<?xml version="1.0"?>
<doc>
<assembly>
<name>ThermoFisher.CommonCore.BackgroundSubtraction</name>
</assembly>
<members>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractionSettings">
<summary>
Settings for the background subtraction algorithm.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractionSettings.Range1EndTime">
<summary>
Gets or sets Background range 1 end time.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractionSettings.Range1StartTime">
<summary>
Gets or sets Background range 1 start time.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractionSettings.Range2EndTime">
<summary>
Gets or sets Background range 2 end time.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractionSettings.Range2StartTime">
<summary>
Gets or sets Background range 2 start time.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractionSettings.SelectedRange1">
<summary>
Gets or sets a value indicating whether Background range 1 will be used.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractionSettings.SelectedRange2">
<summary>
Gets or sets a value indicating whether Background range 1 will be used.
</summary>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractor">
<summary>
Computes and returns the average subtracted scan
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractor.Averager">
<summary>
Gets Averager.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractor.GetForeGroundAvgScan(System.Double,System.Double)">
<summary>
Calculate the foreground average scan.
</summary>
<param name="startTime">
The start time.
</param>
<param name="endTime">
The end time.
</param>
<returns>
The averaged scan
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractor.GetBackGroundAverageScan(ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractionSettings)">
<summary>
Calculate a background average scan.
</summary>
<param name="backSettings">
The background subtraction settings.
</param>
<returns>
The averaged background
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractor.GetScanStatistics(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReaderPlus,System.Int32,System.Int32,System.String)">
<summary>
Get scan statistics.
</summary>
<param name="plus">
The plus.
</param>
<param name="start">
The start scan.
</param>
<param name="end">
The end scan.
</param>
<param name="filter">
The scan filter.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractor.InitializeScanList(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReader,System.Int32,System.Int32,System.String)">
<summary>Initializes the scan list.</summary>
<param name="detectorReader">The detector reader.</param>
<param name="start">The start.</param>
<param name="end">The end.</param>
<param name="filter">The filter.</param>
<exception cref="T:System.ArgumentNullException">detectorReader</exception>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractor.InitializeScanList(ThermoFisher.CommonCore.Data.Interfaces.IRawData,System.Int32,System.Int32,System.String)">
<summary>Initializes the scan list.</summary>
<param name="rawData">The raw data.</param>
<param name="start">The start.</param>
<param name="end">The end.</param>
<param name="filter">The filter.</param>
<exception cref="T:System.ArgumentNullException">rawData</exception>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractor.UpdateScanList(System.String,ThermoFisher.CommonCore.Data.Business.Scan)">
<summary>Updates the scan list.</summary>
<param name="filter">The filter.</param>
<param name="scan">The scan.</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractor.GetBackgroundSubtraction(ThermoFisher.CommonCore.Data.Interfaces.IRawData,System.String,ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractionSettings,System.Double,System.Double)">
<summary>
Computes the average scan and then subtracts the background average scan and
return the average subtracted scan.
</summary>
<param name="rawFile">
Raw file to read scans based on time.
</param>
<param name="filter">
scan filter
</param>
<param name="backSettings">
Background Information.
</param>
<param name="startTime">
Foreground StartTime.
</param>
<param name="endTime">
Foreground EndTime.
</param>
<returns>
Scan object containing the subtracted scan.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractor.GetBackgroundSubtraction(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReader,System.String,ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractionSettings,System.Double,System.Double)">
<summary>
Computes the average scan and then subtracts the background average scan and
return the average subtracted scan.
</summary>
<param name="detectorReader">
Raw file to read scans based on time.
</param>
<param name="filter">
scan filter
</param>
<param name="backSettings">
Background Information.
</param>
<param name="startTime">
Foreground StartTime.
</param>
<param name="endTime">
Foreground EndTime.
</param>
<returns>
Scan object containing the subtracted scan.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractor.GetBackgroundSubtraction(ThermoFisher.CommonCore.Data.Interfaces.IRawData,System.String,ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractionSettings,ThermoFisher.CommonCore.Data.Business.Scan)">
<summary>
Computes the average scan and then subtracts the background average scan and
return the average subtracted scan.
</summary>
<param name="rawFile">
Raw file to read scans based on time.
</param>
<param name="filter">
scan filter
</param>
<param name="backSettings">
Background Information.
</param>
<param name="foreAverageScan">
Scan which data is subtracted from
</param>
<returns>
The subtracted scan.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractor.GetBackgroundSubtraction(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReader,System.String,ThermoFisher.CommonCore.BackgroundSubtraction.BackgroundSubtractionSettings,ThermoFisher.CommonCore.Data.Business.Scan)">
<summary>
Computes the average scan and then subtracts the background average scan and
return the average subtracted scan.
</summary>
<param name="detectorReader">
Detector reader to read scans based on time.
</param>
<param name="filter">
scan filter
</param>
<param name="backSettings">
Background Information.
</param>
<param name="foreAverageScan">
Scan which data is subtracted from
</param>
<returns>
The subtracted scan.
</returns>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint">
<summary>
This internal class is used to capture a point in the centroid scan.
It is specific to the algorithm (internal)
as it includes values such as "index" used for certain sorting features.
Also:
Noise and baseline values are not included in this data structure.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint.Position">
<summary>
Gets or sets the mass to charge ratio
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint.Intensity">
<summary>
Gets or sets the intensity
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint.Resolution">
<summary>
Gets or sets the resolution
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint.Charge">
<summary>
Gets or sets the charge
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint.Index">
<summary>
Gets or sets the index into the mass ordered list
</summary>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.ChargeResult">
<summary>
The charge result, represents a proposed set of isotopes
which have a charge
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.ChargeResult.Charge">
<summary>
Gets or sets the charge.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.ChargeResult.Isotopes">
<summary>
Gets or sets the isotopes.
