public void writeHostOrganism(BinaryInteractionEvidence interaction) throws IOException { Experiment experiment = interaction.getExperiment(); // writes interaction annotations first if (experiment != null){ writeOrganism(experiment.getHostOrganism()); } else{ getWriter().write(MitabUtils.EMPTY_COLUMN); } }
public void writeInteractionDetectionMethod(BinaryInteractionEvidence interaction) throws IOException { Experiment experiment = interaction.getExperiment(); if (experiment != null){ writeCvTerm(experiment.getInteractionDetectionMethod()); } else{ getWriter().write(MitabUtils.EMPTY_COLUMN); } }
public void writeInteractionAnnotations(BinaryInteractionEvidence interaction) throws IOException { // writes interaction annotations first if (!interaction.getAnnotations().isEmpty()){ Iterator<Annotation> interactorAnnotationIterator = interaction.getAnnotations().iterator(); while (interactorAnnotationIterator.hasNext()){ Annotation annot = interactorAnnotationIterator.next(); writeAnnotation(annot); if(interactorAnnotationIterator.hasNext()){ getWriter().write(MitabUtils.FIELD_SEPARATOR); } } if (interaction.getExperiment() != null){ Publication pub = interaction.getExperiment().getPublication(); if (pub != null){ getWriter().write(MitabUtils.FIELD_SEPARATOR); writeInteractionAnnotationTagsFrom(pub); } } } else if (interaction.getExperiment() != null){ Publication pub = interaction.getExperiment().getPublication(); if (pub != null){ // writes curation depth first writeInteractionAnnotationTagsFrom(pub); } } else{ getWriter().write(MitabUtils.EMPTY_COLUMN); } }
public void writeSource(BinaryInteractionEvidence interaction) throws IOException { Experiment experiment = interaction.getExperiment(); if (experiment != null){ Publication pub = experiment.getPublication(); if (pub != null){ writeCvTerm(pub.getSource()); } else { getWriter().write(MitabUtils.EMPTY_COLUMN); } } else{ getWriter().write(MitabUtils.EMPTY_COLUMN); } }
if (interaction.getExperiment() != null){ Publication pub = interaction.getExperiment().getPublication(); else if (interaction.getExperiment() != null){ Publication pub = interaction.getExperiment().getPublication();
public void writeFirstAuthor(BinaryInteractionEvidence interaction) throws IOException { Experiment experiment = interaction.getExperiment(); if (experiment != null){ Publication pub = experiment.getPublication();
public void writePublicationIdentifiers(BinaryInteractionEvidence interaction) throws IOException { Experiment experiment = interaction.getExperiment();