private void setSignatures(Set<Signature> signatures) { for (Signature s : signatures) { addSignature(s); } }
private void createSignature(final SignatureLibraryRelease release, Map<String, String> kdatFileData, final String sigAcc, final String sigName, final String sigDescription) { if (sigName != null) { // If sigName is null, this is the very first one in the file, so nothing to do. String sigAbstract = (storeAbstract) ? kdatFileData.get(sigAcc) : null; final Set<Model> model = Collections.singleton( new Model(sigAcc, sigName, sigDescription) ); release.addSignature( new Signature(sigAcc, sigName, null, sigDescription, sigAbstract, release, model) ); } }
private void createSignature(final SignatureLibraryRelease release, Map<String, String> kdatFileData, final String sigAcc, final String sigName, final String sigDescription) { if (sigName != null) { // If sigName is null, this is the very first one in the file, so nothing to do. String sigAbstract = (storeAbstract) ? kdatFileData.get(sigAcc) : null; final Set<Model> model = Collections.singleton( new Model(sigAcc, sigName, sigDescription) ); release.addSignature( new Signature(sigAcc, sigName, null, sigDescription, sigAbstract, release, model) ); } }
/** * Creates sub family signatures. * * @throws IOException */ private void createSubFamilySignatures(String dirName, Map<String, String> familyIdFamilyNameMap, SignatureLibraryRelease release) throws IOException { for (Resource modelFile : modelFiles) { File subFamilyDir = new File(modelFile.getFile().getPath() + "/books/" + dirName); if (subFamilyDir.exists() && subFamilyDir.getAbsoluteFile() != null) { //TODO: Implement a file filter for a more memory save implementation String[] children = subFamilyDir.getAbsoluteFile().list(new DirectoryFilenameFilter()); if (children != null) { for (String signatureAcc : children) { signatureAcc = dirName + ":" + signatureAcc; String signatureName = familyIdFamilyNameMap.get(signatureAcc); //Create super family signatures release.addSignature(createSignature(signatureAcc, signatureName, release)); } } else { LOGGER.debug("Either dir does not exist or is not a directory."); } } } }
/** * Method to parse a model file and return a SignatureLibraryRelease. * * @return a complete SignatureLibraryRelease object */ @Override public SignatureLibraryRelease parse() throws IOException { LOGGER.debug("Starting to parse hmm file."); SignatureLibraryRelease release = new SignatureLibraryRelease(library, releaseVersion); for (Resource modelFile : modelFiles) { if (modelFile.exists() && modelFile.getFile() != null) { Map<String, String> familyIdFamilyNameMap = readInPantherFamilyNames(modelFile); if (LOGGER.isDebugEnabled()) { LOGGER.debug("number of panther families: " + familyIdFamilyNameMap.keySet().size()); } Map<String, List<String>> pantherParentChildMap = getPantherParentChildMap(familyIdFamilyNameMap.keySet()); for (String parent : pantherParentChildMap.keySet()) { String signatureAcc = parent; String signatureName = familyIdFamilyNameMap.get(signatureAcc); release.addSignature(createSignature(signatureAcc, signatureName, release)); List<String> children = pantherParentChildMap.get(parent); for (String childSignatureAcc : children) { String childSignatureName = familyIdFamilyNameMap.get(childSignatureAcc); release.addSignature(createSignature(childSignatureAcc, childSignatureName, release)); } } } } return release; }
String signatureName = familyIdFamilyNameMap.get(signatureAcc); release.addSignature(createSignature(signatureAcc, signatureName, release));
release.addSignature(createSignature(accession, name, description, release));
release.addSignature(createSignature(accession, name, description, release));
release.addSignature(createSignature(accession, name, description, release, modelBuf)); release.addSignature(createSignature(accession, name, description, release, modelBuf));
release.addSignature(createSignature(accession, id, description, release));
release.addSignature(createSignature(accession, id, description, 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; } }
/** * 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; }
/** * 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 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 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 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; } }
/** * 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 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; } }