</summary>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.NamespaceDoc">
<summary>
This namespace contains code related to averaging and background
subtraction of scans. When data is available via the IRawDataPlus interface
it is often simpler to use these features by extension methods on IRawDataPlus
which are published in the CommonCore.Data namespace, in the Extensions class.
</summary>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.NoisePackets">
<summary>
The noise packets.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.NoisePackets.Mass">
<summary>
Gets or sets the mass.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.NoisePackets.Noise">
<summary>
Gets or sets the noise.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.NoisePackets.BaseLine">
<summary>
Gets or sets the base line.
</summary>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator">
<summary>
<code>
This is a variant of the Patterson algorithm for calculating the charge from
a given set of measured points in a mass segment. The original algorithm
operates on profile points. Because this degrades the performance of the
algorithm significantly for FTMS data (due to their high sampling rate), this
variant operates on the detected centroids in a given mass segment instead.
The algorithm steps through the given centroid segment and calculates the
corresponding charge state for each two neighbors in the segment from their
mass distance. The calculation is made according to:
charge_i,n = dM_iso / (m(i+n) - m(i))
where dM_iso is the general average delta mass between two isotopic peaks.
For each calculated charge a score is calculated according to:
score_i,n = y(i+n) * y(i) / y2
where y(i), and y(i+n) are the intensities of the i-th, and the i-th plus one
centroid, respectively, and y2 is the intensity of the most intense centroid
in between them.
All calculated scores are multiplied to the corresponding entry in the
provided charge map.
The number of comparisons done in the Patterson charge calculation increases
with the square of the number of centroids contained in the segment (exactly
this is 0.5 * n * (n-1). To speed up the Patterson charge calculation in
those cases where we have a large number of centroids, an intensity threshold
is calculated that limits the number of centroid whose intensity is lying
above. The ratio behind this is, that the more intense peaks should be the
more important ones for the isotopic cluster.
POSSIBLE ENHANCEMENTS:
Currently the algorithm does not make benefit of the specific centroids that
have contributed to the score of a certain charge state in the charge map.
This information is available, but thrown away once that a charge is entered
into the map. After determining the charge we have to identify the isotopic
cluster to which the charge should be applied. In this step we need again
the information about the position of the peaks that make up the isotopic
cluster. Thus is might be beneficial if we would combine both.
</code>
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.AverageIsotopicDelta">
<summary>
The average isotopic delta.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.AverageIsotopicDeltaDeviation">
<summary>
The average isotopic delta deviation.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.ChargeMapDensity">
<summary>
The charge map density.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.DeltaCharge">
<summary>
The delta charge.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.MaxCentroidsForPattersonCharge">
<summary>
The max centroids for patterson charge.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.MaxChargeState">
<summary>
The max charge state.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.PattersonHighChargeUpscaleFactor">
<summary>
The patterson high charge upscale factor.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.#ctor">
<summary>
Initializes a new instance of the <see cref="T:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator"/> class.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.CalculatePattersonCharge(System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},System.Int32,System.Int32,System.Double,System.Double)">
<summary>
Calculates a distribution of possible charge states based upon
the pairwise distances between the centroid peaks.
</summary>
<param name="centroids">
data for scan
</param>
<param name="beginRangeIndex">
The start of the centroid segment to analyze.
</param>
<param name="endRangeIndex">
The end of the centroid segment to analyze.
</param>
<param name="profileSpacing">
The spacing of profile points. This spacing is used to calculate the maximum theoretical charge for which the isotopic pattern could be resolved.
</param>
<param name="massAccuracy">
The mass accuracy to apply for the identification of the isotopic cluster peaks.
</param>
<returns>
The calculated patterson charge.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.FastMax(System.Double[])">
<summary>
Find the max value in an array of doubles.
(don't use slow LINQ extension Max() )
</summary>
<param name="arrayOfDoubles">Numbers to examine</param>
<returns>max, or 0 if empty</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.CalculateIntensityThreshold(System.Int32,System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},System.Int32,System.Int32)">
<summary>
Calculate an intensity threshold for a given range of centroids.
</summary>
<param name="maxCentroidsAboveThreshold">
The maximum number of centroids that should lie above the calculated threshold.
</param>
<param name="centroids">
data for scan
</param>
<param name="beginRangeIndex">
begin of the centroid
</param>
<param name="endRangeIndex">
end of the centroid
</param>
<returns>
The calculated intensity threshold.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.FindCount(System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},System.Int32,System.Int32,System.Double)">
<summary>
Finds the count of values above the threshold
</summary>
<param name="centroids">
List of Centroids
</param>
<param name="startIndex">
Start of array slice to analyze
</param>
<param name="endIndex">
End of array slice to analyze
</param>
<param name="intensityThreshold">The smallest counted value
</param>
<returns>
The count above threshold
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.GetChargeMapIndexForCharge(System.Double)">
<summary>
Get the charge map index for a specific charge.
</summary>
<param name="charge">
The charge.
</param>
<returns>
The charge map index for this charge.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.IndexOfMax(System.Double[])">
<summary>
Find the index of max value in an array of doubles
</summary>
<param name="arrayOfDoubles">Numbers to examine</param>
<returns>Index of max, or -1 if list is empty</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PattersonChargeCalculator.NormalizeChargeMap(System.Double[])">
<summary>
Smooth, normalize and transfer the local map to the result charge map.
</summary>
<param name="localChargeMap">
The local charge map.
</param>
<returns>
The smoothed map.
</returns>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator">
<summary>
The peak charge calculator.
