How to use

Signature

in

uk.ac.ebi.interpro.scan.model

@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;
  }
}