private FlankingMassMatch GetBestMatchInTheGraph(ShiftedSequenceGraph seqGraph, ProductSpectrum spec, double?featureMass)
{
FlankingMassMatch match = null;
var bestScore = double.NegativeInfinity;
var protCompositions = seqGraph.GetSequenceCompositions();
for (var modIndex = 0; modIndex < protCompositions.Length; modIndex++)
{
seqGraph.SetSink(modIndex);
var protCompositionWithH2O = seqGraph.GetSinkSequenceCompositionWithH2O();
var sequenceMass = protCompositionWithH2O.Mass;
if (featureMass != null && !_tolerance.IsWithin(sequenceMass, (double)featureMass))
{
continue;
}
var charge =
(int)
Math.Round(sequenceMass /
(spec.IsolationWindow.IsolationWindowTargetMz - Constants.Proton));
var mostAbundantIsotopeMz = Ion.GetIsotopeMz(sequenceMass, charge,
Averagine.GetIsotopomerEnvelope(sequenceMass).MostAbundantIsotopeIndex);
if (!spec.IsolationWindow.Contains(mostAbundantIsotopeMz))
{
continue;
}
//var feature = new TargetFeature(sequenceMass, charge, spec.ScanNum);
if (_featureFinder != null)
{
var ms1Corr = _featureFinder.GetMs1EvidenceScore(spec.ScanNum, sequenceMass, charge);
if (ms1Corr < Ms1CorrThreshold)
{
continue;
}
}
var curScoreAndModifications = seqGraph.GetScoreAndModifications(_ms2Scorer);
var curScore = curScoreAndModifications.Item1;
// var curScore = seqGraph.GetFragmentScore(_ms2Scorer);
if (curScore > bestScore)
{
match = new FlankingMassMatch(curScore,
sequenceMass - Composition.H2O.Mass - seqGraph.ShiftMass, charge, curScoreAndModifications.Item2);
//match = new FlankingMassMatch(curScore,
// sequenceMass - Composition.H2O.Mass - seqGraph.ShiftMass, charge, new ModificationInstance[0]);
bestScore = curScore;
}
}
return(match);
}
public void TestMs1EvidenceScore()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string TestRawFile = @"\\protoapps\UserData\Jungkap\Lewy\Lewy_intact_01.pbf";
if (!File.Exists(TestRawFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, TestRawFile);
}
const string TestResultFile = @"\\protoapps\UserData\Jungkap\Lewy\Lewy_intact_01_IcTda.tsv";
if (!File.Exists(TestResultFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, TestResultFile);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFile);
var tsvParser = new TsvFileParser(TestResultFile);
var featureFinder = new LcMsPeakMatrix(run);
for (var i = 0; i < tsvParser.NumData; i++)
{
var scan = int.Parse(tsvParser.GetData("Scan")[i]);
var charge = int.Parse(tsvParser.GetData("Charge")[i]);
var mass = double.Parse(tsvParser.GetData("Mass")[i]);
var qvalue = double.Parse(tsvParser.GetData("QValue")[i]);
//var targetFeature = new TargetFeature(mass, charge, scan);
var score = featureFinder.GetMs1EvidenceScore(scan, mass, charge);
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", scan, mass, charge, qvalue, score);
}
}
public void TestMs1EvidenceScore()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
var testRawFile = Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"TopDown\Lewy_ManyMods\Lewy_intact_01.pbf");
if (!File.Exists(testRawFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, testRawFile);
}
var testResultFile = Path.Combine(Utils.DEFAULT_TEST_FILE_FOLDER, @"TopDown\Lewy_ManyMods\TestOutput\Lewy_intact_01_IcTda.tsv");
if (!File.Exists(testResultFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, testResultFile);
}
var run = PbfLcMsRun.GetLcMsRun(testRawFile);
var tsvParser = new TsvFileParser(testResultFile);
var featureFinder = new LcMsPeakMatrix(run);
for (var i = 0; i < tsvParser.NumData; i++)
{
var scan = int.Parse(tsvParser.GetData("Scan")[i]);
var charge = int.Parse(tsvParser.GetData("Charge")[i]);
var mass = double.Parse(tsvParser.GetData("Mass")[i]);
var qvalue = double.Parse(tsvParser.GetData("QValue")[i]);
//var targetFeature = new TargetFeature(mass, charge, scan);
var score = featureFinder.GetMs1EvidenceScore(scan, mass, charge);
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", scan, mass, charge, qvalue, score);
}
}
