public void TestGetModifiedAminiacids()
{
var actual = ModificationUtils.GetModifiedAminiacids("^SEETAY*FVWLGK@");
Assert.AreEqual(2, actual.Count);
Assert.AreEqual('Y', actual[5]);
Assert.AreEqual('K', actual[11]);
}
public void TestParseProbability()
{
var probs = ModificationUtils.ParseProbability("S(1): 0.0; S(3): 0.4; S(4): 99.6");
Assert.AreEqual(3, probs.Count);
Assert.IsTrue(probs.All(l => l.Aminoacid.Equals("S")));
Assert.AreEqual(4, probs[2].Site);
Assert.AreEqual(99.6, probs[2].Probability);
}
public void TestFilterSiteProbability()
{
var actual = ModificationUtils.FilterSiteProbability("SQSS*PR", "S(1): 0.0; S(3): 0.4; S(4): 99.6");
Assert.AreEqual("S(4): 99.6", actual);
actual = ModificationUtils.FilterSiteProbability("^SQSS*PR", "S(1): 0.0; S(3): 0.4; S(4): 99.6");
Assert.AreEqual("S(4): 99.6", actual);
actual = ModificationUtils.FilterSiteProbability("^SRK@T*SSVSSSPST*PT*QVT*K@", "Too many isoforms");
Assert.AreEqual("K(3): 0; T(4): 0; T(13): 0; T(15): 0; T(18): 0; K(19): 0", actual);
}
public void TestParseFromOutFileLine()
{
Dictionary <char, double> map =
ModificationUtils.ParseFromOutFileLine(
"(STY* +79.96633) (M# +15.99492) (ST@ -18.00000) C=160.16523 Enzyme:Trypsin(KR) (1)");
Assert.AreEqual(4, map.Count);
Assert.AreEqual(79.96633, map['*'], 0.00001);
Assert.AreEqual(15.99492, map['#'], 0.00001);
Assert.AreEqual(-18.00000, map['@'], 0.00001);
Assert.AreEqual(160.16523, map['C'], 0.00001);
}
public bool Validate(string sequence)
{
if (sequence == null || sequence.Length == 0)
{
return(false);
}
int specialAminoAcidCount = 0;
int modifiedAminoAcidCount = 0;
int i = 0;
while (i < sequence.Length)
{
if (aminoAcids.IndexOf(sequence[i]) < 0)
{
i++;
continue;
}
specialAminoAcidCount++;
i++;
if (i < sequence.Length)
{
if (ModificationUtils.IsModification(sequence[i]))
{
modifiedAminoAcidCount++;
i++;
}
}
}
if (0 == specialAminoAcidCount)
{
return(false);
}
return(0 == modifiedAminoAcidCount || modifiedAminoAcidCount == specialAminoAcidCount);
}
public void TestIsModification()
{
Assert.IsTrue(ModificationUtils.IsModification('*'));
Assert.IsTrue(ModificationUtils.IsModification('p'));
Assert.IsFalse(ModificationUtils.IsModification('A'));
}
