvidenceType evidenceType = graph.getMetaData().getEvidenceType("IMPD");; if (evidenceType != null) { return evidenceType; } return graph.getMetaData().createEvidenceType("IMPD", ((String) args.getUniqueValue(IMPD_FULLNAME_ARG)), ((String) args.getUniqueValue(IMPD_DESCRIPTION_ARG))); }
public Hmmer(String blastDir, String pfamPfad, String tmpDir, String evalue, String bitscore, String hmmThreshold, ONDEXGraph graph, AttributeName seqAtt, ConceptClass conceptType) { super(blastDir, pfamPfad, tmpDir, evalue, bitscore, hmmThreshold, graph, seqAtt, conceptType); this.ccPfam = graph.getMetaData().getConceptClass( MetaData.CC_Pfam); this.dataSourcePfam = graph.getMetaData().getDataSource(MetaData.CV_PFAM); this.hmmer = graph.getMetaData().getEvidenceType(EV_HMMER); }
public static void initialiseMetaData(ONDEXGraph g) { graph = g; ONDEXGraphMetaData metaData = graph.getMetaData(); dataSource = metaData.getFactory().createDataSource("BCSDB", "bacterial carbohydrate structure database"); cc = metaData.getConceptClass("Taxon"); et = metaData.getEvidenceType("IMPD"); external = metaData.getDataSource("TX"); // as used by NCBI Taxonomy parser taxidAttributeName = metaData.getAttributeName("TAXID"); }
public static void initialiseMetaData(ONDEXGraph g) { graph = g; ONDEXGraphMetaData metaData = graph.getMetaData(); // required metadata for a publication dataSource = metaData.getFactory().createDataSource("OGLYCBASE", "o-linked glycoprotein database"); nlm = metaData.getDataSource("NLM"); cc = metaData.getConceptClass("Publication"); // see entries of et = metaData.getEvidenceType("IMPD"); // Attributes for publication authorsAttributeName = metaData.getAttributeName("AUTHORS"); citationAttributeName = metaData.getAttributeName("JOURNAL_REF"); yearPublishedAttributeName = metaData.getAttributeName("YEAR"); }
/** * initialise Ondex meta-data */ private void initMetaData() { // basic concept meta data dsCHEMBL = graph.getMetaData().getDataSource(DS_CHEMBL); dsVO = graph.getMetaData().getDataSource(DS_VO); ccComp = graph.getMetaData().getConceptClass(CC_COMP); ccThing = graph.getMetaData().getConceptClass(CC_THING); evidencetype = graph.getMetaData().getEvidenceType(ET_IMPD); rtIsa = graph.getMetaData().getRelationType(RT_ISA); }
/** * @param graph */ public ProteinTransformer(ONDEXGraph graph) { this.graph = graph; pdb = graph.getMetaData().getFactory().createAttributeName( "Protein3dStructure", Protein3dStructure.class); ccProtein3DStructure = graph.getMetaData().getConceptClass( MetaData.CC_Protein3DStructure); dataSourcePDB = graph.getMetaData().getDataSource(MetaData.CV_PDB); dataSourceUniProt = graph.getMetaData().getDataSource(MetaData.CV_UniProt); dataSourceGenBank = graph.getMetaData().getDataSource(MetaData.CV_GenBank); etIMPD = graph.getMetaData().getEvidenceType("IMPD"); }
public static void initialiseMetaData(ONDEXGraph g) { graph = g; ONDEXGraphMetaData metaData = graph.getMetaData(); dataSource = metaData.getFactory().createDataSource("BCSDB", "bacterial carbohydrate structure database"); ccsd = metaData.getDataSource("CCSD"); cc = metaData.getConceptClass("Comp"); et = metaData.getEvidenceType("IMPD"); linearStructureAttributeName = metaData.getFactory().createAttributeName("linearBCSDB","structure in BCSDB linear format",String.class); structureTypeAttributeName = metaData.getFactory().createAttributeName("typeBCSDB","structure type according to BCSDB classification",String.class); molecularMassAttributeName = metaData.getFactory().createAttributeName("molmass","molecular mass",String.class); aglyconInfoAttributeName = metaData.getFactory().createAttributeName("alglyconinfo","info about biochemical entity to which glycan is bound",String.class); molecularFormulaAttributeName = metaData.getFactory().createAttributeName("molformula","molecular formula",String.class); trivialNameAttributeName = metaData.getFactory().createAttributeName("trivialname","trivial name",String.class); }