@Test
public void test_copy_basic_participant_properties_create_new_features() {
Participant sourceParticipant =
new DefaultParticipant(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"));
((Collection<Feature>) sourceParticipant.getFeatures())
.add(new DefaultFeature("test", "test feature"));
Participant targetParticipant = new DefaultParticipant(new DefaultProtein("p2"));
ParticipantCloner.copyAndOverrideBasicParticipantProperties(
sourceParticipant, targetParticipant, true);
Assert.assertEquals(1, targetParticipant.getFeatures().size());
Assert.assertFalse(
targetParticipant.getFeatures().iterator().next()
== sourceParticipant.getFeatures().iterator().next());
Assert.assertTrue(
DefaultFeatureBaseComparator.areEquals(
(Feature) targetParticipant.getFeatures().iterator().next(),
(Feature) sourceParticipant.getFeatures().iterator().next()));
}
@Test
public void test_copy_modelled_participant_properties() {
ModelledParticipant sourceParticipant =
new DefaultModelledParticipant(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 DefaultModelledFeature("test", "test feature"));
sourceParticipant.setInteraction(new DefaultModelledInteraction());
ModelledParticipant targetParticipant =
new DefaultModelledParticipant(new DefaultProtein("p2"));
ParticipantCloner.copyAndOverrideModelledParticipantProperties(
sourceParticipant, targetParticipant, false);
Assert.assertEquals(1, targetParticipant.getXrefs().size());
Assert.assertEquals(1, targetParticipant.getAnnotations().size());
Assert.assertEquals(1, targetParticipant.getAliases().size());
Assert.assertEquals(1, targetParticipant.getFeatures().size());
Assert.assertNull(targetParticipant.getInteraction());
Assert.assertTrue(
targetParticipant.getXrefs().iterator().next()
== sourceParticipant.getXrefs().iterator().next());
Assert.assertTrue(
targetParticipant.getAliases().iterator().next()
== sourceParticipant.getAliases().iterator().next());
Assert.assertTrue(
targetParticipant.getAnnotations().iterator().next()
== sourceParticipant.getAnnotations().iterator().next());
Assert.assertTrue(
targetParticipant.getFeatures().iterator().next()
== sourceParticipant.getFeatures().iterator().next());
Assert.assertTrue(targetParticipant.getInteractor() == sourceParticipant.getInteractor());
Assert.assertTrue(targetParticipant.getStoichiometry() == sourceParticipant.getStoichiometry());
Assert.assertTrue(
targetParticipant.getBiologicalRole() == sourceParticipant.getBiologicalRole());
Assert.assertTrue(
targetParticipant.getCausalRelationships().iterator().next()
== sourceParticipant.getCausalRelationships().iterator().next());
Assert.assertTrue(
targetParticipant.getFeatures().iterator().next().getParticipant() == sourceParticipant);
}
@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_write_interaction()
throws XMLStreamException, IOException, IllegalRangeException {
BinaryInteractionEvidence interaction = new DefaultNamedBinaryInteractionEvidence();
ParticipantEvidence participant =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
interaction.addParticipant(participant);
elementCache.clear();
XmlNamedBinaryInteractionEvidenceWriter writer =
new XmlNamedBinaryInteractionEvidenceWriter(createStreamWriter(), this.elementCache);
writer.write(interaction);
streamWriter.flush();
Assert.assertEquals(this.interaction, 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);
}
@Test
public void test_write_interaction_attributes()
throws XMLStreamException, IOException, IllegalRangeException {
BinaryInteractionEvidence interaction = new DefaultNamedBinaryInteractionEvidence();
ParticipantEvidence participant =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
interaction.addParticipant(participant);
interaction.getAnnotations().add(new DefaultAnnotation(new DefaultCvTerm("test2")));
interaction.getAnnotations().add(new DefaultAnnotation(new DefaultCvTerm("test3")));
interaction.setComplexExpansion(CvTermUtils.createMICvTerm("spoke expansion", "MI:1060"));
elementCache.clear();
XmlNamedBinaryInteractionEvidenceWriter writer =
new XmlNamedBinaryInteractionEvidenceWriter(createStreamWriter(), this.elementCache);
writer.write(interaction);
streamWriter.flush();
Assert.assertEquals(this.interaction_attributes, output.toString());
}
@Test
public void test_write_interaction_alias()
throws XMLStreamException, IOException, IllegalRangeException {
NamedInteraction interaction = new DefaultNamedBinaryInteractionEvidence();
interaction
.getAliases()
.add(new DefaultAlias(new DefaultCvTerm("synonym"), "interaction synonym"));
interaction.getAliases().add(new DefaultAlias("test"));
ParticipantEvidence participant =
new DefaultNamedParticipantEvidence(InteractorUtils.createUnknownBasicInteractor());
interaction.addParticipant(participant);
elementCache.clear();
XmlNamedBinaryInteractionEvidenceWriter writer =
new XmlNamedBinaryInteractionEvidenceWriter(createStreamWriter(), this.elementCache);
writer.write((BinaryInteractionEvidence) interaction);
streamWriter.flush();
Assert.assertEquals(this.interaction_aliases, output.toString());
}
