.description(tmhmmSignature.getShortDesc()) .signatureLibraryRelease(release) .build();
final Signature signature = builder .name(type.getName()) .description(type.getDescription()) .signatureLibraryRelease(release) .build();
/** * This is rather badly named as there is nothing to parse... * <p/> * however, the point is that it returns a SignatureLibraryRelease for Phobius, * containing the signatures defined in the PhobiusFeatureType enum. * * @return a complete SignatureLibraryRelease object */ @Override public SignatureLibraryRelease parse() throws IOException { final SignatureLibraryRelease release = new SignatureLibraryRelease( this.getSignatureLibrary(), this.getReleaseVersionNumber()); for (final PhobiusFeatureType type : PhobiusFeatureType.values()) { final Model model = new Model(type.getAccession(), type.getName(), type.getDescription()); final Signature.Builder builder = new Signature.Builder(type.getAccession()); final Signature signature = builder .name(type.getName()) .model(model) .description(type.getDescription()) .signatureLibraryRelease(release) .build(); release.addSignature(signature); } return release; } }
/** * This is rather badly named as there is nothing to parse... * <p/> * however, the point is that it returns a SignatureLibraryRelease for Phobius, * containing the signatures defined in the PhobiusFeatureType enum. * * @return a complete SignatureLibraryRelease object */ @Override public SignatureLibraryRelease parse() throws IOException { final SignatureLibraryRelease release = new SignatureLibraryRelease( this.getSignatureLibrary(), this.getReleaseVersionNumber()); for (final PhobiusFeatureType type : PhobiusFeatureType.values()) { final Signature.Builder builder = new Signature.Builder(type.getAccession()); final Signature signature = builder .name(type.getName()) .description(type.getDescription()) .signatureLibraryRelease(release) .build(); release.addSignature(signature); } return release; } }
/** * This is rather badly named as there is nothing to parse... * <p/> * however, the point is that it returns a SignatureLibraryRelease for MOBIDB, * containing one big fat Signature called "mobidb-lite". * * @return a complete SignatureLibraryRelease object */ @Override public SignatureLibraryRelease parse() throws IOException { final SignatureLibraryRelease release = new SignatureLibraryRelease( this.getSignatureLibrary(), this.getReleaseVersionNumber()); final Model model = new Model(MOBIDB_SIGNATURE_ACCESSION, MOBIDB_SIGNATURE_NAME, MOBIDB_SIGNATURE_DESC); final Signature.Builder builder = new Signature.Builder(MOBIDB_SIGNATURE_ACCESSION); final Signature signature = builder.name(MOBIDB_SIGNATURE_NAME) .description(MOBIDB_SIGNATURE_DESC) .model(model) .signatureLibraryRelease(release).build(); release.addSignature(signature); return release; } }
/** * Returns a SignatureLibraryRelease for TMHMM * containing the signatures defined in the {@link uk.ac.ebi.interpro.scan.model.TMHMMSignature} enum. * * @return a complete SignatureLibraryRelease object */ @Override public SignatureLibraryRelease parse() throws IOException { final SignatureLibraryRelease release = new SignatureLibraryRelease( this.getSignatureLibrary(), this.getReleaseVersionNumber()); for (final TMHMMSignature type : TMHMMSignature.values()) { final Model model = new Model(type.getAccession(), type.getShortDesc(), type.getDescription()); final Signature.Builder builder = new Signature.Builder(type.getAccession()); final Signature signature = builder .description(type.getDescription()) .model(model) .signatureLibraryRelease(release) .build(); release.addSignature(signature); } return release; } }
/** * Returns a SignatureLibraryRelease for TMHMM * containing the signatures defined in the {@link uk.ac.ebi.interpro.scan.model.TMHMMSignature} enum. * * @return a complete SignatureLibraryRelease object */ @Override public SignatureLibraryRelease parse() throws IOException { final SignatureLibraryRelease release = new SignatureLibraryRelease( this.getSignatureLibrary(), this.getReleaseVersionNumber()); for (final TMHMMSignature type : TMHMMSignature.values()) { final Signature.Builder builder = new Signature.Builder(type.getAccession()); final Signature signature = builder .description(type.getDescription()) .signatureLibraryRelease(release) .build(); release.addSignature(signature); } return release; } }
private TMHMMMatch createNewTmhmmMatch(TMHMMSignature prediction, Set<TMHMMMatch.TMHMMLocation> locations) { Signature signature = new Signature.Builder(prediction.getAccession()). description(prediction.getShortDesc()). signatureLibraryRelease(signatureLibraryRelease). build(); return new TMHMMMatch(signature, locations); }
private TMHMMMatch createNewTmhmmMatch(TMHMMSignature prediction, Set<TMHMMMatch.TMHMMLocation> locations) { Signature signature = new Signature.Builder(prediction.getAccession()). description(prediction.getShortDesc()). signatureLibraryRelease(signatureLibraryRelease). build(); String signatureModel = signature.getAccession(); return new TMHMMMatch(signature, signatureModel, locations); }
private TMHMMMatch createNewTmhmmMatch(TMHMMSignature prediction, Set<TMHMMMatch.TMHMMLocation> locations) { Signature signature = new Signature.Builder(prediction.getAccession()). description(prediction.getShortDesc()). signatureLibraryRelease(signatureLibraryRelease). build(); String signatureModel = signature.getAccession(); return new TMHMMMatch(signature, signatureModel, locations); } }
private TMHMMMatch createNewTmhmmMatch(TMHMMSignature prediction, Set<TMHMMMatch.TMHMMLocation> locations) { Signature signature = new Signature.Builder(prediction.getAccession()). description(prediction.getShortDesc()). signatureLibraryRelease(signatureLibraryRelease). build(); return new TMHMMMatch(signature, locations); } }