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Interactor.getOrganism
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How to use
getOrganism
method
in
psidev.psi.mi.jami.model.Interactor

Best Java code snippets using psidev.psi.mi.jami.model.Interactor.getOrganism (Showing top 10 results out of 315)

origin: psidev.psi.mi.jami/jami-core

public void onOrganismUpdate(T protein, Organism old) {
  if (old == null){
    interactorChangeLogger.log(Level.INFO, "The organism has been initialised for the interactor " + protein.toString());
  }
  else if (protein.getOrganism() == null){
    interactorChangeLogger.log(Level.INFO, "The organism has been reset for the interactor " + protein.toString());
  }
  else {
    interactorChangeLogger.log(Level.INFO, "The organism " + old.toString() + " has been replaced with " + protein.getOrganism() + " in the interactor " + protein.toString());
  }
}
origin: psidev.psi.mi.jami/jami-mitab

public void writeInteractorOrganism(P participant) throws IOException {
  if (participant != null){
    Interactor interactor = participant.getInteractor();
    writeOrganism(interactor.getOrganism());
  }
  else{
    writer.write(MitabUtils.EMPTY_COLUMN);
  }
}
origin: psidev.psi.mi/psimi-schema-validator

@Override
public Collection<ValidatorMessage> check(Interactor interactor) throws ValidatorException {
  Collection<ValidatorMessage> messages = Collections.EMPTY_LIST;
  if (interactor.getInteractorType() != null && RuleUtils.isProtein(ontologyManager, interactor) && interactor.getOrganism() == null){
    MiContext context = RuleUtils.buildContext(interactor, "interactor");
    messages=Collections.singleton(new ValidatorMessage("The protein does not have an organism and it is required for MIMIx.",
        MessageLevel.ERROR,
        context,
        this));
  }
  else if ( InteractorUtils.doesInteractorHaveType(interactor, Gene.GENE_MI, Gene.GENE) && interactor.getOrganism() == null){
    MiContext context = RuleUtils.buildContext(interactor, "interactor");
    messages=Collections.singleton( new ValidatorMessage( "The gene does not have an organism and it is required for MIMIx.",
        MessageLevel.ERROR,
        context,
        this ) );
  }
  return messages;
}
origin: psidev.psi.mi.jami/jami-core

Organism organism1 = interactor1.getOrganism();
Organism organism2 = interactor2.getOrganism();
origin: psidev.psi.mi.jami/jami-core

Organism organism1 = interactor1.getOrganism();
Organism organism2 = interactor2.getOrganism();
origin: psidev.psi.mi.jami/jami-core

  /**
   *
   * @param interactor
   * @return the hashcode consistent with the equals method for this comparator
   */
  public static int hashCode(Interactor interactor){
    if (unambiguousExactInteractorComparator == null){
      unambiguousExactInteractorComparator = new UnambiguousExactInteractorBaseComparator();
    }

    if (interactor == null){
      return 0;
    }

    int hashcode = 31;
    hashcode = 31*hashcode + UnambiguousCvTermComparator.hashCode(interactor.getInteractorType());
    hashcode = 31*hashcode + OrganismTaxIdComparator.hashCode(interactor.getOrganism());
    hashcode = 31*hashcode + UnambiguousInteractorBaseComparator.hashCode(interactor);

    return hashcode;
  }
}
origin: psidev.psi.mi.jami/jami-core

/***
 * This method will copy properties of interactor source in interactor target and will override all the other properties of Target interactor.
 * @param source
 * @param target
 */
public static void copyAndOverrideBasicInteractorProperties(Interactor source, Interactor target){
  if (source != null && target != null){
    target.setShortName(source.getShortName());
    target.setFullName(source.getFullName());
    target.setInteractorType(source.getInteractorType());
    target.setOrganism(source.getOrganism());
    // copy collections
    target.getAnnotations().clear();
    target.getAnnotations().addAll(source.getAnnotations());
    target.getIdentifiers().clear();
    target.getIdentifiers().addAll(source.getIdentifiers());
    target.getAliases().clear();
    target.getAliases().addAll(source.getAliases());
    target.getXrefs().clear();
    target.getXrefs().addAll(source.getXrefs());
    target.getChecksums().clear();
    target.getChecksums().addAll(source.getChecksums());
  }
}
origin: psidev.psi.mi/psimi-schema-validator

if (interactor.getOrganism() != null){
  checkOrganism(messages, interactor.getOrganism(), interactor, "interactor");
origin: psidev.psi.mi.jami/jami-interactionviewer-json

if (object.getOrganism() != null){
  MIJsonUtils.writeSeparator(writer);
  MIJsonUtils.writePropertyKey("organism", writer);
  getOrganismWriter().write(object.getOrganism());
origin: psidev.psi.mi.jami/jami-interactionviewer-json

if (object.getOrganism() != null){
  MIJsonUtils.writeSeparator(writer);
  MIJsonUtils.writePropertyKey("organism", writer);
  getOrganismWriter().write(object.getOrganism());
psidev.psi.mi.jami.modelInteractorgetOrganism

Javadoc

The original source organism for this interactor. It can be null in case of chemical compounds/synthetic peptides

Popular methods of Interactor

  • getShortName
    The short name of the interactor. It cannot be null or empty. Ex: brca2
  • getAliases
    Collection of aliases for an interactor The Collection cannot be null and if the interactor does not
  • getAnnotations
    Collection of annotations for an interactor. The set cannot be null and if the interactor does not h
  • getIdentifiers
    Set of identifiers for this interactor. The identifiers can be from different databases, can be prim
  • getInteractorType
    The molecule type of this interactor. It is a controlled vocabulary term and cannot be null. Ex: pro
  • getChecksums
    Set of checksums computed for this interactor. The Collection cannot be null so when an interactor d
  • getXrefs
    Collection of other xrefs that give more information about the interactor. Ex: GO references to give
  • getFullName
    The full name of the interactor. It can be null Ex: Breast cancer type 2 susceptibility protein
  • getPreferredIdentifier
    The identifier in the list of identifiers which is the preferred identifier. If no identifiers is pr
  • setFullName
    Sets the full name of the interactor
  • setOrganism
    Sets the source organism of this interactor
  • setInteractorType
    Sets the molecule type for this interactor If the given type is null, this method automatically sets
  • setOrganism,
  • setInteractorType,
  • setShortName

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