Calculates charge for one peak in the centroid list.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.AverageIsotopicDelta">
<summary>
The average isotopic delta.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.AverageIsotopicDeltaDeviation">
<summary>
The average isotopic delta deviation.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.ChargeEvaluationScoreSepartion">
<summary>
The charge evaluation score separation.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.ChargeEvaluationTolerance">
<summary>
The charge evaluation tolerance.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.ChargeMapDensity">
<summary>
The charge map density.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.DefaultMassAccuracy">
<summary>
The default mass accuracy. PPM.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.DeltaCharge">
<summary>
The delta charge.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.MaxHighMassRangeForChargeDetermination">
<summary>
The max high mass range for charge determination.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.MaxIsotopicPeaksPerCluster">
<summary>
The max isotopic peaks per cluster.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.MaxLowMassRangeForChargeDetermination">
<summary>
The max low mass range for charge determination.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.MaxOrder">
<summary>
The max order for FT.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.MinOrder">
<summary>
The min order for FT.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.#ctor">
<summary>
Initializes a new instance of the <see cref="T:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator" /> class.
Default constructor
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.MassAccuracy">
<summary>
Gets or sets the mass accuracy, in PPM. Default 5 PPM.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.CentroidBegin(System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CentroidPositionComparer,ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint)">
<summary>
Find index of first mass in range.
</summary>
<param name="massSortedCentroidList">
The mass sorted centroid list.
</param>
<param name="centroidPositionComparer">
The centroid position comparer.
</param>
<param name="lowerCentroid">
The lower centroid.
</param>
<returns>
The index of first mass in range.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.CalculateChargeForPeak(ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData,System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CentroidPositionComparer,ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint)">
<summary>
Calculate charge for peak.
</summary>
<param name="segmentList">
The segment list.
</param>
<param name="massSortedCentroidList">
The mass sorted centroid list.
</param>
<param name="centroidPositionComparer">
The centroid position comparer.
</param>
<param name="centroid">
The peak whose charge is needed.
</param>
<returns>
The <see cref="T:ThermoFisher.CommonCore.BackgroundSubtraction.ChargeResult"/>.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.CalculateChargeMapScores(System.Double[],System.Int32,System.Double,System.Double[])">
<summary>
The calculate charge map scores.
</summary>
<param name="fftVector">
The FFT vector.
</param>
<param name="halfSize">
The half size.
</param>
<param name="fftSpacing">
The FFT spacing.
</param>
<param name="localChargeMap">
The local charge map.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.CalculateComplexModulus(System.Double[],System.Int32)">
<summary>
The calculate complex modulus.
</summary>
<param name="fftVector">
The FFT vector.
</param>
<param name="halfSize">
The half size.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.CalculateFftCharge(System.Double[],ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData,System.Int32,System.Int32,System.Double)">
<summary>
Calculates a distribution of possible charge states based upon
an FFT analysis of the input profile spectrum.
</summary>
<param name="chargeMap">
charge map object to fill the scores for the Patterson calculation info
</param>
<param name="segments">
Profile data to be analyzed
</param>
<param name="startIndex">
start of the profile segment to analyze
</param>
<param name="endIndex">
end of the profile segment to analyze.
</param>
<param name="profileSpacing">
The spacing of profile points. This spacing is used to calculate the maximum theoretical charge
for which the isotopic pattern could be resolved.
</param>
<returns>
The map
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.CentroidEnd(System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CentroidPositionComparer,ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint)">
<summary>
Find the centroid end.
</summary>
<param name="massSortedCentroidList">
The mass sorted centroid list.
</param>
<param name="centroidPositionComparer">
The centroid position comparer.
</param>
<param name="upperCentroid">
The upper centroid.
</param>
<returns>
The centroid end.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.EvaluateChargeMap(System.Double[])">
<summary>
Evaluate the given charge map and report the best scored charge
if it is both, valid and significant.
</summary>
<param name="chargeMapList">
charge map list to evaluate.
</param>
<returns>
highest scored charge in the map
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.FindProfileSpacing(ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData,System.Int32,System.Int32)">
<summary>
find profile spacing.
</summary>
<param name="segmentList">
The segment list.
</param>
<param name="begin">
The begin.
</param>
<param name="end">
The end.
</param>
<returns>
The profile spacing.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.IdentifyIsotopicCluster(System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},System.Int32,System.Int32,System.Double)">
<summary>
Identifies a possible isotopic cluster.
</summary>
<param name="centroidList">
The list of centroids to process
</param>
<param name="centerPointer">
The center of the isotopic cluster to identify
</param>
<param name="charge">
The charge of the isotopic cluster.
</param>
<param name="massAccuracy">
The mass accuracy to apply for the identification of the isotopic cluster peaks.
</param>
<returns>
The identify isotopic cluster and assign charge.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.IndexOfMax(System.Double[],System.Int32,System.Int32)">
<summary>
The index of max element.
</summary>
<param name="listofDoubles">
The list of doubles.
</param>
<param name="from">
The from.
</param>
<param name="to">
The to.
</param>
<returns>
The index.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.IndexOfMax(System.Double[])">
<summary>
Find the index of max value in a list of doubles
</summary>
<param name="listofDoubles">Numbers to examine</param>
<returns>Index of max, or -1 if list is empty</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.IndexOfMinimum(System.Double[],System.Int32,System.Int32)">
<summary>
Gets the index of minimum.
</summary>
<param name="listofDoubles">
The list of doubles.
</param>
<param name="from">
The from index.
</param>
<param name="to">
The to index.
</param>
<returns>
The index of min.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.LookAboveCenterMass(System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},System.Int32,System.Int32,System.Int32,System.Collections.Generic.List{System.Int32},System.Collections.Generic.List{System.Int32},System.Double,System.Double,System.Double)">
<summary>
Look above center mass.
