/** * 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)); } }
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)); } }
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, 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)); }
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)); }
/** * 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 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, null); 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)); }
public Signature toSignature() { return new Signature(getSignatureAccession()); }
public Signature toSignature() { return new Signature(getSignatureAccession()); }
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); } } }
/** * 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 * @param length Model HMM length */ private void processRecord(SignatureLibraryRelease release, String accession, String name, String description, Integer length) { if (accession != null) { Model model = new Model(name, description, null, length); 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<>()); signature.addModel(model); signatures.put(accession, signature); } } }
/** * Method to parse a model file and return a SignatureLibraryRelease. * * @return a complete SignatureLibraryRelease object */ @Override public SignatureLibraryRelease parse() throws IOException { final Map<String, String> records = parseFileToMap(); // Create signatures final Map<String, Signature> signatureMap = new HashMap<String, Signature>(); for (String modelAc : records.keySet()) { String signatureAc = records.get(modelAc); Signature signature; if (signatureMap.containsKey(signatureAc)) { signature = signatureMap.get(signatureAc); } else { signature = new Signature(signatureAc); signatureMap.put(signatureAc, signature); } signature.addModel(new Model(modelAc)); } // Create release return new SignatureLibraryRelease(library, releaseVersion, new HashSet<Signature>(signatureMap.values())); }
public Signature build() { Signature signature = new Signature(accession); signature.setName(name); signature.setDescription(description); signature.setEntry(entry); signature.setType(type); signature.setAbstract(abstractText); signature.setSignatureLibraryRelease(signatureLibraryRelease); signature.setCreated(created); signature.setUpdated(updated); signature.setMd5(md5); signature.setComment(comment); if (models != null) { signature.setModels(models); } if (!crossReferences.isEmpty()) { for (SignatureXref x : crossReferences) { signature.addCrossReference(x); } } if (deprecatedAccessions != null) { signature.setDeprecatedAccessions(deprecatedAccessions); } return signature; }