uk.ac.ebi.intact.model.InteractorXref java code examples

Add the Codota plugin to your IDE and get smart completions

private void myMethod () {
 OutputStreamWriter o =OutputStream out;new OutputStreamWriter(out)
OutputStream out;String charsetName;new OutputStreamWriter(out, charsetName)
HttpURLConnection connection;new OutputStreamWriter(connection.getOutputStream())
Smart code suggestions by Tabnine
}

private static Collection<InteractorXref> extractCrossReferencesFrom(Protein protein, String databaseMiRef, String qualifierMiRef) {
  Collection<InteractorXref> parents = new ArrayList<InteractorXref>();
  for (InteractorXref ref : protein.getXrefs()) {
    if (ref.getCvDatabase().getIdentifier().equals(databaseMiRef)) {
      if (ref.getCvXrefQualifier().getIdentifier().equals(qualifierMiRef)) {
        parents.add(ref);
      }
    }
  }
  return parents;
}

/**
 * Add all the cross references with qualifier 'identity' to the list of identifiers of the protein (intact cross references are ignored)
 * @param refs : the refs of the protein
 * @param context : the context of the protein
 */
private void addIdentityCrossreferencesToContext(Collection<InteractorXref> refs, UpdateContext context){
  for (InteractorXref ref : refs){
    if (ref.getPrimaryId() != null){
      if (ref.getCvXrefQualifier() != null){
        CvXrefQualifier qualifier = ref.getCvXrefQualifier();
        if (isIdentityCrossReference(qualifier)){
          CvDatabase database = ref.getCvDatabase();
          if (database != null){
            if (database.getIdentifier() != null && !CvDatabase.INTACT_MI_REF.equals(database.getIdentifier())){
              context.addIdentifier(database.getIdentifier(), ref.getPrimaryId());
            }
            else if (database.getShortLabel() != null && !CvDatabase.INTACT.equals(database.getShortLabel())) {
              context.addIdentifier(database.getShortLabel(), ref.getPrimaryId());
            }
          }
        }
      }
    }
  }
}

/**
 * Check if two interactors contain the same identity xrefs, excluding the IMEx partner identities
 *
 * @param interactor1
 * @param interactor2
 * @return
 */
public static boolean containTheSameIdentities(Interactor interactor1, Interactor interactor2) {
  List<InteractorXref> identities1 = getIdentityXrefs(interactor1, true);
  List<InteractorXref> identities2 = getIdentityXrefs(interactor2, true);
  if (identities1.size() != identities2.size()) {
    return false;
  }
  Comparator<InteractorXref> identityXrefComparator = new Comparator<InteractorXref>() {
    public int compare(InteractorXref o1, InteractorXref o2) {
      return o1.getPrimaryId().compareTo(o2.getPrimaryId());
    }
  };
  Collections.sort(identities1, identityXrefComparator);
  Collections.sort(identities2, identityXrefComparator);
  for (int i = 0; i < identities1.size(); i++) {
    if (!(identities1.get(i).equals(identities2.get(i)))) {
      return false;
    }
  }
  return true;
}

/**
 * Retreives Imex identifier stored in the Xrefs.
 *
 * @param interaction the interaction to search on.
 * @return an imex id or null if not found.
 */
public static String getImexIdentifier(Interaction interaction) {
  if (interaction == null) {
    throw new IllegalArgumentException("You must give a non null interaction");
  }
  for (InteractorXref xref : interaction.getXrefs()) {
    if (CvDatabase.IMEX_MI_REF.equals(xref.getCvDatabase().getIdentifier())) {
      return xref.getPrimaryId();
    }
  }
  // Could not find an IMEx id
  return null;
}

private Collection<ProteinImpl> getProteinByXref(String primaryId, CvDatabase database, CvXrefQualifier qualifier) {
  XrefDao<InteractorXref> xrefDao = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao(InteractorXref.class);
  Collection<InteractorXref> xrefs = xrefDao.getByPrimaryId(primaryId, false);
  Collection<ProteinImpl> proteins = new ArrayList<ProteinImpl>();
  for (InteractorXref xref : xrefs) {
    if ((null != database && database.equals(xref.getCvDatabase()))
      ||
      (null == database && null == xref.getCvDatabase())) {
      if ((null != qualifier && qualifier.equals(xref.getCvXrefQualifier()))
        ||
        (null == qualifier && null == xref.getCvXrefQualifier())) {
        proteins.add((ProteinImpl) xref.getParent());
      }
    }
  }
  return proteins;
}

