@Override protected void addParticipant(Participant participant, BinaryInteraction interaction) { if (interaction.getParticipantA() != null){ interaction.setParticipantB(participant); } else { interaction.setParticipantA(participant); } } }
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 BinaryInteraction createBasicBinaryInteractionFrom(Interaction interaction, Participant p1, Participant p2, CvTerm expansionMethod){ BinaryInteraction binary = instantiateNewBinaryInteraction(); binary.setComplexExpansion(expansionMethod); InteractionCloner.copyAndOverrideBasicInteractionProperties(interaction, binary, false, true); binary.setParticipantA(p1); binary.setParticipantB(p2); return binary; }
public ModelledBinaryInteraction createModelledBinaryInteractionFrom(ModelledInteraction interaction, ModelledParticipant p1, ModelledParticipant p2, CvTerm expansionMethod) { ModelledBinaryInteraction binary = instantiateNewModelledBinaryInteraction(); binary.setComplexExpansion(expansionMethod); InteractionCloner.copyAndOverrideModelledInteractionProperties(interaction, binary, false, true); binary.setParticipantA(p1); binary.setParticipantB(p2); return binary; }
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 writeComplexExpansion(T binary) throws IOException { if (binary.getComplexExpansion() != null){ writeCvTerm(binary.getComplexExpansion()); } else { getWriter().write(MitabUtils.EMPTY_COLUMN); } }
@Override protected void initialiseExpansionMethod(Collection<MitabCvTerm> expansion, ModelledBinaryInteraction 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()); } } }
@Override protected void initialiseExpansionMethod(Collection<MitabCvTerm> expansion, BinaryInteraction 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()); } }
@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 writeInteractionType(T interaction) throws IOException { writeCvTerm(interaction.getInteractionType()); }
public void writeSource(ModelledBinaryInteraction interaction) throws IOException { writeCvTerm(interaction.getSource()); }
public void writeNegativeProperty(BinaryInteractionEvidence interaction) throws IOException { if (interaction.isNegative()){ getWriter().write("true"); } else { getWriter().write(MitabUtils.EMPTY_COLUMN); } }
public void writeInteractionParameters(ModelledBinaryInteraction interaction) throws IOException { if (!interaction.getModelledParameters().isEmpty()){ Iterator<ModelledParameter> parameterIterator = interaction.getModelledParameters().iterator(); while(parameterIterator.hasNext()){ writeParameter(parameterIterator.next()); if (parameterIterator.hasNext()){ getWriter().write(MitabUtils.FIELD_SEPARATOR); } } } else { getWriter().write(MitabUtils.EMPTY_COLUMN); } }
public void writeInteractionChecksums(T interaction) throws IOException { if (!interaction.getChecksums().isEmpty()){ Iterator<Checksum> checksumIterator = interaction.getChecksums().iterator(); while(checksumIterator.hasNext()){ writeChecksum(checksumIterator.next()); if (checksumIterator.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 writeInteractionConfidences(ModelledBinaryInteraction interaction) throws IOException { if (!interaction.getModelledConfidences().isEmpty()){ Iterator<ModelledConfidence> confIterator = interaction.getModelledConfidences().iterator(); while (confIterator.hasNext()) { writeConfidence(confIterator.next()); if (confIterator.hasNext()){ getWriter().write(MitabUtils.FIELD_SEPARATOR); } } } else { getWriter().write(MitabUtils.EMPTY_COLUMN); } }
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 writeInteractionAnnotations(ModelledBinaryInteraction 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); } } } 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 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); } }