public static String getDoiId(Experiment exp){ if (exp == null){ return null; } else if (exp.getPublication() == null){ return null; } else{ return exp.getPublication().getDoi(); } }
public static String getPubmedId(Experiment exp){ if (exp == null){ return null; } else if (exp.getPublication() == null){ return null; } else{ return exp.getPublication().getPubmedId(); } }
@Override protected CvTerm extractInteractionDetectionMethodFrom(InteractionEvidence interaction) { return interaction.getExperiment() != null ? interaction.getExperiment().getInteractionDetectionMethod() : null; } }
public String getPARIdentifier() { return this.parIdentifier != null ? this.parIdentifier.getId() : null; }
/** * 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()); } }
@Override protected void createDefinitionFor(String def, OntologyTerm term) { if (term.getDefinition() != null){ term.setDefinition(term.getDefinition() + LINE_BREAK + def); } else{ term.setDefinition(def); } }
public void setInteractionAndAddParticipant(I interaction) { if (this.interaction != null){ this.interaction.removeParticipant(this); } if (interaction != null){ interaction.addParticipant(this); } }
public static String getParameterValueAsString(Parameter param){ if (param == null){ return null; } return param.getValue().toString() + (param.getUncertainty() != null ? " ~" + param.getUncertainty().toString() : ""); }
public void setExperimentAndAddInteractionEvidence(Experiment experiment) { if (this.experiment != null){ this.experiment.removeInteractionEvidence(this); } if (experiment != null){ experiment.addInteractionEvidence(this); } }
public void setPublicationAndAddExperiment(Publication publication) { if (this.publication != null){ this.publication.removeExperiment(this); } if (publication != null){ publication.addExperiment(this); } }
public void setExperimentAndAddVariableParameter(Experiment experiment) { if (this.experiment != null){ this.experiment.removeVariableParameter(this); } if (experiment != null){ experiment.addVariableParameter(this); } }
public void setParticipantAndAddFeature(P participant) { if (this.participant != null){ this.participant.removeFeature(this); } if (participant != null){ participant.addFeature(this); } }
public Collection<Checksum> getChecksums() { return wrappedInteraction.getChecksums(); }
public void setInteractionType(CvTerm term) { wrappedInteraction.setInteractionType(term); }
public String getShortName() { return wrappedInteraction.getShortName(); }
public void setCreatedDate(Date created) { wrappedInteraction.setCreatedDate(created); }
public Date getCreatedDate() { return wrappedInteraction.getCreatedDate(); }
public String getEntrezGeneId() { return this.entrezGeneId != null ? this.entrezGeneId.getId() : null; }
public void setExperimentAndAddInteractionEvidence(Experiment experiment) { if (this.experiment != null){ this.experiment.removeInteractionEvidence(this); } if (experiment != null){ experiment.addInteractionEvidence(this); } }
public String getPubmedId() { return this.pubmedId != null ? this.pubmedId.getId() : null; }