  public int compare(InteractorXref o1, InteractorXref o2) {
    return o1.getPrimaryId().compareTo(o2.getPrimaryId());
  }
};

protected void fixSourceReferenceXrefsIfNecessary(Interaction interaction) {
  InteractorXref xrefToFix = null;
  if( ConverterContext.getInstance().isAutoFixInteractionSourceReference() ) {
    // Look up source reference xref and only try to fix identity if there is no source ref present.
    // if the qualifier is identity, we will check if the owner identity MI is the same as the database MI
    for (InteractorXref xref : interaction.getXrefs()) {
      if (xref.getCvXrefQualifier() != null &&
          getInstitutionPrimaryId() != null &&
          getInstitutionPrimaryId().equals( xref.getPrimaryId() ) &&
          !CvXrefQualifier.SOURCE_REFERENCE_MI_REF.equals(xref.getCvXrefQualifier().getIdentifier())) {
        xrefToFix = xref;
        break;
      }
    }
    if ( xrefToFix != null ) {
      log.warn("Interaction identity xref found pointing to the source database. It should be of type 'source-reference'. Will be fixed automatically: "+xrefToFix);
      CvXrefQualifier sourceReference = CvObjectUtils.createCvObject(interaction.getOwner(), CvXrefQualifier.class, CvXrefQualifier.SOURCE_REFERENCE_MI_REF, CvXrefQualifier.SOURCE_REFERENCE);
      xrefToFix.setCvXrefQualifier(sourceReference);
      addMessageToContext(MessageLevel.WARN, "Interaction identity xref found pointing to the source database. It should be of type 'source-reference'. Fixed.", true);
    }
  }
}

protected ProteinImpl getProteinTranscriptsMasterProtein( Protein proteinTranscript, String cvXRefQualifier) {
  if ( proteinTranscript == null ) {
    throw new NullPointerException( "proteinTranscript must not be null." );
  }
  if ( cvXRefQualifier == null ) {
    throw new NullPointerException( "The Cv Xref qualifier must not be null." );
  }
  String masterProtAc = null;
  for (InteractorXref xref : proteinTranscript.getXrefs()) {
    if (xref.getCvXrefQualifier() != null && cvXRefQualifier.equals(xref.getCvXrefQualifier().getIdentifier())) {
      if (masterProtAc == null) {
        masterProtAc = xref.getPrimaryId();
      } else {
        throw new IntactException("This protein transcript contains more than one "+cvXRefQualifier+" xrefs: "+proteinTranscript.getShortLabel() );
      }
    }
  }
  // search protein by AC
  return getByAc(masterProtAc);
}

public Interaction createInteractionRandomBinary(String imexId) {
  CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION);
  CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.INTERACTION_MI_REF, CvInteractorType.INTERACTION );
  Experiment experimentEmpty = createExperimentEmpty();
  Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(experimentEmpty)),
                         cvInteractionType, intType, nextString("label"), getInstitution());
  experimentEmpty.getInteractions().add(interaction);
  createComponentBait(interaction, createProteinRandom());
  createComponentPrey(interaction, createProteinRandom());
  String shortLabel = InteractionUtils.calculateShortLabel(interaction);
  interaction.setShortLabel(shortLabel);
  if (imexId != null) {
    CvObjectBuilder cvBuilder = new CvObjectBuilder();
    CvXrefQualifier idQual = cvBuilder.createIdentityCvXrefQualifier(getInstitution());
    CvDatabase imexDb = createCvObject(CvDatabase.class, CvDatabase.IMEX_MI_REF, CvDatabase.IMEX);
    interaction.addXref(new InteractorXref(getInstitution(), imexDb, imexId, idQual));
  }
  return interaction;
}

