*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testTranslateCdna_withUntranslatableCodons()
throws IOException
{
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testTranslateCdna_withUntranslatableCodonsAndHiddenColumns()
throws IOException
{
}
/**
- * Test simple translation to Amino Acids (with STOP codons translated to X).
+ * Test simple translation to Amino Acids (with STOP codons translated to *).
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testTranslateCdna_simple() throws IOException
{
AlignmentI alf = new FormatAdapter().readFile(fasta,
AlignmentI translated = dna.translateCdna();
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals(
- "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYYXXX",
+ "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
aa);
}
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testTranslateCdna_hiddenColumns() throws IOException
{
AlignmentI alf = new FormatAdapter().readFile(fasta,
/**
* Use this test to help debug into any cases of interest.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testCompareCodonPos_oneOnly()
{
assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
/**
* Tests for method that compares 'alignment' of two codon position triplets.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testCompareCodonPos()
{
/*
* reorders the cDNA and retranslates, and verifies that the translations are
* the same (apart from ordering).
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testTranslateCdna_sequenceOrderIndependent()
{
/*
* Test that all the cases in testCompareCodonPos have a 'symmetric'
* comparison (without checking the actual comparison result).
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testCompareCodonPos_isSymmetric()
{
assertSymmetric("AAA", "GGG");
/**
* Weirdly, maybe worth a test to prove the helper method of this test class.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testConvertCodon()
{
assertEquals("[0, 1, 2]", convertCodon("AAA").toString());