</summary>
<param name="centroidList">
The centroid list.
</param>
<param name="charge">
The charge.
</param>
<param name="endPointer">
The end pointer.
</param>
<param name="centerPointer">
The center pointer.
</param>
<param name="isotopes">
The isotopes.
</param>
<param name="tempIsotopes">
The temp isotopes.
</param>
<param name="maxStep">
The max step.
</param>
<param name="massAccuracy">
The mass accuracy.
</param>
<param name="minStep">
The min step.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.LookBelowCenterMass(System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},System.Int32,System.Int32,System.Int32,System.Collections.Generic.List{System.Int32},System.Collections.Generic.List{System.Int32},System.Double,System.Double,System.Double)">
<summary>
Look below the center mass.
</summary>
<param name="centroidList">
The centroid list.
</param>
<param name="charge">
The charge.
</param>
<param name="beginPointer">
The begin pointer.
</param>
<param name="centerPointer">
The center pointer.
</param>
<param name="isotopes">
The isotopes.
</param>
<param name="tempIsotopes">
The temp isotopes.
</param>
<param name="maxStep">
The max step.
</param>
<param name="massAccuracy">
The mass accuracy.
</param>
<param name="minStep">
The min step.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.LowerBound(ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData,System.Double)">
<summary>
Lower bound. This method returns the first value which is within range
</summary>
<param name="segmentList">
The segment list.
</param>
<param name="lower">
The lower.
</param>
<returns>
The lower bound.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.NormalizeChargeMap(System.Double[],System.Double[])">
<summary>
Normalize the charge map.
</summary>
<param name="chargeMap">
The charge map.
</param>
<param name="localChargeMap">
The local charge map.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.UpperBound(ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData,System.Double)">
<summary>
Upper bound. This method returns the first value which is out of range
</summary>
<param name="segmentList">
The segment list.
</param>
<param name="upper">
The upper mass limit.
</param>
<returns>
The upper bound.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.PeakChargeCalculator.CalculateCharge(ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData,System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},System.Int32,System.Int32,System.Double,System.Int32,System.Double,System.Int32)">
<summary>
Calculate the charge.
</summary>
<param name="segmentList">
The segment list.
</param>
<param name="massSortedCentroidList">
The mass sorted centroid list.
</param>
<param name="end">
The end.
</param>
<param name="begin">
The begin.
</param>
<param name="profileSpacing">
The profile spacing.
</param>
<param name="centroidBegin">
The centroid begin.
</param>
<param name="massAccuracy">
The mass accuracy.
</param>
<param name="centroidEnd">
The centroid end.
</param>
<returns>
The calculated charge.
</returns>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager">
<summary>
This class owns and manages a Scan that is produced by averaging a list of scans.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.RawDataReaderPlus">
<summary>
Gets the raw data plus.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.ScanCreator">
<summary>
Gets or sets the scan reader.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.CacheLimit">
<summary>
Gets or sets the limit to the number of scans which may be kept in a cache.
This is valuable when many scan averages are requested from a raw file, with overlapping scan ranges.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.FromFile(ThermoFisher.CommonCore.Data.Interfaces.IRawData,System.Int32)">
<summary>
Factory Method to return the IScanAverage interface.
</summary>
<param name="data">
Access to the raw data, to read the scans.
</param>
<param name="cacheLimit">
Permits the FT averaging algorithm to cache a number of scans. Default 20
</param>
<returns>
An interface to average scans.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.FromDetector(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReader,System.Int32)">
<summary>
Factory Method to return the IScanAverage interface.
</summary>
<param name="rawDataReader">
Access to the raw data, to read the scans.
</param>
<param name="cacheLimit">
Permits the FT averaging algorithm to cache a number of scans. Default 20
</param>
<returns>
An interface to average scans.
</returns>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.FtOptions">
<summary>
Gets or sets options For FT or Orbitrap data.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.GetAverageScanInTimeRange(System.Double,System.Double,System.String)">
<summary>
Gets the average scan between the given times.
Mass tolerance is taken from default values in the raw file
If "PermitRedirection" and the supplied raw file reader supports IScanAverage,
then the averaging is performed by the file reading tool.
</summary>
<param name="startTime">
start time
</param>
<param name="endTime">
end time
</param>
<param name="filter">
filter string
</param>
<returns>
returns the averaged scan.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.GetAverageScanInTimeRange(System.Double,System.Double,System.String,System.Double,ThermoFisher.CommonCore.Data.ToleranceMode)">
<summary>
Gets the average scan between the given times.
If "PermitRedirection" and the supplied raw file reader supports IScanAverage,
then the averaging is performed by the file reading tool.
</summary>
<param name="startTime">
start time
</param>
<param name="endTime">
end time
</param>
<param name="filter">
filter string
</param>
<param name="tolerance">
mass tolerance
</param>
<param name="toleranceMode">
unit of tolerance
</param>
<returns>
returns the averaged scan.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.ScanRangeFromTimeRange(System.Tuple{System.Double,System.Double})">
<summary>
Convert a time range to a scan range
</summary>
<param name="timeRange">
The time range.
</param>
<returns>
The scan range.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.AverageScanInScanRange(System.String,System.Double,ThermoFisher.CommonCore.Data.ToleranceMode,System.Tuple{System.Int32,System.Int32})">
<summary>
Average scan in a given scan range.
</summary>
<param name="filter">
The filter.
</param>
<param name="tolerance">
The tolerance.
</param>
<param name="toleranceMode">
The tolerance mode.
</param>
<param name="scans">
The start scan (Item1) and end scan (Item2).
