public static void TestGlycanCompositionHypothesis()
{
String testGlycanCompositionFile = @"TestData\Glycresoft glycan hypothesis.csv";
CompositionHypothesis glycanHypothesis = new CompositionHypothesis();
glycanHypothesis.ParseCompositionHypothesisCsv<GlycanComposition>(testGlycanCompositionFile);
Console.WriteLine(glycanHypothesis);
}
public static void TestGlycoPeptideHypothesis()
{
String testGlycopeptideCompositionFile = @"TestData\HA-USSR-Glycopeptide hypothesis.csv";
CompositionHypothesis glycopeptideHypothesis = new CompositionHypothesis();
glycopeptideHypothesis.ParseCompositionHypothesisCsv<GlycopeptideComposition>(testGlycopeptideCompositionFile);
Console.WriteLine(glycopeptideHypothesis);
}
public static void TestBuildGlycoPeptideHypothesis()
{
String testGlycanCompositionFile = @"TestData\Glycresoft glycan hypothesis.csv";
CompositionHypothesis glycanHypothesis = new CompositionHypothesis();
glycanHypothesis.ParseCompositionHypothesisCsv<GlycanComposition>(testGlycanCompositionFile);
String testMSDigestFile = @"TestData\KK-USSR-digest-Prospector output.xml";
MSDigestReport msdigest = MSDigestReport.Load(testMSDigestFile);
int counter = 0;
foreach (MSDigestPeptide pep in msdigest.Peptides)
{
counter += pep.NumGlycosylations;
if (counter > 30)
{
pep.NumGlycosylations = 0;
}
}
try
{
GlycopeptideCompositionHypothesisBuilder builder = new GlycopeptideCompositionHypothesisBuilder(glycanHypothesis, msdigest.Peptides);
Console.WriteLine("Building Hypothesis");
builder.BuildCompositionHypothesis();
Console.WriteLine(builder.GlycopeptideComposition);
builder.GlycopeptideComposition.WriteCompositionHypothesisCsv("TestData/TestOutputHypothesis.csv");
}
catch (OutOfMemoryException ex)
{
Console.WriteLine("\n\n\n!!!!!!!!!!!!!!!!Combinatorics exceeded memory size!", ex.Message, "\n\n\n!!!!!!!!!!!!!!!!!!!!!!!!!!");
}
}