@Override public String toString() { return new ToStringBuilder(this) .append("accession", accession) .append("name", name) .append("description", getDescription()) .append("definition", getDefinition()) .append("signature-ac", (signature == null ? null : signature.getAccession())) .append("md5", md5) .toString(); }
/** * Utility method to check that a given Signature is valid. * This method is light-weight - it is NOT checking that the * SignatureLibrary associated with the Signature is of the correct * type. * * @param signature being checked. * @return true of the Signature accession and name are recognised. */ public static boolean isValidSignature(Signature signature) { for (TMHMMSignature type : TMHMMSignature.values()) { if (type.getAccession().equals(signature.getAccession())) { return true; } } return false; } }
/** * Utility method to check that a given Signature is valid. * This method is light-weight - it is NOT checking that the * SignatureLibrary associated with the Signature is of the correct * type. * * @param signature being checked. * @return true of the Signature accession and name are recognised. */ public static boolean isValidSignature(Signature signature) { for (PhobiusFeatureType type : PhobiusFeatureType.values()) { if (type.getAccession().equals(signature.getAccession()) && type.getName().equals(signature.getName())) { return true; } } return false; }
@Transactional public void persist(Set<TMHMMProtein> proteins) { //load TMHMM signatures from database and map them by accession Map<String, Signature> sigAccToDbSignatureMap = loadPersistedSignatures(); //load proteins from database and map them by protein identifier Map<String, Protein> proteinIdToProteinMap = getProteinIdToProteinMap(proteins); for (TMHMMProtein protein : proteins) { final Protein persistentProtein = proteinIdToProteinMap.get(protein.getProteinIdentifier()); if (persistentProtein == null) { throw new IllegalArgumentException("Attempting to store a TMHMM match for a protein with id " + protein.getProteinIdentifier() + ", however this does not exist in the database."); } for (TMHMMMatch match : protein.getMatches()) { final Signature signature = sigAccToDbSignatureMap.get(match.getSignature().getAccession()); TMHMMMatch newMatch = new TMHMMMatch(signature, signature.getAccession(), match.getLocations()); persistentProtein.addMatch(newMatch); entityManager.persist(newMatch); } } }
String signatureAcc = tmhmmSignature.getAccession(); for (final Signature retrievedSignature : retrievedSignatures) { if (tmhmmSignature.getAccession().equals(retrievedSignature.getAccession()) && tmhmmSignature.getAccession().equals(retrievedSignature.getAccession())) { signatures.put(signatureAcc, retrievedSignature); found = true;
/** * Persists a set of ParseCoilsMatch objects as filtered matches: * there is no filtering step with Coils. * * @param coilsMatches being a Set of ParseCoilsMatch objects to be persisted. */ @Transactional public void persist(Set<ParseCoilsMatch> coilsMatches) { Signature coilsSignature = loadPersistedSignature(); Map<String, Protein> proteinIdToProteinMap = getProteinIdToProteinMap(coilsMatches); for (ParseCoilsMatch parseCoilsMatch : coilsMatches) { final Protein persistentProtein = proteinIdToProteinMap.get(parseCoilsMatch.getProteinDatabaseIdentifier()); if (persistentProtein == null) { throw new IllegalArgumentException("Attempting to store a Coils match for a protein with id " + parseCoilsMatch.getProteinDatabaseIdentifier() + ", however this does not exist in the database."); } Set<CoilsMatch.CoilsLocation> locations = Collections.singleton( new CoilsMatch.CoilsLocation(parseCoilsMatch.getStartCoordinate(), parseCoilsMatch.getEndCoordinate()) ); CoilsMatch match = new CoilsMatch(coilsSignature, coilsSignature.getAccession(), locations); persistentProtein.addMatch(match); entityManager.persist(match); } }
final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName();
for (Match match : matches) { final Signature signature = match.getSignature(); final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = analysisI5toI4.get(signatureLibrary.getName());
for (Match match : matches) { final Signature signature = match.getSignature(); final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName();
new PhobiusMatch.PhobiusLocation(feature.getStart(), feature.getStop()) ); PhobiusMatch match = new PhobiusMatch(signature, signature.getAccession(), locations); persistentProtein.addMatch(match); entityManager.persist(match);
for (Match match : matches) { final Signature signature = match.getSignature(); final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = analysisI5toI4.get(signatureLibrary.getName());
final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName();
if (type.getName().equals(retrievedSignature.getName()) && type.getAccession().equals(retrievedSignature.getAccession()) && type.getDescription().equals(retrievedSignature.getDescription())) {
final String signatureAc = signature.getAccession(); final String signatureModels = match.getSignatureModels(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary();
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); }
for (Match match : matches) { final Signature signature = match.getSignature(); final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName();
for (Match match : matches) { final Signature signature = match.getSignature(); final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName();