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psidev.psi.mi.jami.model
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How to use psidev.psi.mi.jami.model

Best Java code snippets using psidev.psi.mi.jami.model (Showing top 20 results out of 315)

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

public static String getDoiId(Experiment exp){
  if (exp == null){
    return null;
  }
  else if (exp.getPublication() == null){
    return null;
  }
  else{
    return exp.getPublication().getDoi();
  }
}
origin: psidev.psi.mi.jami/jami-core

public static String getPubmedId(Experiment exp){
  if (exp == null){
   return null; 
  }
  else if (exp.getPublication() == null){
    return null; 
  }
  else{
    return exp.getPublication().getPubmedId();
  }
}
origin: uk.ac.ebi.intact.dataexchange/structured-abstract

  @Override
  protected CvTerm extractInteractionDetectionMethodFrom(InteractionEvidence interaction) {
    return interaction.getExperiment() != null ? interaction.getExperiment().getInteractionDetectionMethod() : null;
  }
}
origin: psidev.psi.mi.jami/jami-core

public String getPARIdentifier() {
  return this.parIdentifier != null ? this.parIdentifier.getId() : null;
}
origin: psidev.psi.mi.jami/jami-core

/**
 * All properties are copied from source to target excepted the participant
 * @param source
 * @param target
 */
public static void copyAndOverrideRangeProperties(Range source, Range target){
  if (source != null && target != null){
    target.setPositions(source.getStart(), source.getEnd());
    target.setLink(source.isLink());
    target.setResultingSequence(source.getResultingSequence());
  }
}
origin: psidev.psi.mi.jami.bridges/jami-obo

@Override
protected void createDefinitionFor(String def, OntologyTerm term) {
  if (term.getDefinition() != null){
    term.setDefinition(term.getDefinition() + LINE_BREAK + def);
  }
  else{
    term.setDefinition(def);
  }
}
origin: psidev.psi.mi.jami/jami-core

public void setInteractionAndAddParticipant(I interaction) {
  if (this.interaction != null){
    this.interaction.removeParticipant(this);
  }
  if (interaction != null){
    interaction.addParticipant(this);
  }
}
origin: psidev.psi.mi.jami/jami-core

public static String getParameterValueAsString(Parameter param){
  if (param == null){
    return null;
  }
  return param.getValue().toString() + (param.getUncertainty() != null ? " ~" + param.getUncertainty().toString() : "");
}
origin: psidev.psi.mi.jami/jami-core

public void setExperimentAndAddInteractionEvidence(Experiment experiment) {
  if (this.experiment != null){
    this.experiment.removeInteractionEvidence(this);
  }
  if (experiment != null){
    experiment.addInteractionEvidence(this);
  }
}
origin: psidev.psi.mi.jami/jami-core

public void setPublicationAndAddExperiment(Publication publication) {
  if (this.publication != null){
    this.publication.removeExperiment(this);
  }
  if (publication != null){
    publication.addExperiment(this);
  }
}
origin: psidev.psi.mi.jami/jami-core

public void setExperimentAndAddVariableParameter(Experiment experiment) {
  if (this.experiment != null){
    this.experiment.removeVariableParameter(this);
  }
  if (experiment != null){
    experiment.addVariableParameter(this);
  }
}
origin: psidev.psi.mi.jami/jami-core

public void setParticipantAndAddFeature(P participant) {
  if (this.participant != null){
    this.participant.removeFeature(this);
  }
  if (participant != null){
    participant.addFeature(this);
  }
}
origin: psidev.psi.mi.jami/jami-core

public Collection<Checksum> getChecksums() {
  return wrappedInteraction.getChecksums();
}
origin: psidev.psi.mi.jami/jami-core

public void setInteractionType(CvTerm term) {
  wrappedInteraction.setInteractionType(term);
}
origin: psidev.psi.mi.jami/jami-core

public String getShortName() {
  return wrappedInteraction.getShortName();
}
origin: psidev.psi.mi.jami/jami-core

public void setCreatedDate(Date created) {
  wrappedInteraction.setCreatedDate(created);
}
origin: psidev.psi.mi.jami/jami-core

public Date getCreatedDate() {
  return wrappedInteraction.getCreatedDate();
}
origin: psidev.psi.mi.jami/jami-core

public String getEntrezGeneId() {
  return this.entrezGeneId != null ? this.entrezGeneId.getId() : null;
}
origin: psidev.psi.mi.jami/jami-core

public void setExperimentAndAddInteractionEvidence(Experiment experiment) {
  if (this.experiment != null){
    this.experiment.removeInteractionEvidence(this);
  }
  if (experiment != null){
    experiment.addInteractionEvidence(this);
  }
}
origin: psidev.psi.mi.jami/jami-core

public String getPubmedId() {
  return this.pubmedId != null ? this.pubmedId.getId() : null;
}
psidev.psi.mi.jami.model

Most used classes

  • CvTerm
  • Xref
    Cross reference to an external database/resource which can give more information about an object. Ex
  • Publication
    A scientific publication which has been curated by an interaction database.
  • Experiment
    Experiment in which some interactions has been determined.
  • InteractionEvidence
    Interaction involving one to several molecules supported by experiments.
  • Organism,
  • ParticipantEvidence,
  • Annotation,
  • Interaction,
  • Protein,
  • Source,
  • DefaultSource,
  • Alias,
  • Confidence,
  • Feature,
  • Parameter,
  • Participant,
  • DefaultCvTerm,
  • Checksum
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