public SmallMolecule createSmallMolecule(String chebiId, String shortLabel) { CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.SMALL_MOLECULE_MI_REF, CvInteractorType.SMALL_MOLECULE); SmallMolecule smallMolecule = new SmallMoleculeImpl(shortLabel, getInstitution(), intType); InteractorXref idXref = createIdentityXrefChebi(smallMolecule, chebiId); smallMolecule.addXref(idXref); InteractorAlias alias = createAliasGeneName(smallMolecule, shortLabel.toUpperCase()); smallMolecule.addAlias(alias); return smallMolecule; }
public NucleicAcid createNucleicAcid( String emblGenbankDdbjId, BioSource biosource, String shortlabel ) { CvInteractorType type = createCvObject(CvInteractorType.class, CvInteractorType.NUCLEIC_ACID_MI_REF, CvInteractorType.NUCLEIC_ACID); NucleicAcid na = new NucleicAcidImpl(getInstitution(), biosource, shortlabel, type); InteractorXref idXref = createIdentityXrefEmblGenbankDdbj(na, emblGenbankDdbjId); na.addXref(idXref); InteractorAlias alias = createAliasGeneName(na, shortlabel.toUpperCase()); na.addAlias(alias); return na; }
public SmallMolecule createSmallMolecule(String chebiId, String shortLabel) { CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.SMALL_MOLECULE_MI_REF, CvInteractorType.SMALL_MOLECULE); SmallMolecule smallMolecule = new SmallMoleculeImpl(shortLabel, getInstitution(), intType); InteractorXref idXref = createIdentityXrefChebi(smallMolecule, chebiId); smallMolecule.addXref(idXref); InteractorAlias alias = createAliasGeneName(smallMolecule, shortLabel.toUpperCase()); smallMolecule.addAlias(alias); return smallMolecule; }
public NucleicAcid createNucleicAcid( String emblGenbankDdbjId, BioSource biosource, String shortlabel ) { CvInteractorType type = createCvObject(CvInteractorType.class, CvInteractorType.NUCLEIC_ACID_MI_REF, CvInteractorType.NUCLEIC_ACID); NucleicAcid na = new NucleicAcidImpl(getInstitution(), biosource, shortlabel, type); InteractorXref idXref = createIdentityXrefEmblGenbankDdbj(na, emblGenbankDdbjId); na.addXref(idXref); InteractorAlias alias = createAliasGeneName(na, shortlabel.toUpperCase()); na.addAlias(alias); return na; }
public Protein createProtein(String uniprotId, String shortLabel, BioSource bioSource) { CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.PROTEIN_MI_REF, CvInteractorType.PROTEIN); Protein protein = new ProteinImpl(getInstitution(), bioSource, shortLabel, intType); InteractorXref idXref = createIdentityXrefUniprot(protein, uniprotId); protein.addXref(idXref); InteractorAlias alias = createAliasGeneName(protein, shortLabel.toUpperCase()); protein.addAlias(alias); String sequence = randomPeptideSequence(); String crc64 = Crc64.getCrc64(sequence); protein.setSequence(sequence); protein.setCrc64(crc64); return protein; }
private Protein createProtein(String uniprotId, String shortLabel, String geneName, BioSource bioSource, CvInteractorType intType) { Protein protein = new ProteinImpl(getInstitution(), bioSource, shortLabel, intType); InteractorXref idXref = createIdentityXrefUniprot(protein, uniprotId); protein.addXref(idXref); InteractorAlias alias = createAliasGeneName(protein, geneName); protein.addAlias(alias); String sequence = randomPeptideSequence(); String crc64 = Crc64.getCrc64(sequence); protein.setSequence(sequence); protein.setCrc64(crc64); return protein; }
private Protein createProtein(String uniprotId, String shortLabel, String geneName, BioSource bioSource, CvInteractorType intType) { Protein protein = new ProteinImpl(getInstitution(), bioSource, shortLabel, intType); InteractorXref idXref = createIdentityXrefUniprot(protein, uniprotId); protein.addXref(idXref); InteractorAlias alias = createAliasGeneName(protein, geneName); protein.addAlias(alias); String sequence = randomPeptideSequence(); String crc64 = Crc64.getCrc64(sequence); protein.setSequence(sequence); protein.setCrc64(crc64); return protein; }