public CompositeScorerFactory(
DPbfLcMsRun run,
IMassBinning comparer,
AminoAcidSet aaSet,
int minProductCharge = 1, int maxProductCharge = 20,
double productTolerancePpm = 10,
int isotopeOffsetTolerance = 2,
double filteringWindowSize = 1.1
)
: this(run, comparer, aaSet, minProductCharge, maxProductCharge, new Tolerance(productTolerancePpm), isotopeOffsetTolerance, filteringWindowSize)
{
}
public CompositeScorerFactory(
DPbfLcMsRun run,
IMassBinning comparer,
AminoAcidSet aaSet,
int minProductCharge, int maxProductCharge,
Tolerance productTolerance,
int isotopeOffsetTolerance = 2,
double filteringWindowSize = 1.1)
{
_run = run;
_minProductCharge = minProductCharge;
_maxProductCharge = maxProductCharge;
_productTolerance = productTolerance;
FilteringWindowSize = filteringWindowSize;
IsotopeOffsetTolerance = isotopeOffsetTolerance;
_ms2Scorer = new ConcurrentDictionary <int, IScorer>();
_comparer = comparer;
_scoringGraphFactory = new ProteinScoringGraphFactory(comparer, aaSet);
}
public void CountScansTest()
{
var file = @"C:\Users\wilk011\Documents\DataFiles\MSPF\Ecoli_Ribosome\Ecoli_intact_UVPD-3pulse0p5mJ_05-20-2017.pbf";
var pbfLcmsRun = PbfLcMsRun.GetLcMsRun(file);
var deconvoluter = new Deconvoluter(1, 20, 2, 0.1, new Tolerance(10, ToleranceUnit.Ppm));
var lcmsRunDecon = new LcmsRunDeconvoluter(pbfLcmsRun, deconvoluter, 2, 6);
var dlcms = new DPbfLcMsRun(file, lcmsRunDecon, keepDataReaderOpen: true);
int count = 0;
var scans = pbfLcmsRun.GetScanNumbers(2);
foreach (var scan in scans)
{
var spectrum = pbfLcmsRun.GetSpectrum(scan) as ProductSpectrum;
if (spectrum.Peaks.Length < 50 || spectrum.IsolationWindow.Charge == null)
{
continue;
}
count++;
}
Console.WriteLine(count);
}
/// <summary>
/// Initializes a new instance of the <see cref="FlipScorerFactory" /> class with a new scoring parameter set.
/// </summary>
/// <param name="lcmsRun">LcmsRun for selected deconvoluted spectra required for scoring.</param>
/// <param name="isTopDown">A value indicating whether the experiment is an intact experiment or not.</param>
public FlipScorerFactory(DPbfLcMsRun lcmsRun, bool isTopDown = true)
: this(lcmsRun, new ScoringParameterSet(isTopDown))
{
}
/// <summary>
/// Initializes a new instance of the <see cref="FlipScorerFactory" /> class with a preloaded scoring parameter set.
/// </summary>
/// <param name="lcmsRun">LcmsRun for selected deconvoluted spectra required for scoring.</param>
/// <param name="scoringParameterSet">Existing scoring parameters to select from.</param>
public FlipScorerFactory(DPbfLcMsRun lcmsRun, ScoringParameterSet scoringParameterSet)
{
this.lcmsRun = lcmsRun;
this.scoringParameterSet = scoringParameterSet;
this.scorerHash = new Dictionary <int, IScorer>();
}
