/** * 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; } }
for (final TMHMMSignature tmhmmSignature : TMHMMSignature.values()) { boolean found = false; 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; Signature.Builder builder = new Signature.Builder(tmhmmSignature.getAccession()); final Signature signature = builder .description(tmhmmSignature.getShortDesc())
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); }
/** * 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; } }