public void testAndOptimizeAllNone() {
optimizeExact(all_and_all, FilterUtils.all());
optimizeExact(FilterUtils.and(all_and_all, all_and_all), FilterUtils.all());
optimizeExact(all_and_none, FilterUtils.none());
optimizeExact(FilterUtils.and(all_and_none, FilterUtils.all()), FilterUtils.none());
optimizeExact(none_and_none, FilterUtils.none());
}
public void testAndOrAllNone() {
optimizeExact(FilterUtils.or(all_and_all, FilterUtils.all()), FilterUtils.all());
optimizeExact(FilterUtils.or(all_and_none, FilterUtils.all()), FilterUtils.all());
optimizeExact(FilterUtils.or(all_and_all, FilterUtils.none()), FilterUtils.all());
optimizeExact(FilterUtils.or(all_and_none, FilterUtils.none()), FilterUtils.none());
optimizeExact(FilterUtils.and(all_or_all, FilterUtils.all()), FilterUtils.all());
}
public void testUseCases() {
// schemas for our database features
FeatureFilter transcript = FilterUtils.byType("transcript");
FeatureFilter exon = FilterUtils.byType("exon");
FeatureFilter repeat = FilterUtils.byType("repeat");
AnnotationType.Impl tsType = new AnnotationType.Impl();
tsType.setConstraints(
"transcript.id", new PropertyConstraint.ByClass(String.class), CardinalityConstraint.ONE);
tsType.setDefaultConstraints(PropertyConstraint.NONE, CardinalityConstraint.NONE);
FeatureFilter tsID = FilterUtils.byAnnotationType(tsType);
AnnotationType.Impl exType = new AnnotationType.Impl();
exType.setConstraints(
"id", new PropertyConstraint.ByClass(String.class), CardinalityConstraint.ONE);
exType.setDefaultConstraints(PropertyConstraint.NONE, CardinalityConstraint.NONE);
FeatureFilter exID = FilterUtils.byAnnotationType(exType);
AnnotationType.Impl rpType = new AnnotationType.Impl();
rpType.setConstraints("id", PropertyConstraint.ANY, CardinalityConstraint.ONE);
rpType.setDefaultConstraints(PropertyConstraint.NONE, CardinalityConstraint.NONE);
FeatureFilter repeatID = FilterUtils.byAnnotationType(rpType);
FeatureFilter tsSchema = FilterUtils.and(transcript, tsID);
FeatureFilter exSchema = FilterUtils.and(exon, exID);
FeatureFilter reSchema = FilterUtils.and(repeat, repeatID);
FeatureFilter dbFilter = FilterUtils.or(new FeatureFilter[] {tsSchema, exSchema, reSchema});
// pull out a feature by transcript.id
FeatureFilter aTranscript = FilterUtils.byAnnotation("transcript.id", "ts:42");
// let the fun commence
optimizeEquals(
FilterUtils.and(tsSchema, aTranscript), FilterUtils.and(transcript, aTranscript));
optimizeExact(FilterUtils.and(exSchema, aTranscript), FilterUtils.none());
optimizeExact(FilterUtils.and(reSchema, aTranscript), FilterUtils.none());
optimizeEquals(dbFilter, dbFilter);
optimizeEquals(
FilterUtils.and(dbFilter, aTranscript), FilterUtils.and(transcript, aTranscript));
}
public void testAndOrMethods() {
checkEquals(
FilterUtils.and(FilterUtils.and(tf1, tf2), tf3),
FilterUtils.and(new FeatureFilter[] {tf1, tf2, tf3}));
checkEquals(
FilterUtils.and(tf1, FilterUtils.and(tf2, tf3)),
FilterUtils.and(new FeatureFilter[] {tf1, tf2, tf3}));
checkEquals(
FilterUtils.or(FilterUtils.or(tf1, tf2), tf3),
FilterUtils.or(new FeatureFilter[] {tf1, tf2, tf3}));
checkEquals(
FilterUtils.or(tf1, FilterUtils.or(tf2, tf3)),
FilterUtils.or(new FeatureFilter[] {tf1, tf2, tf3}));
}
