public double GetScoreTest(Sequence sequence, ProductSpectrum spectrum)
{
var score = 0d;
var tol = new Tolerance(10);
var matchCounter = new CorrMatchedPeakCounter(spectrum, tol, 1, 20);
var prefixCompArr = sequence.GetPrefixCompositions().ToArray();
foreach (var c in prefixCompArr)
{
if (c.Equals(Composition.Zero))
{
Console.WriteLine("found zero");
}
}
var suffixCompArr = sequence.GetSuffixCompositions().ToArray();
for (int i = 0; i < prefixCompArr.Length; i++)
{
score += matchCounter.GetFragmentScore(prefixCompArr[i], suffixCompArr[i]);
}
return(score);
}
public void TestCorrMatchedPeakCounter()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
// Parameters
var precursorIonTolerance = new Tolerance(10);
var productIonTolerance = new Tolerance(10);
var sw = new System.Diagnostics.Stopwatch();
var aaSet = new AminoAcidSet();
const string protAnnotation = "_.TMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFIADATINTPNGHLVASAKHEDMYTAINELINKLERQLNKVQHKGEAR._";
// Create a sequence graph
var seqGraph = SequenceGraph.CreateGraph(aaSet, protAnnotation);
Assert.NotNull(seqGraph, "Invalid sequence: {0}", protAnnotation);
const string specFilePath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\SBEP_STM_001_02272012_Aragon.raw";
if (!File.Exists(specFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath);
}
var run = InMemoryLcMsRun.GetLcMsRun(specFilePath, 1.4826, 1.4826);
sw.Start();
var precursorFilter = new Ms1ContainsIonFilter(run, precursorIonTolerance);
var seqCompositionArr = seqGraph.GetSequenceCompositions();
Console.WriteLine("Length: {0}\tNumCompositions: {1}", protAnnotation.Length - 4, seqCompositionArr.Length);
const int charge = 9;
const int modIndex = 0;
const int ms2ScanNum = 3633;
var seqComposition = seqCompositionArr[modIndex];
var peptideComposition = seqComposition + Composition.H2O;
peptideComposition.GetIsotopomerEnvelopeRelativeIntensities();
Console.WriteLine("Composition: {0}, AveragineMass: {1}", seqComposition, seqComposition.Mass);
seqGraph.SetSink(modIndex);
var precursorIon = new Ion(peptideComposition, charge);
Assert.True(precursorFilter.IsValid(precursorIon, ms2ScanNum));
var spec = run.GetSpectrum(ms2ScanNum) as ProductSpectrum;
Assert.True(spec != null);
//var scorer = new MatchedPeakCounter(spec, productIonTolerance, 1, 10);
var scorer = new CorrMatchedPeakCounter(spec, productIonTolerance, 1, 10);
var score = seqGraph.GetFragmentScore(scorer);
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", protAnnotation, charge, precursorIon.GetMostAbundantIsotopeMz(), ms2ScanNum, score);
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}