/**
* Test 'standard' codon translations (no ambiguity codes)
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testCodonTranslate()
{
// standard translation table order column 1/2/3/4
* Test a sample of codon translations involving ambiguity codes. Should
* return a protein value where the ambiguity does not affect the translation.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testCodonTranslate_ambiguityCodes()
{
// Y is C or T
assertNull(ResidueProperties.codonTranslate("WSK"));
}
- @Test
+ @Test(groups ={ "Functional" })
public void testGetResidues_nucleotide()
{
/*
assertEquals("[A, C, G, I, N, R, T, U, X, Y]", residues.toString());
}
- @Test
+ @Test(groups ={ "Functional" })
public void testGetResidues_peptide()
{
/*
"[ALA, ARG, ASN, ASP, ASX, CYS, GLN, GLU, GLX, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, XAA]",
residues.toString());
}
+
+ @Test(groups = { "Functional" })
+ public void testGetCanonicalAminoAcid()
+ {
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MET"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSE"));
+ assertEquals(null, ResidueProperties.getCanonicalAminoAcid(null));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetSingleCharacterCode()
+ {
+ assertEquals('0', ResidueProperties.getSingleCharacterCode(null));
+ assertEquals('0', ResidueProperties.getSingleCharacterCode(null));
+ assertEquals('0', ResidueProperties.getSingleCharacterCode(""));
+ assertEquals('Q', ResidueProperties.getSingleCharacterCode("GLN"));
+ assertEquals('Q', ResidueProperties.getSingleCharacterCode("Gln"));
+ assertEquals('Q', ResidueProperties.getSingleCharacterCode("gln"));
+ }
}