/// <summary>
/// Resets all parameters to default values.
/// </summary>
private void Clear()
{
m_userTolerances = new FeatureMatcherTolerances();
m_useEllipsoid = true;
m_shouldCalculateShiftFDR = true;
m_shouldCalculateSTAC = true;
m_shouldCalculateHistogramFDR = false;
m_shouldCalculateSLiC = true;
m_useDriftTime = false;
m_usePriors = true;
m_chargeStateList = new List <int>();
m_shiftAmount = 11.0;
m_histogramBinWidth = 0.02;
m_histogramMultiplier = 0.1;
}
/// <summary>
/// Sets the internal flag as to whether the match is within the given tolerances.
/// </summary>
/// <param name="tolerances">Tolerances to use for matching.</param>
/// <param name="useElllipsoid">Whether to use ellipsoidal region for matching.</param>
/// <returns></returns>
public bool InRegion(FeatureMatcherTolerances tolerances, bool useElllipsoid)
{
if (m_targetFeature == new TTarget())
{
throw new InvalidOperationException("Match must be populated before using functions involving the match.");
}
var toleranceMatrix = tolerances.AsVector(true);
if (m_reducedDifferenceVector != new DenseMatrix(2, 1))
{
var dimensions = m_reducedDifferenceVector.RowCount;
if (useElllipsoid)
{
double distance = 0;
for (var i = 0; i < dimensions; i++)
{
distance += m_reducedDifferenceVector[i, 0] * m_reducedDifferenceVector[i, 0] / toleranceMatrix[i, 0] / toleranceMatrix[i, 0];
}
m_withinRefinedRegion = (distance <= 1);
}
else
{
var truthValue = true;
for (var i = 0; i < dimensions; i++)
{
truthValue = (truthValue && Math.Abs(m_reducedDifferenceVector[i, 0]) <= toleranceMatrix[i, 0]);
}
m_withinRefinedRegion = truthValue;
}
}
else
{
if (useElllipsoid)
{
double distance = 0;
var massDiff = m_observedFeature.MassMonoisotopicAligned - m_targetFeature.MassMonoisotopicAligned;
var netDiff = m_observedFeature.NetAligned - m_targetFeature.NetAligned;
distance += massDiff * massDiff / toleranceMatrix[0, 0] / toleranceMatrix[0, 0];
distance += netDiff * netDiff / toleranceMatrix[1, 0] / toleranceMatrix[1, 0];
// TODO: Add drift time difference.
m_withinRefinedRegion = (distance <= 1);
}
}
return(m_withinRefinedRegion);
}