/** * 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 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; } }
/** * This is rather badly named as there is nothing to parse... * <p/> * However, the point is that it returns a SignatureLibraryRelease for SignalP, * containing two Signature objects called "SignalP-TM" and "SignalP-noTM". * * @return a complete SignatureLibraryRelease object */ @Override public SignatureLibraryRelease parse() throws IOException { final SignatureLibraryRelease release = new SignatureLibraryRelease( this.getSignatureLibrary(), this.getReleaseVersionNumber()); final Model model1 = new Model(SIGNALP_SIGNATURE_NAME1, SIGNALP_SIGNATURE_NAME1, null, null); final Signature.Builder builder1 = new Signature.Builder(SIGNALP_SIGNATURE_NAME1); final Signature signature1 = builder1.name(SIGNALP_SIGNATURE_NAME1).model(model1).signatureLibraryRelease(release).build(); release.addSignature(signature1); final Model model2 = new Model(SIGNALP_SIGNATURE_NAME2, SIGNALP_SIGNATURE_NAME2, null, null); final Signature.Builder builder2 = new Signature.Builder(SIGNALP_SIGNATURE_NAME2); final Signature signature2 = builder2.name(SIGNALP_SIGNATURE_NAME2).model(model2).signatureLibraryRelease(release).build(); release.addSignature(signature2); return release; }
/** * This is rather badly named as there is nothing to parse... * <p/> * however, the point is that it returns a SignatureLibraryRelease for Coils, * containing one big fat Signature called "Coil". * * @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(COILS_SIGNATURE_NAME, COILS_SIGNATURE_NAME, null); final Signature.Builder builder = new Signature.Builder(COILS_SIGNATURE_NAME); final Signature signature = builder.name(COILS_SIGNATURE_NAME) .signatureLibraryRelease(release) .model(model) .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; } }
/** * This is rather badly named as there is nothing to parse... * <p/> * However, the point is that it returns a SignatureLibraryRelease for SignalP, * containing two Signature objects called "SignalP-TM" and "SignalP-noTM". * * @return a complete SignatureLibraryRelease object */ @Override public SignatureLibraryRelease parse() throws IOException { final SignatureLibraryRelease release = new SignatureLibraryRelease( this.getSignatureLibrary(), this.getReleaseVersionNumber()); final Model model1 = new Model(SIGNALP_SIGNATURE_NAME1, SIGNALP_SIGNATURE_NAME1, null); final Signature.Builder builder1 = new Signature.Builder(SIGNALP_SIGNATURE_NAME1); final Signature signature1 = builder1.name(SIGNALP_SIGNATURE_NAME1).model(model1).signatureLibraryRelease(release).build(); release.addSignature(signature1); final Model model2 = new Model(SIGNALP_SIGNATURE_NAME2, SIGNALP_SIGNATURE_NAME2, null); final Signature.Builder builder2 = new Signature.Builder(SIGNALP_SIGNATURE_NAME2); final Signature signature2 = builder2.name(SIGNALP_SIGNATURE_NAME2).model(model2).signatureLibraryRelease(release).build(); release.addSignature(signature2); return release; }