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Added tests for mostFrequentBaseFraction() and reverseComplementString() 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@944 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-06-09 00:53:45 +00:00
parent 681e67c72c
commit af0b03a257
1 changed files with 18 additions and 3 deletions
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21
java/test/org/broadinstitute/sting/utils/BaseUtilsTest.java
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@ -18,6 +18,11 @@ public class BaseUtilsTest extends BaseTest {
compareFrequentBaseFractionToExpected("ACCCCTTTTG", 4.0/10.0);
}
private void compareFrequentBaseFractionToExpected(String sequence, double expected) {
double fraction = BaseUtils.mostFrequentBaseFraction(sequence.getBytes());
Assert.assertTrue(MathUtils.compareDoubles(fraction, expected) == 0);
}
@Test
public void testTransitionTransversion() {
logger.warn("Executing testTransitionTransversion");
@ -45,8 +50,18 @@ public class BaseUtilsTest extends BaseTest {
Assert.assertTrue( BaseUtils.SNPSubstitutionType( 'a', 'c' ) == BaseUtils.BaseSubstitutionType.TRANSVERSION );
}
private void compareFrequentBaseFractionToExpected(String sequence, double expected) {
double fraction = BaseUtils.mostFrequentBaseFraction(sequence.getBytes());
Assert.assertTrue(MathUtils.compareDoubles(fraction, expected) == 0);
@Test
public void testReverseComplementString() {
logger.warn("Executing testReverseComplementString");
compareRCStringToExpected("ACGGT", "ACCGT");
compareRCStringToExpected("TCGTATATCTCGCTATATATATATAGCTCTAGTATA", "TATACTAGAGCTATATATATATAGCGAGATATACGA");
compareRCStringToExpected("AAAN", "NTTT");
}
private void compareRCStringToExpected(String fw, String rcExp) {
String rcObs = BaseUtils.simpleReverseComplement(fw);
Assert.assertTrue(rcObs.equals(rcExp));
}
}