/// <summary>
/// Takes a List of UMCLight data and applies the NET/Mass Function to the dataset and
/// aligns it to the baseline. Updates the data in place for the calibrated Masses and
/// Alignment.
/// </summary>
/// <param name="data"></param>
public List <UMCLight> ApplyNetMassFunctionToAligneeDatasetFeatures(List <UMCLight> data)
{
var sortedData = data.OrderBy(x => x.Id).ToList();
IEnumerable <UMCLight> featureData;
if (_aligningToMassTagDb)
{
featureData = _lcmsWarp.GetFeatureCalibratedMassesAndAlignedNets();
}
else
{
featureData = _lcmsWarp.GetFeatureCalibratedMassesAndAlignedNets(_minReferenceDatasetScan,
_maxReferenceDatasetScan, _minReferenceDatasetTime, _maxReferenceDatasetTime);
}
// Update sortedData using featureData
var i = 0;
foreach (var point in featureData.OrderBy(x => x.Id))
{
while (i < data.Count - 1 && sortedData[i].Id < point.Id)
{
i++;
}
while (i > 0 && sortedData[i].Id > point.Id)
{
i--;
}
if (sortedData[i].Id != point.Id)
{
Console.WriteLine("Possible code bug; id {0} not found in sortedData: ", point.Id);
sortedData.Add(point);
continue;
}
if (this._options.AlignType == LcmsWarpAlignmentType.NET_MASS_WARP)
{
sortedData[i].MassMonoisotopicAligned = point.MassMonoisotopicAligned;
}
else
{
sortedData[i].MassMonoisotopicAligned = sortedData[i].MassMonoisotopic;
}
sortedData[i].MassMonoisotopicOriginal = point.MassMonoisotopicOriginal;
sortedData[i].NetAligned = point.NetAligned;
sortedData[i].NetStart = point.NetStart;
sortedData[i].NetEnd = point.NetEnd;
sortedData[i].DriftTime = point.DriftTime;
if (!_aligningToMassTagDb)
{
sortedData[i].ScanAligned = point.ScanAligned;
sortedData[i].DriftTimeAligned = point.DriftTimeAligned;
}
i++;
}
return(sortedData);
}
/// <summary>
/// Takes a List of UMCLight data and applies the NET/Mass Function to the dataset and
/// aligns it to the baseline. Updates the data in place for the calibrated Masses and
/// Alignment.
/// </summary>
/// <param name="data"></param>
public void ApplyNetMassFunctionToAligneeDatasetFeatures(ref List <UMCLight> data)
{
if (m_lcmsWarp == null)
{
m_lcmsWarp = new LcmsWarp();
}
var umcIndices = new List <int>();
var umcCalibratedMasses = new List <double>();
var umcAlignedNets = new List <double>();
var umcAlignedScans = new List <int>();
var umcDriftTimes = new List <double>();
if (AligningToMassTagDb)
{
m_lcmsWarp.GetFeatureCalibratedMassesAndAlignedNets(ref umcIndices, ref umcCalibratedMasses,
ref umcAlignedNets, ref umcDriftTimes);
for (var i = 0; i < umcIndices.Count; i++)
{
var point = new UMCLight
{
Id = umcIndices[i],
MassMonoisotopicAligned = umcCalibratedMasses[i],
NetAligned = umcAlignedNets[i],
DriftTime = umcDriftTimes[i]
};
if (i < data.Count)
{
// Update the data without stomping the data that shouldn't change.
data[i].MassMonoisotopicAligned = point.MassMonoisotopicAligned;
data[i].NetAligned = point.NetAligned;
data[i].DriftTime = point.DriftTime;
}
else
{
data.Add(point);
}
}
}
else
{
m_lcmsWarp.GetFeatureCalibratedMassesAndAlignedNets(ref umcIndices, ref umcCalibratedMasses,
ref umcAlignedNets, ref umcAlignedScans,
ref umcDriftTimes, m_minReferenceDatasetScan,
m_maxReferenceDatasetScan);
for (var i = 0; i < umcIndices.Count; i++)
{
var point = new UMCLight
{
Id = umcIndices[i],
MassMonoisotopicAligned = umcCalibratedMasses[i],
NetAligned = umcAlignedNets[i],
ScanAligned = umcAlignedScans[i],
DriftTime = umcDriftTimes[i]
};
if (i < data.Count)
{
// Update the data without stomping the data that shouldn't change.
data[i].MassMonoisotopicAligned = point.MassMonoisotopicAligned;
data[i].NetAligned = point.NetAligned;
data[i].ScanAligned = point.ScanAligned;
data[i].DriftTime = point.DriftTime;
}
else
{
data.Add(point);
}
}
}
}