/** Ensures that boundaries can be determined correctly based on lower and upper limits. */
@Test
public void insideBoundary() {
CopyNumberAlterationCriterion criterion = new CopyNumberAlterationCriterion();
CopyNumberAlterationCriterionHandler handler =
CopyNumberAlterationCriterionHandler.create(criterion);
criterion.setLowerLimit(2f);
criterion.setUpperLimit(1f);
assertFalse(criterion.isInsideBoundaryType());
assertEquals(
GenomicCriteriaMatchTypeEnum.MATCH_POSITIVE_OR_NEGATIVE,
handler.getSegmentValueMatchCriterionType(2f));
criterion.setLowerLimit(1f);
criterion.setUpperLimit(2f);
assertTrue(criterion.isInsideBoundaryType());
assertEquals(
GenomicCriteriaMatchTypeEnum.NO_MATCH, handler.getSegmentValueMatchCriterionType(3f));
criterion.setLowerLimit(3f);
criterion.setUpperLimit(1f);
assertFalse(criterion.isInsideBoundaryType());
assertEquals(
GenomicCriteriaMatchTypeEnum.MATCH_POSITIVE_OR_NEGATIVE,
handler.getSegmentValueMatchCriterionType(4f));
}
/** Tests for various segment value match criterion. */
@Test
public void matchCriterion() {
CopyNumberAlterationCriterion criterion = new CopyNumberAlterationCriterion();
CopyNumberAlterationCriterionHandler handler =
CopyNumberAlterationCriterionHandler.create(criterion);
assertEquals(
GenomicCriteriaMatchTypeEnum.MATCH_POSITIVE_OR_NEGATIVE,
handler.getSegmentValueMatchCriterionType(2f));
criterion.setLowerLimit(1f);
assertEquals(
GenomicCriteriaMatchTypeEnum.MATCH_POSITIVE_OR_NEGATIVE,
handler.getSegmentValueMatchCriterionType(2f));
assertEquals(
GenomicCriteriaMatchTypeEnum.NO_MATCH, handler.getSegmentValueMatchCriterionType(0f));
criterion.setLowerLimit(null);
criterion.setUpperLimit(4f);
assertEquals(
GenomicCriteriaMatchTypeEnum.MATCH_POSITIVE_OR_NEGATIVE,
handler.getSegmentValueMatchCriterionType(4f));
assertEquals(
GenomicCriteriaMatchTypeEnum.NO_MATCH, handler.getSegmentValueMatchCriterionType(5f));
criterion.setLowerLimit(2f);
assertEquals(
GenomicCriteriaMatchTypeEnum.MATCH_POSITIVE_OR_NEGATIVE,
handler.getSegmentValueMatchCriterionType(2f));
assertEquals(
GenomicCriteriaMatchTypeEnum.NO_MATCH, handler.getSegmentValueMatchCriterionType(1f));
assertEquals(
GenomicCriteriaMatchTypeEnum.NO_MATCH, handler.getSegmentValueMatchCriterionType(5f));
}
/**
* Tests segment data retrieval.
*
* @throws InvalidCriterionException on unexpected invalid criterion error
*/
@Test
public void getSegmentDataMatches() throws InvalidCriterionException {
CopyNumberAlterationCriterion criterion = new CopyNumberAlterationCriterion();
CopyNumberAlterationCriterionHandler handler =
CopyNumberAlterationCriterionHandler.create(criterion);
Set<SegmentData> segments = handler.getSegmentDataMatches(dao, study, null);
assertEquals(1, segments.size());
assertEquals(segmentData, segments.iterator().next());
}
/**
* Tests match retrieval.
*
* @throws InvalidCriterionException on unexpected invalid criterion error
*/
@Test
public void getMatches() throws InvalidCriterionException {
CopyNumberAlterationCriterion criterion = new CopyNumberAlterationCriterion();
CopyNumberAlterationCriterionHandler handler =
CopyNumberAlterationCriterionHandler.create(criterion);
Set<ResultRow> rows =
handler.getMatches(dao, arrayDataService, query, new HashSet<EntityTypeEnum>());
assertEquals(1, rows.size());
}
/** Tests that the handler doesn't attempt to deal with data is should not. */
@Test
public void capabilities() {
CopyNumberAlterationCriterion criterion = new CopyNumberAlterationCriterion();
CopyNumberAlterationCriterionHandler handler =
CopyNumberAlterationCriterionHandler.create(criterion);
assertFalse(handler.hasReporterCriterion());
assertFalse(handler.isReporterMatchHandler());
assertTrue(handler.hasCriterionSpecifiedSegmentValues());
assertFalse(handler.hasCriterionSpecifiedReporterValues());
}
/** Tests for handling calls value criterion type. */
@Test
public void callsValues() {
Set<Integer> callsValues = new HashSet<Integer>();
callsValues.add(1);
CopyNumberAlterationCriterion criterion = new CopyNumberAlterationCriterion();
criterion.setCopyNumberCriterionType(CopyNumberCriterionTypeEnum.CALLS_VALUE);
criterion.setCallsValues(callsValues);
CopyNumberAlterationCriterionHandler handler =
CopyNumberAlterationCriterionHandler.create(criterion);
assertTrue(handler.hasCriterionSpecifiedSegmentValues());
assertTrue(handler.hasCriterionSpecifiedSegmentCallsValues());
assertEquals(
GenomicCriteriaMatchTypeEnum.MATCH_POSITIVE_OR_NEGATIVE,
handler.getSegmentCallsValueMatchCriterionType(1));
assertFalse(
GenomicCriteriaMatchTypeEnum.MATCH_POSITIVE_OR_NEGATIVE.equals(
handler.getSegmentCallsValueMatchCriterionType(2)));
}
