@Test
public void foldUnknownExpressionIsUnknownExpression() {
BaselineProfile profileWithUnknownExpression = buildProfileWithUnknownExpression();
BaselineProfile sumProfile = profileWithUnknownExpression.foldProfile(3);
assertThat(sumProfile.getExpression(factor1).isKnown(), is(false));
}
private BaselineProfile buildProfileWithUnknownExpression() {
BaselineExpression unknownExpression1 =
new BaselineExpression("NT", new FactorSet().add(factor1));
BaselineProfile profileWithUnknownExpression = new BaselineProfile("OTHER_ID", "OTHER_NAME");
profileWithUnknownExpression.add(QUERY_FACTOR_TYPE, unknownExpression1);
return profileWithUnknownExpression;
}
@Test
public void testSumProfile() {
subject.sumProfile(buildOtherProfile());
assertThat(subject.getId(), is(subject.getId()));
assertThat(subject.getKnownExpressionLevel(factor1), is(2.2D + 1D));
assertThat(subject.getKnownExpressionLevel(factor2), is(3D + 2D));
assertThat(subject.getKnownExpressionLevel(factor3), is(3.001D + 3D));
assertThat(subject.getKnownExpressionLevel(factor4), is(300D));
}
@Test
public void nonTissueExpressionsDoNotAffectMinOrMax() {
assertThat(subject.getMinExpressionLevel(), is(2.2));
assertThat(subject.getMaxExpressionLevel(), is(3.001));
subject.add(QUERY_FACTOR_TYPE, new BaselineExpression("NT", new FactorSet().add(factor1)));
assertThat(subject.getMinExpressionLevel(), is(2.2));
assertThat(subject.getMaxExpressionLevel(), is(3.001));
}
@Test
public void averageExpressionLevel() {
double averageExpressionLevel =
subject.getAverageExpressionLevelOn(Sets.newHashSet(factor1, factor3));
assertThat(averageExpressionLevel, is(2.6005000000000003D));
averageExpressionLevel =
subject.getAverageExpressionLevelOn(
Sets.newHashSet(factor1, factor3, new Factor(QUERY_FACTOR_TYPE, "leg")));
assertThat(averageExpressionLevel, is(1.733666666666667D));
}
@Test
public void sumOfUnknownExpressionAndKnownExpressionIsUnknownExpression() {
BaselineProfile profileWithUnknownExpression = buildProfileWithUnknownExpression();
assertThat(subject.getExpression(factor1).isKnown(), is(true));
assertThat(subject.getExpression(factor2).isKnown(), is(true));
subject.sumProfile(profileWithUnknownExpression);
assertThat(subject.getExpression(factor1).isKnown(), is(false));
assertThat(subject.getExpression(factor2).isKnown(), is(true));
}
BaselineProfile buildOtherProfile() {
BaselineExpression expression_1 = new BaselineExpression(1D, new FactorSet().add(factor1));
BaselineExpression expression_2 = new BaselineExpression(2D, new FactorSet().add(factor2));
BaselineExpression expression_3 = new BaselineExpression(3D, new FactorSet().add(factor3));
BaselineExpression expression_4 = new BaselineExpression(300D, new FactorSet().add(factor4));
BaselineProfile baselineProfile = new BaselineProfile("OTHER_ID", "OTHER_NAME");
return baselineProfile
.add(QUERY_FACTOR_TYPE, expression_1)
.add(QUERY_FACTOR_TYPE, expression_2)
.add(QUERY_FACTOR_TYPE, expression_3)
.add(QUERY_FACTOR_TYPE, expression_4);
}
@Before
public void setUp() throws Exception {
subject = new BaselineProfile(GENE_ID, GENE_NAME);
subject
.add(QUERY_FACTOR_TYPE, expression_1)
.add(QUERY_FACTOR_TYPE, expression_2)
.add(QUERY_FACTOR_TYPE, expression_3);
}
@Test
public void averageExpressionLevelOnEmptyCollection() {
// given
Set<Factor> queryFactors = Sets.newHashSet(mock(Factor.class));
// when
double averageExpressionLevel = subject.getAverageExpressionLevelOn(queryFactors);
// then
assertThat(averageExpressionLevel, is(0D));
}
@Test
public void sumProfileShouldPreserveLevelsThatAreNotExpressedInOtherProfile() {
BaselineProfile otherProfile =
new BaselineProfile("other profile", "other name").add(QUERY_FACTOR_TYPE, expression_2);
subject.sumProfile(otherProfile);
assertThat(subject.getId(), is(GENE_ID));
assertThat(
subject.getKnownExpressionLevel(factor1), is(subject.getKnownExpressionLevel(factor1)));
assertThat(subject.getKnownExpressionLevel(factor2), is(6D));
assertThat(
subject.getKnownExpressionLevel(factor3), is(subject.getKnownExpressionLevel(factor3)));
assertThat(subject.getKnownExpressionLevel(factor4), is(nullValue()));
}
@Test
public void testFold() {
BaselineProfile sumProfile = subject.foldProfile(3);
assertThat(sumProfile.getId(), is(subject.getId()));
assertThat(sumProfile.getKnownExpressionLevel(factor1), is(0.7D));
assertThat(sumProfile.getKnownExpressionLevel(factor2), is(1.0D));
assertThat(sumProfile.getKnownExpressionLevel(factor3), is(1.0D));
assertThat(sumProfile.getKnownExpressionLevel(factor4), is(nullValue()));
}
@Test(expected = IllegalArgumentException.class)
public void shouldThrowExceptionWhenQueryFactorsIsEmpty() {
subject.getAverageExpressionLevelOn(new HashSet<Factor>());
}
@Test
public void testGetGeneSpecificity() throws Exception {
assertThat(subject.getSpecificity(), is(3));
}
