/// <summary>
/// Constructor.
/// </summary>
public AnalysisOptions()
{
AlignmentOptions = new AlignmentOptions();
DriftTimeAlignmentOptions = new DriftTimeAlignmentOptions();
ClusterOptions = new LCMSFeatureClusteringOptions();
STACOptions = new StacOptions();
ConsolidationOptions = new FeatureConsolidatorOptions();
}
AlignDriftTimes(List <UMCLight> features, List <UMCLight> baselineFeatures, DriftTimeAlignmentOptions options)
{
UpdateStatus("Correcting drift times.");
var baselineUmCs = new List <UMCLight>();
var aligneeUmCs = new List <UMCLight>();
UpdateStatus("Mapping data structures.");
var featureIdMap = new Dictionary <int, UMCLight>();
foreach (var feature in features)
{
var umc = new UMCLight
{
MassMonoisotopicAligned = feature.MassMonoisotopicAligned,
NetAligned = feature.NetAligned,
DriftTime = Convert.ToSingle(feature.DriftTime),
Id = feature.Id,
ChargeState = feature.ChargeState
};
aligneeUmCs.Add(umc);
featureIdMap.Add(feature.Id, feature);
}
foreach (var feature in baselineFeatures)
{
var umc = new UMCLight
{
MassMonoisotopicAligned = feature.MassMonoisotopicAligned,
NetAligned = feature.Net,
DriftTime = Convert.ToSingle(feature.DriftTime),
Id = feature.Id,
ChargeState = feature.ChargeState
};
baselineUmCs.Add(umc);
}
// filter based on charge state.
var chargeMax = options.MaxChargeState;
var chargeMin = options.MinChargeState;
UpdateStatus(string.Format("Filtering Features Min Charge: {0} <= charge <= Max Charge {1}", chargeMin,
chargeMax));
var filteredQuery = from feature in aligneeUmCs
where feature.ChargeState <= chargeMax && feature.ChargeState >= chargeMin
select feature;
var filteredUmCs = filteredQuery.ToList();
UpdateStatus("Finding Aligned Matches and correcting drift times.");
var alignedResults =
DriftTimeAlignment <UMCLight, UMCLight> .AlignObservedEnumerable(aligneeUmCs,
filteredUmCs,
baselineUmCs,
options.MassPPMTolerance,
options.NETTolerance);
DriftTimeAlignmentResults <UMCLight, UMCLight> offsetResults = null;
if (options.ShouldPerformOffset)
{
UpdateStatus("Adjusting drift time offsets.");
var aligneeData = aligneeUmCs;
if (!options.ShouldUseAllObservationsForOffsetCalculation)
{
UpdateStatus("Using only filtered matches for offset correction.");
aligneeData = filteredUmCs;
}
else
{
UpdateStatus("Using all feature matches for offset correction.");
}
offsetResults = DriftTimeAlignment <UMCLight, UMCLight> .CorrectForOffset(aligneeData, baselineUmCs,
options.MassPPMTolerance, options.NETTolerance, options.DriftTimeTolerance);
}
UpdateStatus("Remapping data structures for persistence to database.");
foreach (var umc in aligneeUmCs)
{
featureIdMap[umc.Id].DriftTime = umc.DriftTimeAligned;
}
var pair =
new KeyValuePair
<DriftTimeAlignmentResults <UMCLight, UMCLight>, DriftTimeAlignmentResults <UMCLight, UMCLight> >(
alignedResults,
offsetResults);
return(pair);
}
/// <summary>
/// Correct for the drift times.
/// </summary>
/// <param name="features"></param>
/// <param name="baselineFeatures"></param>
/// <param name="options"></param>
public KeyValuePair<DriftTimeAlignmentResults<UMCLight, UMCLight>, DriftTimeAlignmentResults<UMCLight, UMCLight>> AlignDriftTimes(List<UMCLight> features, List<UMCLight> baselineFeatures, DriftTimeAlignmentOptions options)
{
UpdateStatus("Correcting drift times.");
var baselineUmCs = new List<UMCLight>();
var aligneeUmCs = new List<UMCLight>();
UpdateStatus("Mapping data structures.");
var featureIdMap = new Dictionary<int, UMCLight>();
foreach (var feature in features)
{
var umc = new UMCLight
{
MassMonoisotopicAligned = feature.MassMonoisotopicAligned,
NetAligned = feature.NetAligned,
DriftTime = Convert.ToSingle(feature.DriftTime),
Id = feature.Id,
ChargeState = feature.ChargeState
};
aligneeUmCs.Add(umc);
featureIdMap.Add(feature.Id, feature);
}
foreach (var feature in baselineFeatures)
{
var umc = new UMCLight
{
MassMonoisotopicAligned = feature.MassMonoisotopicAligned,
NetAligned = feature.Net,
DriftTime = Convert.ToSingle(feature.DriftTime),
Id = feature.Id,
ChargeState = feature.ChargeState
};
baselineUmCs.Add(umc);
}
// filter based on charge state.
var chargeMax = options.MaxChargeState;
var chargeMin = options.MinChargeState;
UpdateStatus(string.Format("Filtering Features Min Charge: {0} <= charge <= Max Charge {1}", chargeMin,
chargeMax));
var filteredQuery = from feature in aligneeUmCs
where feature.ChargeState <= chargeMax && feature.ChargeState >= chargeMin
select feature;
var filteredUmCs = filteredQuery.ToList();
UpdateStatus("Finding Aligned Matches and correcting drift times.");
var alignedResults =
DriftTimeAlignment<UMCLight, UMCLight>.AlignObservedEnumerable(aligneeUmCs,
filteredUmCs,
baselineUmCs,
options.MassPPMTolerance,
options.NETTolerance);
DriftTimeAlignmentResults<UMCLight, UMCLight> offsetResults = null;
if (options.ShouldPerformOffset)
{
UpdateStatus("Adjusting drift time offsets.");
var aligneeData = aligneeUmCs;
if (!options.ShouldUseAllObservationsForOffsetCalculation)
{
UpdateStatus("Using only filtered matches for offset correction.");
aligneeData = filteredUmCs;
}
else
{
UpdateStatus("Using all feature matches for offset correction.");
}
offsetResults = DriftTimeAlignment<UMCLight, UMCLight>.CorrectForOffset(aligneeData, baselineUmCs,
options.MassPPMTolerance, options.NETTolerance, options.DriftTimeTolerance);
}
UpdateStatus("Remapping data structures for persistence to database.");
foreach (var umc in aligneeUmCs)
{
featureIdMap[umc.Id].DriftTime = umc.DriftTimeAligned;
}
var pair =
new KeyValuePair
<DriftTimeAlignmentResults<UMCLight, UMCLight>, DriftTimeAlignmentResults<UMCLight, UMCLight>>(
alignedResults,
offsetResults);
return pair;
}