/**
 * Checks if the current protein is a chain
 *
 * @param protein the protein to check
 * @return true if the protein is a chain
 */
public static boolean isFeatureChain(Protein protein) {
  Collection<InteractorXref> xrefs = protein.getXrefs();
  for (InteractorXref xref : xrefs) {
    if (xref.getCvXrefQualifier() != null) {
      String qualifierIdentity = xref.getCvXrefQualifier().getIdentifier();
      if (CvXrefQualifier.CHAIN_PARENT_MI_REF.equals(qualifierIdentity)) {
        return true;
      }
    }
  }
  return false;
}

  public Collection<GeneralMessage> check( SmallMolecule smallMolecule ) throws SanityRuleException {
    Collection<GeneralMessage> messages = new ArrayList<GeneralMessage>();

    final Collection<InteractorXref> identities = XrefUtils.getIdentityXrefs( smallMolecule );
    switch( identities.size() ) {
      case 0:
        messages.add( new GeneralMessage( MessageDefinition.SMALL_MOLECULE_IDENTITY_MISSING, smallMolecule ) );
        break;

      case 1:
        final InteractorXref xref = identities.iterator().next();
        if ( ! CvObjectUtils.hasIdentity( xref.getCvDatabase(), CvDatabase.CHEBI_MI_REF ) ) {
          messages.add( new GeneralMessage(MessageDefinition.SMALL_MOLECULE_IDENTITY_INVALID_DB, smallMolecule ) );
        }
        break;

      default:
        // more than 1
        messages.add( new GeneralMessage( MessageDefinition.SMALL_MOLECULE_IDENTITY_MULTIPLE, smallMolecule ) );
    }

    return messages;
  }
}

  public int compare(InteractorXref o1, InteractorXref o2) {
    return o1.getPrimaryId().compareTo(o2.getPrimaryId());
  }
};

/**
 * Retreives Imex identifier stored in the Xrefs.
 *
 * @param interaction the interaction to search on.
 * @return an imex id or null if not found.
 */
public static String getImexIdentifier(Interaction interaction) {
  if (interaction == null) {
    throw new IllegalArgumentException("You must give a non null interaction");
  }
  for (InteractorXref xref : interaction.getXrefs()) {
    if (CvDatabase.IMEX_MI_REF.equals(xref.getCvDatabase().getIdentifier())) {
      return xref.getPrimaryId();
    }
  }
  // Could not find an IMEx id
  return null;
}

private Collection<ProteinImpl> getProteinByXref(String primaryId, CvDatabase database, CvXrefQualifier qualifier) {
  XrefDao<InteractorXref> xrefDao = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao(InteractorXref.class);
  Collection<InteractorXref> xrefs = xrefDao.getByPrimaryId(primaryId, false);
  Collection<ProteinImpl> proteins = new ArrayList<ProteinImpl>();
  for (InteractorXref xref : xrefs) {
    if ((null != database && database.equals(xref.getCvDatabase()))
      ||
      (null == database && null == xref.getCvDatabase())) {
      if ((null != qualifier && qualifier.equals(xref.getCvXrefQualifier()))
        ||
        (null == qualifier && null == xref.getCvXrefQualifier())) {
        proteins.add((ProteinImpl) xref.getParent());
      }
    }
  }
  return proteins;
}

protected ProteinImpl getProteinTranscriptsMasterProtein( Protein proteinTranscript, String cvXRefQualifier) {
  if ( proteinTranscript == null ) {
    throw new NullPointerException( "proteinTranscript must not be null." );
  }
  if ( cvXRefQualifier == null ) {
    throw new NullPointerException( "The Cv Xref qualifier must not be null." );
  }
  String masterProtAc = null;
  for (InteractorXref xref : proteinTranscript.getXrefs()) {
    if (xref.getCvXrefQualifier() != null && cvXRefQualifier.equals(xref.getCvXrefQualifier().getIdentifier())) {
      if (masterProtAc == null) {
        masterProtAc = xref.getPrimaryId();
      } else {
        throw new IntactException("This protein transcript contains more than one "+cvXRefQualifier+" xrefs: "+proteinTranscript.getShortLabel() );
      }
    }
  }
  // search protein by AC
  return getByAc(masterProtAc);
}