</param>
<returns>
The average of the scans in range which match the filter.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.GetAverageScanInScanRange(System.Int32,System.Int32,System.String)">
<summary>
Gets the average scan between the given times.
Mass tolerance is taken from default values in the raw file
If "PermitRedirection" and the supplied raw file reader supports IScanAverage,
then the averaging is performed by the file reading tool.
</summary>
<param name="startScan">
start scan
</param>
<param name="endScan">
end scan
</param>
<param name="filter">
filter string
</param>
<returns>
returns the averaged scan.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.GetAverageScanInScanRange(System.Int32,System.Int32,System.String,System.Double,ThermoFisher.CommonCore.Data.ToleranceMode)">
<summary>
Gets the average scan between the given times.
If "PermitRedirection" and the supplied raw file reader supports IScanAverage,
then the averaging is performed by the file reading tool.
</summary>
<param name="startScan">
start scan
</param>
<param name="endScan">
end scan
</param>
<param name="filter">
filter string
</param>
<param name="tolerance">
mass tolerance
</param>
<param name="toleranceMode">
unit of tolerance
</param>
<returns>
returns the averaged scan.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.AverageSpectra(System.Collections.Generic.List{ThermoFisher.CommonCore.Data.Business.ScanStatistics})">
<summary>
Calculates the average spectra based upon the list supplied.
If "PermitRedirection" and the supplied raw file reader supports IScanAverage,
then the averaging is performed by the file reading tool.
</summary>
<param name="scanStatsList">
list of ScanStatistics
</param>
<returns>
The average of all scans in the list
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.#ctor(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReaderBase)">
<summary>
Initializes a new instance of the <see cref="T:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager"/> class.
</summary>
<param name="data">
The data.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.AverageScans(System.Boolean,System.Double,ThermoFisher.CommonCore.Data.ToleranceMode,System.Boolean)">
<summary>
Calculates the average scan given the list of scans.
</summary>
<param name="userTolerance">
To use User Tolerance or not
</param>
<param name="tolerance">
Tolerance value
</param>
<param name="unitType">
Types of Tolerance units (MMU,PPM...)
</param>
<param name="alwaysMergeSegments">Always merge segments, regardless of mass range (where there is only one segment)</param>
<returns>
The averaged scans.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.AverageFtProfiles(ThermoFisher.CommonCore.Data.Business.Scan,ThermoFisher.CommonCore.Data.Interfaces.IScanCreator)">
<summary>
Average ft profiles.
</summary>
<param name="firstScan">
The first scan.
</param>
<param name="ftmsScanCreator">tool to read and cache scans</param>
<returns>
The average of the listed scans.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.AddAllScansToAverage(System.Int32,ThermoFisher.CommonCore.Data.Business.Scan,System.Int32@)">
<summary>
Add all scans to the average.
</summary>
<param name="scanInList">
The scan in list.
</param>
<param name="averageScan">
The average scan so far.
</param>
<param name="scanCount">
The scan count.
</param>
<returns>
The averaged scan.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.AddScanToAverage(ThermoFisher.CommonCore.Data.Business.Scan,System.Int32@,System.Int32)">
<summary>
Add a scan to the average, provided it can be merged (is compatible) with the
average so far.
</summary>
<param name="averageScan">
Average so far
</param>
<param name="scanCount">
Count of scans successfully added to the average
</param>
<param name="indexOfScanToAdd">
Index into table of scans
</param>
<returns>
The updated scan
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.GetIndexOfScanWithHighestTic(System.Int32)">
<summary>
Find the scan number with the highest TIC value
</summary>
<param name="scansInList">
number of scans to search
</param>
<returns>
index into ScanStatsList with largest TIC
</returns>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.RawFileToleranceMode">
<summary>
Gets RawFileToleranceMode.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.ConvertToleranceMode(ThermoFisher.CommonCore.Data.ToleranceUnits)">
<summary>
convert tolerance mode.
</summary>
<param name="unit">
The unit.
</param>
<returns>
The <see cref="T:ThermoFisher.CommonCore.Data.ToleranceMode"/>.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.GetScanStatistics(System.Int32,System.Int32,System.String)">
<summary>
Get the scan statistics.
</summary>
<param name="start">
The start scan.
</param>
<param name="end">
The end scan.
</param>
<param name="filter">
The filter.
</param>
<returns>
The list of scan statistics for scans matching the filter.
</returns>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAverager.ScansCached">
<summary>
Gets or sets the number of scans which may be cached.
Setting ScansCached >0 will enable caching of recently read scans.
This is useful if averaging multiple overlapping ranges of scans.
</summary>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAveragerPlus">
<summary>
Implements the IScanAveragePlus interface against a raw file
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAveragerPlus.#ctor(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReaderPlus)">
<summary>
Initializes a new instance of the <see cref="T:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAveragerPlus"/> class.
</summary>
<param name="rawDataReaderPlus">
The raw data reader plus.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAveragerPlus.FromFile(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReaderPlus)">
<summary>
Factory Method to return the IScanAverage interface.
</summary>
<param name="rawData">
Access to the raw data, to read the scans.
</param>
<returns>
An interface to average scans.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAveragerPlus.FromDetector(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReader)">
<summary>
Factory Method to return the IScanAverage interface.
</summary>
<param name="detectorReader">
Access to the raw data, to read the scans.
</param>
<returns>
An interface to average scans.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAveragerPlus.AverageScansInTimeRange(System.Double,System.Double,System.String,ThermoFisher.CommonCore.Data.Business.MassOptions)">
<summary>
Gets the average scan between the given times.
