/** * This method retrieves the persisted Signatures for all of the * PhobiusFeatureTypes. If any of them they do not exist in the database, this * method creates the required Signatures. * * @return the persisted Signatures for all of the * PhobiusFeatureTypes. */ private Signature loadPersistedSignature() { // Check first to see if the SignatureLibraryRelease exists. If not, create it. final SignatureLibraryRelease release = loadCoilsRelease(); // Now try to retrieve the Signatures for Phobius. If they do not exist, create them. final Query query = entityManager.createQuery("select s from Signature s where s.signatureLibraryRelease = :release"); query.setParameter("release", release); @SuppressWarnings("unchecked") List<Signature> retrievedSignatures = query.getResultList(); if (retrievedSignatures.size() == 0) { // The Signature record does not exist yet, so create it. final Signature.Builder builder = new Signature.Builder("Coil"); final Signature signature = builder.name("Coil").signatureLibraryRelease(release).build(); entityManager.persist(signature); return signature; } else if (retrievedSignatures.size() > 1) { // Error detected - more than one Signature record for this release of Coils throw new IllegalStateException("There is more than one Signature record for version " + coilsReleaseVersion + " of Coils in the database."); } else { // return the previously persisted Signature. return retrievedSignatures.get(0); } }
final Signature signature = mobiSignatureBuilder.name("mobidb-lite").signatureLibraryRelease(release).build();
final Signature signature = builder .description(tmhmmSignature.getShortDesc()) .signatureLibraryRelease(release) .build(); entityManager.persist(signature);
.name(type.getName()) .description(type.getDescription()) .signatureLibraryRelease(release) .build(); entityManager.persist(signature);
/** * 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 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; } }
/** * 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); 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; }
/** * 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; } }
/** * 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 Signature.Builder builder = new Signature.Builder(COILS_SIGNATURE_NAME); final Signature signature = builder.name(COILS_SIGNATURE_NAME).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(); 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); } }