public BinaryInteractionEvidence createBinaryInteractionEvidenceFrom(InteractionEvidence interaction, ParticipantEvidence p1, ParticipantEvidence p2, CvTerm expansionMethod) { BinaryInteractionEvidence binary = instantiateNewBinaryInteractionEvidence(); binary.setComplexExpansion(expansionMethod); InteractionCloner.copyAndOverrideInteractionEvidenceProperties(interaction, binary, false, true); binary.setParticipantA(p1); binary.setParticipantB(p2); return binary; }
public void writeInteractionConfidences(BinaryInteractionEvidence interaction) throws IOException { if (!interaction.getConfidences().isEmpty()){ Iterator<Confidence> confIterator = interaction.getConfidences().iterator(); while (confIterator.hasNext()) { writeConfidence(confIterator.next()); if (confIterator.hasNext()){ getWriter().write(MitabUtils.FIELD_SEPARATOR); } } } else { getWriter().write(MitabUtils.EMPTY_COLUMN); } }
public void writeInteractionParameters(BinaryInteractionEvidence interaction) throws IOException { if (!interaction.getParameters().isEmpty()){ Iterator<Parameter> parameterIterator = interaction.getParameters().iterator(); while(parameterIterator.hasNext()){ writeParameter(parameterIterator.next()); if (parameterIterator.hasNext()){ getWriter().write(MitabUtils.FIELD_SEPARATOR); } } } 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 writeInteractionDetectionMethod(BinaryInteractionEvidence interaction) throws IOException { Experiment experiment = interaction.getExperiment(); if (experiment != null){ writeCvTerm(experiment.getInteractionDetectionMethod()); } else{ getWriter().write(MitabUtils.EMPTY_COLUMN); } }
@Override protected void initialiseExpansionMethod(Collection<MitabCvTerm> expansion, BinaryInteractionEvidence interaction) { if (expansion.size() > 1){ if (getParserListener() != null){ getParserListener().onSeveralCvTermsFound(expansion, expansion.iterator().next(), expansion.size()+" complex expansions found. Only the first one will be loaded."); } interaction.setComplexExpansion(expansion.iterator().next()); } else if (!expansion.isEmpty()){ interaction.setComplexExpansion(expansion.iterator().next()); } } }
public void writeInteractionIdentifiers(BinaryInteractionEvidence interaction) throws IOException { if (!interaction.getIdentifiers().isEmpty()){ Iterator<Xref> identifierIterator = interaction.getIdentifiers().iterator(); if (interaction.getImexId() != null){ getWriter().write(MitabUtils.FIELD_SEPARATOR); getWriter().write(Xref.IMEX); getWriter().write(MitabUtils.XREF_SEPARATOR); escapeAndWriteString(interaction.getImexId()); else if (interaction.getImexId() != null) { getWriter().write(Xref.IMEX); getWriter().write(MitabUtils.XREF_SEPARATOR); escapeAndWriteString(interaction.getImexId());
target.setParticipantA(null); target.setParticipantB(null); target.setParticipantA(first); if (self){ ParticipantEvidence clone = new DefaultParticipantEvidence(first.getInteractor()); clone.setStoichiometry(0); target.setParticipantB(clone); target.setParticipantB(iterator.next()); target.setParticipantB(null); ParticipantEvidence clone = new DefaultParticipantEvidence(first.getInteractor()); ParticipantCloner.copyAndOverrideParticipantEvidenceProperties(first, clone, true); target.setParticipantA(clone); clone.setInteraction(target); target.setParticipantB(clone2); ParticipantEvidence clone2 = new DefaultParticipantEvidence(second.getInteractor()); ParticipantCloner.copyAndOverrideParticipantEvidenceProperties(second, clone2, true); target.setParticipantB(clone2); clone2.setInteraction(target); target.setParticipantB(null);
public void writeNegativeProperty(BinaryInteractionEvidence interaction) throws IOException { if (interaction.isNegative()){ getWriter().write("true"); } else { getWriter().write(MitabUtils.EMPTY_COLUMN); } }
@Override public void writeInteractionAnnotations(BinaryInteractionEvidence interaction) throws IOException { Collection<Annotation> noExportAnnotations = AnnotationUtils.collectAllAnnotationsHavingTopic(interaction.getAnnotations(), null, "no-export"); Collection<Annotation> exportAnnotations = new ArrayList<Annotation>(interaction.getAnnotations()); exportAnnotations.removeAll(noExportAnnotations); if (interaction.getExperiment() != null){ Publication pub = interaction.getExperiment().getPublication(); else if (interaction.getExperiment() != null){ Publication pub = interaction.getExperiment().getPublication();
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 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); } }
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();