/** * Creates and returns an instance of signature. */ private Signature createSignature(String accession, String name, SignatureLibraryRelease release) { Model model = new Model(accession, name, null); //TODO Also populate hmmLength from the panther.hmm now? Maybe for PANTHER 13.0+ return new Signature(accession, name, null, null, null, release, Collections.singleton(model)); } }
public Model build() { Model model = new Model(accession, name, description, definition); model.setSignature(signature); model.setMd5(md5); return model; }
protected Signature createSignature(String accession, String name, String description, SignatureLibraryRelease release, StringBuffer modelBuffer) { Model model = new Model(accession, name, description); modelBuffer.delete(0, modelBuffer.length()); return new Signature(accession, name, null, description, null, release, Collections.singleton(model)); }
private Signature createSignature(String accession, String name, String description, SignatureLibraryRelease release) { Model model = new Model(accession, name, description); return new Signature(accession, name, null, description, null, release, Collections.singleton(model)); } }
/** * Creates and returns an instance of signature. */ private Signature createSignature(String accession, String name, SignatureLibraryRelease release) { Model model = new Model(accession, name, null); return new Signature(accession, name, null, null, null, release, Collections.singleton(model)); } }
private Signature createSignature(String accession, String name, String description, SignatureLibraryRelease release) { Model model = new Model(accession, name, description, null); return new Signature(accession, name, null, description, null, release, Collections.singleton(model)); } }
protected Signature createSignature(String accession, String name, String description, SignatureLibraryRelease release, StringBuffer modelBuffer) { Model model = new Model(accession, name, description, null); modelBuffer.delete(0, modelBuffer.length()); return new Signature(accession, name, null, description, null, release, Collections.singleton(model)); }
protected Signature createSignature(String accession, String name, String description, SignatureLibraryRelease release) { Model model = new Model(accession, name, description, null); return new Signature(accession, name, null, description, null, release, Collections.singleton(model)); }
protected Signature createSignature(String accession, String name, String description, int length, SignatureLibraryRelease release, StringBuffer modelBuf) { // Model model = new Model(accession, name, description, modelBuf.toString()); Model model = new Model(accession, name, description, length); modelBuf.delete(0, modelBuf.length()); return new Signature(accession, name, null, description, null, release, Collections.singleton(model)); }
protected Signature createSignature(String accession, String name, String description, SignatureLibraryRelease release, StringBuffer modelBuf) { // Model model = new Model(accession, name, description, modelBuf.toString()); Model model = new Model(accession, name, description, null); modelBuf.delete(0, modelBuf.length()); return new Signature(accession, name, null, description, null, release, Collections.singleton(model)); }
protected Signature createSignature(String accession, String name, String description, SignatureLibraryRelease release) { Model model = new Model(accession, name, description); return new Signature(accession, name, null, description, null, release, Collections.singleton(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) ); } }
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) ); } }
public static Collection<Signature> createSignatures(Collection<CathDomainListRecord> records) { Map<String, Signature> map = new HashMap<String, Signature>(); for (CathDomainListRecord record : records) { String ac = createSignatureAccession(record); Signature signature; if (map.containsKey(ac)) { signature = map.get(ac); } else { signature = new Signature(ac); map.put(ac, signature); } signature.addModel(new Model(record.getDomainName())); } return map.values(); }
public static Collection<Signature> createSignatures(Collection<CathDomainListRecord> records) { Map<String, Signature> map = new HashMap<String, Signature>(); for (CathDomainListRecord record : records) { String ac = createSignatureAccession(record); Signature signature; if (map.containsKey(ac)) { signature = map.get(ac); } else { signature = new Signature(ac); map.put(ac, signature); } signature.addModel(new Model(record.getDomainName())); } return map.values(); }
/** * Add record details to the signatures object. Could involve adding a new signature and model to the existing * signatures object, or just adding a new model to an existing signature. * * @param release Signature library release details * @param accession Signature accession, if NULL then this method does nothing * @param name Model Id * @param description Signature and model names */ private void processRecord(SignatureLibraryRelease release, String accession, String name, String description) { if (accession != null) { Model model = new Model(name, description, null, null); if (signatures.containsKey(accession)) { Signature signature = signatures.get(accession); signature.addModel(model); } else { Signature signature = new Signature(accession, description, null, null, null, release, new HashSet<Model>()); signature.addModel(model); signatures.put(accession, signature); } } }
/** * 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 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; } }