// ReSharper restore StringLiteralTypo
public void TestComputeAminoAcidMassModifiedResidues(string strSequence, string residueModList, double expectedMass)
{
var residueMods = residueModList.Split(';');
var modifiedResidues = new List <PeptideMassCalculator.PeptideSequenceModInfo>();
foreach (var modifiedResidue in residueMods)
{
var modParts = modifiedResidue.Split(':');
var residueLocation = int.Parse(modParts[0]);
var modMass = double.Parse(modParts[1]);
var modInfo = new PeptideMassCalculator.PeptideSequenceModInfo
{
ResidueLocInPeptide = residueLocation,
ModificationMass = modMass,
AffectedAtom = PeptideMassCalculator.NO_AFFECTED_ATOM_SYMBOL
};
modifiedResidues.Add(modInfo);
}
var computedMass = mPeptideMassCalculator.ComputeSequenceMass(strSequence, modifiedResidues);
Console.WriteLine("{0,-30} is {1:F5}; expected {2:F5}", strSequence, computedMass, expectedMass);
Assert.AreEqual(expectedMass, computedMass, 0.0001, "Unexpected mass for the amino acid sequence");
}
private static void TestMSGFPlusParamFileParsing(string msgfPlusParamFilePath)
{
var modFileProcessor = new MSGFPlusParamFileModExtractor("MSGF+");
modFileProcessor.ErrorEvent += ErrorEventHandler;
modFileProcessor.WarningEvent += WarningEventHandler;
var peptideMassCalculator = new PeptideMassCalculator();
MSGFPlusSynFileReader.UpdateMassCalculatorMasses(msgfPlusParamFilePath, modFileProcessor, peptideMassCalculator, out _);
var modifiedResidues = new List <PeptideMassCalculator.PeptideSequenceModInfo>();
var monoMass = peptideMassCalculator.ComputeSequenceMass("PEPTIDE", modifiedResidues);
Console.WriteLine("Mono mass of PEPTIDE: " + monoMass.ToString("0.0000"));
var modifiedResidue = new PeptideMassCalculator.PeptideSequenceModInfo
{
ResidueLocInPeptide = 4,
ModificationMass = 79.966
};
modifiedResidues.Add(modifiedResidue);
var monoMassModified = peptideMassCalculator.ComputeSequenceMass("PEPTIDE", modifiedResidues);
Console.WriteLine("Mono mass of PEPT*IDE: " + monoMassModified.ToString("0.0000"));
const double MONO_MASS_EXPECTED = 799.359926865;
const double MODIFIED_MONO_MASS_EXPECTED = 879.325926865;
if (Math.Abs(monoMass - MONO_MASS_EXPECTED) > 1E-07)
{
PRISM.ConsoleMsgUtils.ShowWarning("Computed mass of {0:F6} does not match the expected mass, {1:F6}", monoMass, MONO_MASS_EXPECTED);
}
if (Math.Abs(monoMassModified - MODIFIED_MONO_MASS_EXPECTED) > 1E-07)
{
PRISM.ConsoleMsgUtils.ShowWarning("Modified computed mass of {0:F6} does not match the expected mass, {1:F6}", monoMassModified, MODIFIED_MONO_MASS_EXPECTED);
}
}
