public void RankScore()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const int ranks = 20;
const string filePath = @"\\protoapps\UserData\Wilkins\DIA\DIA.txt";
if (!File.Exists(filePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, filePath);
}
var rankScorer = new RankScore(filePath);
for (int charge = 1; charge < 4; charge++)
{
var ionTypes = rankScorer.GetIonTypes(charge, 0);
foreach (var ionType in ionTypes)
{
for (int r = 0; r <= ranks; r++)
{
Console.WriteLine("Charge: {0}, Ion Type: {1}, Rank: {2}, Score: {3}",
charge, ionType.Name, r, rankScorer.GetScore(ionType, r, charge, 0.0));
}
}
}
}
public ScoredSpectrum(Spectrum spec, RankScore scorer, int charge, double massWithH2O, Tolerance tolerance)
{
_rankedSpec = new RankedSpectrum(spec);
_scorer = scorer;
_charge = charge;
_sequenceMass = massWithH2O;
_tolerance = tolerance;
}
public InformedBottomUpScorer(LcMsRun run, AminoAcidSet aaSet, int minProductCharge, int maxProductCharge, Tolerance tolerance)
{
Run = run;
AminoAcidSet = aaSet;
MinProductCharge = minProductCharge;
MaxProductCharge = maxProductCharge;
Tolerance = tolerance;
_rankScorer = new RankScore(ActivationMethod.HCD, Ms2DetectorType.Orbitrap, Enzyme.Trypsin, Protocol.Standard);
_scoredSpectra = new Dictionary<int, ScoredSpectrum>();
}
public void RankScoreParamResources()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const int ranks = 20;
var rankScorer = new RankScore(ActivationMethod.HCD, Ms2DetectorType.Iontrap, Enzyme.Trypsin,
Protocol.Standard);
for (int charge = 1; charge < 4; charge++)
{
var ionTypes = rankScorer.GetIonTypes(charge, 0);
foreach (var ionType in ionTypes)
{
for (int r = 0; r <= ranks; r++)
{
Console.WriteLine(@"Charge: {0}, Ion Type: {1}, Rank: {2}, Score: {3}",
charge, ionType.Name, r, rankScorer.GetScore(ionType, r, charge, 0.0));
}
}
}
}
public DiaRankScore(string fileName)
{
_rankScore = new RankScore(fileName);
}
public DiaRankScore(string fileName)
{
_rankScore = new RankScore(fileName);
}