public void BuildResult(Dictionary <string, MaxQuantModificationItem> shortModMap, string noredundantFile, string iniFile, List <IIdentifiedSpectrum> spectra)
{
var proteins = new IdentifiedProteinBuilder().Build(spectra);
var groups = new IdentifiedProteinGroupBuilder().Build(proteins);
var ir = new IdentifiedResultBuilder(DefaultAccessNumberParser.GetInstance(), "").Build(groups);
new MascotResultTextFormat().WriteToFile(noredundantFile, ir);
Aminoacids samAminoacids, refAminoacids;
InitializeAminoacids(out samAminoacids, out refAminoacids);
using (var sw = new StreamWriter(iniFile))
{
for (var idx = 0; idx < samAminoacids.Count; idx++)
{
var samAA = samAminoacids[idx];
var refAA = refAminoacids[idx];
if (samAA.Visible)
{
sw.WriteLine("<{0}>\tSAM\tREF", samAA.OneName);
WriteAtom(sw, samAA, refAA, new[] { Atom.C }, "C");
WriteAtom(sw, samAA, refAA, new[] { Atom.H }, "H");
WriteAtom(sw, samAA, refAA, new[] { Atom.O }, "O");
WriteAtom(sw, samAA, refAA, new[] { Atom.N }, "N");
WriteAtom(sw, samAA, refAA, new[] { Atom.S }, "S");
WriteAtom(sw, samAA, refAA, new[] { Atom.P }, "P");
WriteAtom(sw, samAA, refAA, new[] { Atom.N15, Atom.Nx }, "15N");
WriteAtom(sw, samAA, refAA, new[] { Atom.H2, Atom.Hx }, "2H");
WriteAtom(sw, samAA, refAA, new[] { Atom.C13, Atom.Cx }, "13C");
WriteAtom(sw, samAA, refAA, new[] { Atom.O18, Atom.Ox }, "18O", false);
sw.WriteLine();
}
}
var terms = new[] { new MaxQuantModificationItem()
{
Symbol = "NTERM", Composition = new AtomComposition("H")
},
new MaxQuantModificationItem()
{
Symbol = "CTERM", Composition = new AtomComposition("OH")
} };
var usedMods = (from v in shortModMap.Values
orderby v.Symbol
select v).ToList();
usedMods.AddRange(terms);
foreach (var mod in usedMods)
{
mod.WriteToSilacINI(sw);
}
}
}
public override IEnumerable <string> Process(string fileName)
{
var proteins = ParseProteins(fileName);
Progress.SetMessage("Building protein groups ...");
var groups = new IdentifiedProteinGroupBuilder().Build(proteins);
Progress.SetMessage("Building result ...");
var ir = new IdentifiedResultBuilder(null, null).Build(groups);
var result = FileUtils.ChangeExtension(fileName, ".noredundant");
RefineModifications(ir);
Progress.SetMessage("Saving result ...");
new SequestResultTextFormat(SequestHeader.SEQUEST_PROTEIN_HEADER, SequestHeader.SEQUEST_PEPTIDE_HEADER + "\tModification").WriteToFile(result, ir);
Progress.SetMessage("Finished.");
return(new string[] { result });
}
public void TestBuild()
{
List<IIdentifiedSpectrum> spectra = new SequestPeptideTextFormat().ReadFromFile(@"../../../data/TestBuilder.peptides");
Assert.AreEqual(4, spectra.Count);
IAccessNumberParser parser = AccessNumberParserFactory.FindOrCreateParser(@"(IPI\d+)", "IPI");
List<IIdentifiedProtein> proteins = new IdentifiedProteinBuilder().Build(spectra);
Assert.AreEqual(4, proteins.Count);
List<IIdentifiedProteinGroup> groups = new IdentifiedProteinGroupBuilder().Build(proteins);
Assert.AreEqual(2, groups.Count);
Assert.AreEqual(1, groups[0].Count);
Assert.AreEqual("IPI:IPI00784154.1|SW", groups[0][0].Name);
Assert.AreEqual(2, groups[1].Count);
Assert.AreEqual("REVERSED_00000001", groups[1][0].Name);
Assert.AreEqual("REVERSED_00000002", groups[1][1].Name);
IIdentifiedResult result = new IdentifiedResultBuilder(parser,"").Build(groups);
}