@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(); }
/** * 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); } } }
@Override public boolean equals(Object o) { if (this == o) return true; if (!(o instanceof Signature)) return false; final Signature s = (Signature) o; return new EqualsBuilder() .append(accession, s.accession) .append(name, s.name) .append(type, s.type) .append(created, s.created) .append(updated, s.updated) .append(getSafeMd5(md5), getSafeMd5(s.md5)) .append(comment, s.comment) .append(getSignatureLibraryRelease(),s.getSignatureLibraryRelease()) // .append(getCrossReferences(), s.getCrossReferences()) // .append(getDescription(), s.getDescription()) // .append(getAbstract(), s.getAbstract()) // .append(models, s.models) // .append(deprecatedAccessions, s.deprecatedAccessions) .isEquals(); }
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; }
public Signature addSignature(Signature signature) throws IllegalArgumentException { if (signature == null) { throw new IllegalArgumentException("'Signature' must not be null"); } if (signature.getSignatureLibraryRelease() != null) { signature.getSignatureLibraryRelease().removeSignature(signature); } signature.setSignatureLibraryRelease(this); signatures.add(signature); return signature; }
final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String description = signature.getDescription(); Entry interProEntry = signature.getEntry(); if (interProEntry != null) { mappingFields.add(interProEntry.getAccession());
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()); if (analysis == null) { final String signatureName = signature.getName(); final Entry interProEntry = signature.getEntry(); if (interProEntry != null) {
boolean found = false; for (final Signature retrievedSignature : retrievedSignatures) { if (type.getName().equals(retrievedSignature.getName()) && type.getAccession().equals(retrievedSignature.getAccession()) && type.getDescription().equals(retrievedSignature.getDescription())) { signatures.put(type, retrievedSignature); found = true;
/** * 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)); } }
final String signatureAc = signature.getAccession(); final String signatureModels = match.getSignatureModels(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String version = signature.getSignatureLibraryRelease().getVersion(); final String description = signature.getDescription();
/** * 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; }
final String signatureAc = signature.getAccession(); final SignatureLibrary signatureLibrary = signature.getSignatureLibraryRelease().getLibrary(); final String analysis = signatureLibrary.getName(); final String version = signature.getSignatureLibraryRelease().getVersion();
private void setModels(Collection<Model> models) { // Ensure Signature reference is set ("this.models = models" won't do) for (Model m : models) { addModel(m); } }
private void setCrossReferences(Set<SignatureXref> crossReferences) { for (SignatureXref xref : crossReferences) { addCrossReference(xref); } }
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(); final String description = signature.getDescription(); Entry interProEntry = signature.getEntry(); if (interProEntry != null) { mappingFields.add(interProEntry.getAccession());
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()); if (analysis == null) { final String signatureName = signature.getName(); final Entry interProEntry = signature.getEntry(); if (interProEntry != null) {
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)); } }
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(); final String description = signature.getDescription(); final String matchId = MATCH_STRING + getMatchCounter(); .append(locEnd); GFF3Feature matchFeature = buildMatchFeature(seqId, analysis, locStart, locEnd, score, description, status, date, matchIdLocation.toString(), targetId, signatureAc, signature.getEntry(), writeAllAttributes);
/** * 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); } } }
/** * 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; } }