public void TestParsingGlycoMods()
{
const string modFilePath = @"C:\cygwin\home\kims336\Data\Debug\MSPathFinder_Mods.txt";
var aaSet = new AminoAcidSet(modFilePath);
aaSet.Display();
}
public void TestCreatingAminoAcidSet()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Configure amino acid set
var pyroGluQ = new SearchModification(Modification.PyroGluQ, 'Q', SequenceLocation.PeptideNTerm, false);
var acetylN = new SearchModification(Modification.Acetylation, '*', SequenceLocation.ProteinNTerm, false);
var oxM = new SearchModification(Modification.Oxidation, 'M', SequenceLocation.Everywhere, false);
var searchModifications = new List <SearchModification>
{
acetylN,
pyroGluQ,
oxM
};
const int numMaxModsPerProtein = 2;
var aaSet = new AminoAcidSet(searchModifications, numMaxModsPerProtein);
//var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
aaSet.Display();
}
public void TestReadingModFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var modFilePath = Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"TopDown\ProductionQCShew\Mods.txt");
var modFile = Utils.GetTestFile(methodName, modFilePath);
var modFileParser = new ModFileParser(modFile.FullName);
Console.WriteLine("MaxNumDynModsPerSequence: {0}", modFileParser.MaxNumDynModsPerSequence);
foreach (var searhMod in modFileParser.SearchModifications)
{
Console.WriteLine("{0}\t{1}\t{2}\t{3}", searhMod.TargetResidue, searhMod.Location, searhMod.IsFixedModification, searhMod.Modification);
}
var aaSet = new AminoAcidSet(modFile.FullName);
aaSet.Display();
}
public void TestReadingModFile()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string modFilePath = @"..\..\..\TestFiles\Mods.txt";
if (!File.Exists(modFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, modFilePath);
}
var modFileParser = new ModFileParser(modFilePath);
Console.WriteLine("MaxNumDynModsPerSequence: {0}", modFileParser.MaxNumDynModsPerSequence);
foreach (var searhMod in modFileParser.SearchModifications)
{
Console.WriteLine("{0}\t{1}\t{2}\t{3}", searhMod.TargetResidue, searhMod.Location, searhMod.IsFixedModification, searhMod.Modification);
}
var aaSet = new AminoAcidSet(modFilePath);
aaSet.Display();
}