</summary>
<param name="startTime">
start time
</param>
<param name="endTime">
end time
</param>
<param name="filter">
filter string
</param>
<param name="options">mass tolerance settings. If not supplied, these are default from the raw file</param>
<returns>
the averaged scan. Use Scan.ScansCombined to find how many scans were averaged.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAveragerPlus.AverageScansInTimeRange(System.Double,System.Double,ThermoFisher.CommonCore.Data.Interfaces.IScanFilter,ThermoFisher.CommonCore.Data.Business.MassOptions)">
<summary>
Gets the average scan between the given times.
</summary>
<param name="startTime">
start time
</param>
<param name="endTime">
end time
</param>
<param name="filter">
filter rules
</param>
<param name="options">mass tolerance settings. If not supplied, these are default from the raw file</param>
<returns>
the averaged scan. Use Scan.ScansCombined to find how many scans were averaged.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAveragerPlus.AverageScansInScanRange(System.Int32,System.Int32,System.String,ThermoFisher.CommonCore.Data.Business.MassOptions)">
<summary>
Gets the average scan between the given times.
</summary>
<param name="startScan">
start scan
</param>
<param name="endScan">
end scan
</param>
<param name="filter">
filter string
</param>
<param name="options">mass tolerance settings. If not supplied, these are default from the raw file</param>
<returns>
the averaged scan. Use Scan.ScansCombined to find how many scans were averaged.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAveragerPlus.AverageScansInScanRange(System.Int32,System.Int32,ThermoFisher.CommonCore.Data.Interfaces.IScanFilter,ThermoFisher.CommonCore.Data.Business.MassOptions)">
<summary>
Gets the average scan between the given times.
</summary>
<param name="startScan">
start scan
</param>
<param name="endScan">
end scan
</param>
<param name="filter">
filter rules
</param>
<param name="options">mass tolerance settings. If not supplied, these are default from the raw file</param>
<returns>
the averaged scan. Use Scan.ScansCombined to find how many scans were averaged.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAveragerPlus.MakeScanStatsListPlus(System.Int32,System.Int32,ThermoFisher.CommonCore.Data.Business.ScanFilterHelper)">
<summary>
Make scan stats list plus.
</summary>
<param name="startScan">
The start scan.
</param>
<param name="endScan">
The end scan.
</param>
<param name="filterHelper">
The filter helper.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAveragerPlus.AverageScans(System.Collections.Generic.List{ThermoFisher.CommonCore.Data.Business.ScanStatistics},ThermoFisher.CommonCore.Data.Business.MassOptions)">
<summary>
Calculates the average spectra based upon the list supplied.
The application should filter the data before making this code, to ensure that
the scans are of equivalent format. The result, when the list contains scans of
different formats (such as linear trap MS centroid data added to orbitrap MS/MS profile data) is undefined.
If the first scan in the list contains "FT Profile",
then the FT data profile is averaged for each
scan in the list. The combined profile is then centroided.
If the first scan is profile data, but not orbitrap data:
All scans are summed, starting from the final scan in this list, moving back to the first scan in
the list, and the average is then computed.
For simple centroid data formats: The scan stats "TIC" value is used to find the "most abundant scan".
This scan is then used as the "first scan of the average".
Scans are then added to this average, taking scans alternatively before and after
the apex, merging data within tolerance.
</summary>
<param name="scanStatsList">
list of ScanStatistics
</param>
<param name="options">mass tolerance settings. If not supplied, these are default from the raw file</param>
<returns>
The average of the listed scans. Use Scan.ScansCombined to find how many scans were averaged.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAveragerPlus.AverageScans(System.Collections.Generic.List{System.Int32},ThermoFisher.CommonCore.Data.Business.MassOptions,System.Boolean)">
<summary>
Calculates the average spectra based upon the list supplied.
The application should filter the data before making this code, to ensure that
the scans are of equivalent format. The result, when the list contains scans of
different formats (such as linear trap MS centroid data added to orbitrap MS/MS profile data) is undefined.
If the first scan in the list contains "FT Profile",
then the FT data profile is averaged for each
scan in the list. The combined profile is then centroided.
If the first scan is profile data, but not orbitrap data:
All scans are summed, starting from the final scan in this list, moving back to the first scan in
the list, and the average is then computed.
For simple centroid data formats: The scan stats "TIC" value is used to find the "most abundant scan".
This scan is then used as the "first scan of the average".
Scans are then added to this average, taking scans alternatively before and after
the apex, merging data within tolerance.
</summary>
<param name="scans">
list of scans to average
</param>
<param name="options">mass tolerance settings. If not supplied, these are default from the raw file</param>
<param name="alwaysMergeSegments">
Merge data from scans
which were not scanned over a similar range.
Only applicable when scans only have a single segment.
By default: Scans are considered incompatible if:
The span of the scanned mass range differs by 10%
The start or end of the scanned mass range differs by 10%
If this is set as "true" then any mass ranges will be merged.
Default: false
</param>
<returns>
The average of the listed scans. Use Scan.ScansCombined to find how many scans were averaged.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAveragerPlus.SubtractScans(ThermoFisher.CommonCore.Data.Business.Scan,ThermoFisher.CommonCore.Data.Business.Scan,ThermoFisher.CommonCore.Data.Business.MassOptions)">
<summary>
Subtracts the background scan from the foreground scan
</summary>
<param name="foreground">Foreground data (Left of "scan-scan" operation</param>
<param name="background">Background data (right of"scan-scan" operation)</param>
<param name="options">(optional) mass tolerance options. If this is null,
tolerance which is already configured in "foreground" is used</param>
<returns>The result of foreground-background</returns>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.ScanAveragerPlus.ScanReader">
<summary>
Gets or sets the scan reader.
</summary>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromFileCreator">
<summary>
Get scan data from a raw data, based on a know list of scans.