public Interaction createInteractionRandomBinary(String imexId) {
  CvInteractionType cvInteractionType = createCvObject(CvInteractionType.class, CvInteractionType.DIRECT_INTERACTION_MI_REF, CvInteractionType.DIRECT_INTERACTION);
  CvInteractorType intType = createCvObject(CvInteractorType.class, CvInteractorType.INTERACTION_MI_REF, CvInteractorType.INTERACTION );
  Experiment experimentEmpty = createExperimentEmpty();
  Interaction interaction = new InteractionImpl(new ArrayList<Experiment>(Arrays.asList(experimentEmpty)),
                         cvInteractionType, intType, nextString("label"), getInstitution());
  experimentEmpty.getInteractions().add(interaction);
  createComponentBait(interaction, createProteinRandom());
  createComponentPrey(interaction, createProteinRandom());
  String shortLabel = InteractionUtils.calculateShortLabel(interaction);
  interaction.setShortLabel(shortLabel);
  if (imexId != null) {
    CvObjectBuilder cvBuilder = new CvObjectBuilder();
    CvXrefQualifier idQual = cvBuilder.createIdentityCvXrefQualifier(getInstitution());
    CvDatabase imexDb = createCvObject(CvDatabase.class, CvDatabase.IMEX_MI_REF, CvDatabase.IMEX);
    interaction.addXref(new InteractorXref(getInstitution(), imexDb, imexId, idQual));
  }
  return interaction;
}

/**
 * Checks if the current protein is a splice variant
 *
 * @param protein the protein to check
 * @return true if the protein is a splice variant
 */
public static boolean isSpliceVariant(Protein protein) {
  Collection<InteractorXref> xrefs = protein.getXrefs();
  for (InteractorXref xref : xrefs) {
    if (xref.getCvXrefQualifier() != null) {
      String qualifierIdentity = xref.getCvXrefQualifier().getIdentifier();
      if (CvXrefQualifier.ISOFORM_PARENT_MI_REF.equals(qualifierIdentity)) {
        return true;
      }
    }
  }
  return false;
}

private static Collection<InteractorXref> extractCrossReferencesFrom(Protein protein, String databaseMiRef, String qualifierMiRef) {
  Collection<InteractorXref> parents = new ArrayList<InteractorXref>();
  for (InteractorXref ref : protein.getXrefs()) {
    if (ref.getCvDatabase().getIdentifier().equals(databaseMiRef)) {
      if (ref.getCvXrefQualifier().getIdentifier().equals(qualifierMiRef)) {
        parents.add(ref);
      }
    }
  }
  return parents;
}

  /**
   * Get the uniprot primary ID from Protein and Splice variant.
   *
   * @param protein the Protein for which we want the uniprot ID.
   *
   * @return the uniprot ID as a String or null if none is found (should not occur)
   */
  public String getUniprotPrimaryAc(final Protein protein) {

    if (protAcToUniprotIdCache.containsKey(protein.getAc())) {
      return protAcToUniprotIdCache.get(protein.getAc());
    }

    String uniprotId = null;

    Collection<InteractorXref> xrefs = protein.getXrefs();

    for (InteractorXref xref : xrefs) {
      if (getUniprot().equals(xref.getCvDatabase()) &&
          getIdentity().equals(xref.getCvXrefQualifier())) {
        uniprotId = xref.getPrimaryId();
        break;
      }
    }

    protAcToUniprotIdCache.put(protein.getAc(), uniprotId);

    return uniprotId;
  }
}

  public int compare(InteractorXref o1, InteractorXref o2) {
    return o1.getPrimaryId().toLowerCase().compareTo(o2.getPrimaryId().toLowerCase());
  }
});

Javadoc

TODO comment this!

Most used methods

Popular in Java

Creating JSON documents from java classes using gson
setContentView (Activity)
startActivity (Activity)
findViewById (Activity)
Font (java.awt)
The Font class represents fonts, which are used to render text in a visible way. A font provides the
SQLException (java.sql)
An exception that indicates a failed JDBC operation. It provides the following information about pro
SimpleDateFormat (java.text)
Formats and parses dates in a locale-sensitive manner. Formatting turns a Date into a String, and pa
BitSet (java.util)
The BitSet class implements abit array [http://en.wikipedia.org/wiki/Bit_array]. Each element is eit
HashMap (java.util)
HashMap is an implementation of Map. All optional operations are supported.All elements are permitte
BlockingQueue (java.util.concurrent)
A java.util.Queue that additionally supports operations that wait for the queue to become non-empty
Top plugins for WebStorm

How to useInteractorXref in uk.ac.ebi.intact.model

Best Java code snippets using uk.ac.ebi.intact.model.InteractorXref (Showing top 20 results out of 315)

How to use
InteractorXref
in
uk.ac.ebi.intact.model