/// <summary>
/// Public constructor for the LCMS Alignment Processor
/// Initializes a new LCMSWarp object using the LCMS Alignment options
/// which were passed into the Processor
/// </summary>
public LcmsWarpAlignmentProcessor()
{
m_lcmsWarp = new LcmsWarp();
Options = new LcmsWarpAlignmentOptions();
ApplyAlignmentOptions();
AligningToMassTagDb = false;
}
/// <summary>
/// Method to return the heatmap of the alignment (as a 2D array of doubles) based on
/// the output scores taht
/// </summary>
/// <param name="outputScores"></param>
/// <param name="xIntervals"></param>
/// <param name="yIntervals"></param>
public void GetAlignmentHeatMap(out double[,] outputScores, out double[] xIntervals,
out double[] yIntervals)
{
if (m_lcmsWarp == null)
{
m_lcmsWarp = new LcmsWarp();
}
var alignmentScores = new List <double>();
var aligneeIntervals = new List <double>();
var baselineIntervals = new List <double>();
// Original .cpp code did not include the boolean standardize. Hard coding to false for the moment
// Mike - 3/10/14
m_lcmsWarp.GetSubsectionMatchScore(ref alignmentScores, ref aligneeIntervals, ref baselineIntervals, true);
var numBaselineSections = baselineIntervals.Count;
var numAligneeSections = aligneeIntervals.Count;
outputScores = new double[numBaselineSections, numAligneeSections];
var numTotalSections = alignmentScores.Count;
if (numTotalSections != numBaselineSections * numAligneeSections)
{
throw new ApplicationException("Error in Alignment heatmap scores. Total section is not as expected");
}
var aligneeSection = 0;
var baselineSection = 0;
for (var i = 0; i < numTotalSections; i++)
{
outputScores[baselineSection, aligneeSection] = alignmentScores[i];
baselineSection++;
if (baselineSection != numBaselineSections)
{
continue;
}
baselineSection = 0;
aligneeSection++;
}
xIntervals = new double[numAligneeSections];
for (var i = 0; i < numAligneeSections; i++)
{
xIntervals[i] = aligneeIntervals[i];
}
yIntervals = new double[numBaselineSections];
for (var i = 0; i < numBaselineSections; i++)
{
yIntervals[i] = baselineIntervals[i];
}
}
/// <summary>
/// Public constructor for the LCMS Alignment Processor
/// Initializes a new LCMSWarp object using the LCMS Alignment options
/// that are passed into the Processor
/// </summary>
/// <remarks>
/// Store data using SetReferenceDatasetFeatures and SetAligneeDatasets,
/// then call PerformAlignmentToMsFeatures, which calls either PerformNetWarp or PerformNetMassWarp</remarks>
public LcmsWarpAlignmentProcessor(LcmsWarpAlignmentOptions options)
{
_options = options;
_lcmsWarp = new LcmsWarp(_options);
_lcmsWarp.Progress += lcmsWarp_Progress;
_currentTaskPercentCompleteAtStart = new Dictionary <CurrentLcmsWarpTask, double>
{
{ CurrentLcmsWarpTask.Unstarted, 0 },
{ CurrentLcmsWarpTask.GenerateCandidateMatches, 0 },
{ CurrentLcmsWarpTask.GetMatchProbabilities, 10 },
{ CurrentLcmsWarpTask.CalculateAlignmentMatrix, 90 },
{ CurrentLcmsWarpTask.CalculateAlignmentFunction, 93 },
{ CurrentLcmsWarpTask.GetTransformedNets, 96 },
{ CurrentLcmsWarpTask.CalculateAlignmentMatches, 98 },
{ CurrentLcmsWarpTask.Complete, 100 }
};
_percentCompleteAtStartOfTask = 0;
_percentCompleteAtEndOfTask = 100;
_aligningToMassTagDb = false;
}
/// <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);
}
}
}
}