Can avoid getting the same can multiple times, using a cache.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromFileCreator.CacheLimit">
<summary>
Gets or sets the cache limit.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromFileCreator.Initialize(System.Collections.Generic.List{System.Int32},System.Int32)">
<inheritdoc />
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromFileCreator.#ctor(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReaderBase)">
<summary>
Initializes a new instance of the <see cref="T:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromFileCreator"/> class.
</summary>
<param name="rawDataReader">
The raw file.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromFileCreator.CreateSegmentedScan(System.Int32)">
<summary>
create segmented scan.
</summary>
<param name="index">
The index into the supplied table of scans (on construction)
</param>
<returns>
The <see cref="T:ThermoFisher.CommonCore.Data.Business.SegmentedScan"/>.
</returns>
<exception cref="T:System.ArgumentOutOfRangeException">when index is outside of the scan numbers array
</exception>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromFileCreator.CreateCentroidStream(System.Int32)">
<summary>
Create a centroid stream.
</summary>
<param name="index">
The index into the supplied table of scans (on construction)
</param>
<returns>
The <see cref="T:ThermoFisher.CommonCore.Data.Business.CentroidStream"/>.
</returns>
<exception cref="T:System.ArgumentOutOfRangeException">when index is outside of the scan numbers array
</exception>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromListCreator">
<summary>
Class to support background subtract, which uses a scan list, instead of a raw file for a data
source.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromListCreator.#ctor(System.Collections.Generic.List{ThermoFisher.CommonCore.Data.Business.Scan})">
<summary>
Initializes a new instance of the <see cref="T:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromListCreator"/> class.
</summary>
<param name="scanList">
The scan list.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromListCreator.CreateSegmentedScan(System.Int32)">
<summary>
create segmented scan.
</summary>
<param name="index">
The index into the scan table.
</param>
<returns>
The <see cref="T:ThermoFisher.CommonCore.Data.Business.SegmentedScan"/>.
</returns>
<exception cref="T:System.ArgumentOutOfRangeException">when index is out of range for the scan list
</exception>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromListCreator.CreateCentroidStream(System.Int32)">
<summary>
create centroid stream.
</summary>
<param name="index">
The index into the scan list.
</param>
<returns>
The <see cref="T:ThermoFisher.CommonCore.Data.Business.CentroidStream"/>.
</returns>
<exception cref="T:System.ArgumentOutOfRangeException">when index is out of range
</exception>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromThreadedFileCreator">
<summary>
Get scan data from a file, based on a known list of scans.
Using multiple threads read scans in parallel, up to the cache limit.
If multiple passes over data are needed,
this can avoid getting the same scan more than once from the raw file,
if the cache is large enough.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromThreadedFileCreator.#ctor(ThermoFisher.CommonCore.Data.Interfaces.IRawFileThreadManager,ThermoFisher.CommonCore.Data.Business.InstrumentSelection,System.Boolean)">
<summary>
Initializes a new instance of the <see cref="T:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromThreadedFileCreator"/> class.
</summary>
<param name="rawFile">
The raw file.
</param>
<param name="requiredInstrument">Instrument whole scans are to be read</param>
<param name="includeReferencePeaks">set if reference and exception peaks must be read. Default false</param>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromThreadedFileCreator.CacheLimit">
<summary>
Gets or sets the cache limit.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromThreadedFileCreator.CreateCentroidStream(System.Int32)">
<summary>
Create a centroid stream.
</summary>
<param name="index">
The index into the supplied table of scans (on construction)
</param>
<returns>
The <see cref="T:ThermoFisher.CommonCore.Data.Business.CentroidStream"/>.
</returns>
<exception cref="T:System.ArgumentOutOfRangeException">when index is outside of the scan numbers array
</exception>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromThreadedFileCreator.CreateSegmentedScan(System.Int32)">
<summary>
create segmented scan.
</summary>
<param name="index">
The index into the supplied table of scans (on construction)
</param>
<returns>
The <see cref="T:ThermoFisher.CommonCore.Data.Business.SegmentedScan"/>.
</returns>
<exception cref="T:System.ArgumentOutOfRangeException">when index is outside of the scan numbers array
</exception>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromThreadedFileCreator.Initialize(System.Collections.Generic.List{System.Int32},System.Int32)">
<inheritdoc />
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.ScanFromThreadedFileCreator.CacheScans(System.Collections.Generic.List{System.Int32},System.Int32,System.Int32)">
<summary>
Add some scans to the cache.
</summary>
<param name="scanNumbers">
The scan numbers.
</param>
<param name="startCacheIndex">
The start cache index. Cache from this index in the scan numbers.
</param>
<param name="endCacheIndexExclusive">
The end cache index exclusive. Cache up to but not including this index in scan numbers.
</param>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager">
<summary>
Class for averaging a set of spectra.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.FtOptions">
<summary>
Gets or sets Options which can be used to control the Ft / Orbitrap averaging
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.#ctor">
<summary>
Initializes a new instance of the <see cref="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager"/> class.
Default constructor
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.MaxPeakSamplesForDetection">
<summary>
The max peak samples for detection.
</summary>
</member>
<member name="F:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ZeroPointCompressionLimit">
<summary>
The zero point compression limit.
</summary>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.FindSegmentedScan">
<summary>
Find a segmented scan.
</summary>
<param name="scanNumber">
The scan number.
</param>
<returns>The found scan</returns>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.FindCentroids">
<summary>
Find centroid data.
</summary>
<param name="scanNumber">
The scan number.
