@Override
protected void writeAttributes(ParticipantEvidence object) throws XMLStreamException {
// write attributes
Stoichiometry stc = object.getStoichiometry();
Collection<Annotation> noExportAnnotations =
AnnotationUtils.collectAllAnnotationsHavingTopic(
object.getAnnotations(), null, "no-export");
Collection<Annotation> exportAnnotations = new ArrayList<Annotation>(object.getAnnotations());
exportAnnotations.removeAll(noExportAnnotations);
if (!exportAnnotations.isEmpty()) {
// write start attribute list
getStreamWriter().writeStartElement("attributeList");
for (Object ann : exportAnnotations) {
getAttributeWriter().write((Annotation) ann);
}
// write stoichiometry attribute if not null
writeOtherAttributes(object, false);
// write end attributeList
getStreamWriter().writeEndElement();
}
// write stoichiometry attribute if not null
else {
writeOtherAttributes(object, true);
}
}
@Override
protected void writeXref(ParticipantEvidence object) throws XMLStreamException {
if (object instanceof IntactParticipantEvidence) {
IntactParticipantEvidence intactParticipant = (IntactParticipantEvidence) object;
if (intactParticipant.getAc() != null) {
writeIntactAc("primaryRef", intactParticipant.getAc());
if (!object.getXrefs().isEmpty()) {
writeXrefFromIntactParticipantXrefs(object);
}
} else if (!object.getXrefs().isEmpty()) {
writeXrefFromParticipantXrefs(object);
}
} else {
super.writeXref(object);
}
}
protected void writeXrefFromIntactParticipantXrefs(ParticipantEvidence object)
throws XMLStreamException {
Iterator<Xref> refIterator = object.getXrefs().iterator();
// default qualifier is null as we are not processing identifiers
getXrefWriter().setDefaultRefType(null);
getXrefWriter().setDefaultRefTypeAc(null);
// write start xref
getStreamWriter().writeStartElement("xref");
while (refIterator.hasNext()) {
Xref ref = refIterator.next();
// write secondaryref
getXrefWriter().write(ref, "secondaryRef");
}
// write end xref
getStreamWriter().writeEndElement();
}
@Test
@Ignore
public void test_write_interaction_inferred()
throws XMLStreamException, IOException, IllegalRangeException {
BinaryInteractionEvidence interaction = new DefaultNamedBinaryInteractionEvidence();
ParticipantEvidence participant =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
ParticipantEvidence participant2 =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
ParticipantEvidence participant3 =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
ParticipantEvidence participant4 =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
// two inferred interactiosn f1, f2, f3 and f3,f4
FeatureEvidence f1 = new DefaultFeatureEvidence();
f1.getRanges().add(RangeUtils.createRangeFromString("1-4"));
FeatureEvidence f2 = new DefaultFeatureEvidence();
f2.getRanges().add(RangeUtils.createRangeFromString("1-4"));
FeatureEvidence f3 = new DefaultFeatureEvidence();
f1.getLinkedFeatures().add(f2);
f1.getLinkedFeatures().add(f3);
f2.getLinkedFeatures().add(f1);
f2.getLinkedFeatures().add(f3);
f3.getLinkedFeatures().add(f1);
f3.getLinkedFeatures().add(f2);
participant.addFeature(f1);
participant2.addFeature(f2);
participant3.addFeature(f3);
interaction.addParticipant(participant);
interaction.addParticipant(participant2);
elementCache.clear();
XmlNamedBinaryInteractionEvidenceWriter writer =
new XmlNamedBinaryInteractionEvidenceWriter(createStreamWriter(), this.elementCache);
writer.write(interaction);
streamWriter.flush();
Assert.assertEquals(this.interaction_inferred, output.toString());
}
@Test
public void test_copy_participant_evidence_properties_create_new_features() {
ParticipantEvidence sourceParticipant =
new DefaultParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
sourceParticipant.setStoichiometry(new DefaultStoichiometry(3));
sourceParticipant
.getCausalRelationships()
.add(
new DefaultCausalRelationship(
new DefaultCvTerm("decrease"), new DefaultParticipant(new DefaultProtein("p1"))));
sourceParticipant.setBiologicalRole(new DefaultCvTerm("enzyme"));
sourceParticipant.getAliases().add(new DefaultAlias("test alias"));
sourceParticipant.getXrefs().add(new DefaultXref(new DefaultCvTerm("test database"), "xxxx"));
sourceParticipant
.getAnnotations()
.add(new DefaultAnnotation(new DefaultCvTerm("test comment"), "comment"));
sourceParticipant.addFeature(new DefaultFeatureEvidence("test", "test feature"));
sourceParticipant.setInteraction(new DefaultInteractionEvidence());
sourceParticipant.setExperimentalRole(new DefaultCvTerm("bait"));
sourceParticipant.setExpressedInOrganism(new DefaultOrganism(-1));
sourceParticipant.getExperimentalPreparations().add(new DefaultCvTerm("test preparation"));
sourceParticipant
.getConfidences()
.add(new DefaultConfidence(new DefaultCvTerm("author-score"), "high"));
sourceParticipant
.getParameters()
.add(new DefaultParameter(new DefaultCvTerm("kd"), new ParameterValue(new BigDecimal(3))));
ParticipantEvidence targetParticipant =
new DefaultParticipantEvidence(new DefaultProtein("p2"));
ParticipantCloner.copyAndOverrideParticipantEvidenceProperties(
sourceParticipant, targetParticipant, true);
Assert.assertEquals(1, targetParticipant.getFeatures().size());
Assert.assertFalse(
targetParticipant.getFeatures().iterator().next()
== sourceParticipant.getFeatures().iterator().next());
Assert.assertTrue(
DefaultFeatureBaseComparator.areEquals(
targetParticipant.getFeatures().iterator().next(),
sourceParticipant.getFeatures().iterator().next()));
Assert.assertTrue(
targetParticipant.getFeatures().iterator().next().getParticipant() == targetParticipant);
}