</param>
<returns>The found centroids.</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.GetAverage(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReaderBase,System.Collections.Generic.List{ThermoFisher.CommonCore.Data.Business.ScanStatistics},ThermoFisher.CommonCore.Data.Business.Scan,System.Int32,ThermoFisher.CommonCore.Data.Interfaces.IScanCreator)">
<summary>
Create the average scan from a collection of raw scans.
</summary>
<param name="rawFile">The file containing scans to average.
</param>
<param name="scanStatistics">
The collection of raw scans to average
</param>
<param name="firstScan">
The first scan in the set to average.
</param>
<param name="cacheLimit">
(optional) set the number of items which can be internally cached (default 20)
</param>
<param name="scanCreator">optional tool to provide scans.
If this is not supplied, then scan data is read in a single threaded manner using the supplied raw
data interface, and cached as per the supplied cache limits. </param>
<returns>
The averaged scan.
</returns>
<exception cref="T:System.ArgumentNullException">
<c>rawFile</c> is null.
</exception>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.GetAverage(ThermoFisher.CommonCore.Data.Interfaces.IRawData,System.Collections.Generic.List{System.Int32},ThermoFisher.CommonCore.Data.Business.Scan,System.Int32)">
<summary>
Create the average scan from a collection of raw scans.
</summary>
<param name="rawFile">The file containing scans to average
</param>
<param name="scanNumbers">
The collection of raw scans to average
</param>
<param name="firstScan">
The first scan in the set to average.
</param>
<param name="cacheLimit">
(optional) set the number of items which can be internally cached (default 20)
</param>
<returns>
The averaged scan.
</returns>
<exception cref="T:System.ArgumentNullException">
<c>rawFile</c> is null.
</exception>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData">
<summary>
Internal representation of re-sampled data
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData.#ctor(System.Int32)">
<summary>
Initializes a new instance of the <see cref="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData"/> class.
</summary>
<param name="totalPoints">
The total points.
</param>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData.Masses">
<summary>
Gets or sets Masses.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData.Intensities">
<summary>
Gets or sets Intensities.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData.Length">
<summary>
Gets Length.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.GetAverage(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReaderBase,ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.FindSegmentedScan,System.Collections.Generic.List{System.Int32},ThermoFisher.CommonCore.Data.Business.Scan,ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.FindCentroids)">
<summary>
Create the average scan from a collection of raw scans.
</summary>
<param name="rawDataReader">file which has data to average</param>
<param name="segmentedScanCreator">
method to return segmented scans when requested (by scan list index)
</param>
<param name="scanNumbers">
The collection of raw scans to average
</param>
<param name="firstScan">
The first scan in the set to average.
</param>
<param name="centroidStreamCreator">
method to return centroids streams from the list of scans when requested
</param>
<returns>
The number of scans that were actually averaged.
</returns>
<exception cref="T:System.ArgumentNullException">
<c>rawFile</c> is null.
</exception>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.Subtract(ThermoFisher.CommonCore.Data.Business.Scan,ThermoFisher.CommonCore.Data.Business.Scan)">
<summary>
Creates a difference of two raw scans.
The returned scans count of "scans combined" is
the total number of scans combined in each of the
foreground and background scans.
</summary>
<param name="foregroundScan">
The scan containing signal.
</param>
<param name="backgroundScan">
The scan containing background
</param>
<returns>
foregroundScan - backgroundScan
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.Add(ThermoFisher.CommonCore.Data.Business.Scan,ThermoFisher.CommonCore.Data.Business.Scan)">
<summary>
Creates a sum of two scans.
The returned scans count of "scans combined" is
the total number of scans combined in each of the
first and second scans.
</summary>
<param name="firstScan">
The first scan.
</param>
<param name="secondScan">
The second scan
</param>
<returns>
first scan + second scan
</returns>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.PartProfileMasses">
<summary>
The part profile masses.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.PartProfileMasses.Mass">
<summary>
Gets or sets a set of masses for profile points.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.PartProfileMasses.Filled">
<summary>
Gets or sets number of filled array points.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CreateTargetSpectrum(ThermoFisher.CommonCore.Data.Business.Scan,ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.FindSegmentedScan,System.Int32,ThermoFisher.CommonCore.Data.Business.MassToFrequencyConverter@)">
<summary>
Create the target array for keeping the averaged profile points.
</summary>
<param name="firstScan">
The first Scan.
</param>
<param name="findSegmentedScan">
The find Segmented Scan.
</param>
<param name="scans">
The scans.
</param>
<param name="massToFrequencyConverter">
The target Spectrum Parameters.
</param>
<returns>
The created target spectrum.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CreateProfilePoints(System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.PartProfileMasses})">
<summary>
create profile points.
</summary>
<param name="massTable">
The mass table.
</param>
<returns>
Points containing masses and 0 intensity
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CreateMassTable(ThermoFisher.CommonCore.Data.Business.MassToFrequencyConverter)">
<summary>
The create mass table.
</summary>
<param name="massToFrequencyConverter">
The target spectrum parameters.
</param>
<returns>
The masses for each profile point.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.SumUpSpectraResampled(ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.FindSegmentedScan,ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData,System.Int32)">
<summary>
Create the average profile spectrum.
</summary>
<param name="scanCreator">
tool to return scans
</param>
<param name="segmentList">
segment List
</param>
<param name="scans">
The number of scans to sum
</param>
<returns>
The summed up spectra.
</returns>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.Resampler">
<summary>
The re-sampler.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.Resampler.#ctor(System.Double[],ThermoFisher.CommonCore.Data.Business.SegmentedScan,System.Int32)">
<summary>
Initializes a new instance of the <see cref="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.Resampler"/> class.
</summary>
<param name="masses">
The masses.
</param>
<param name="scanData">
The scan data.
</param>
<param name="scans">
The scans.
</param>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.Resampler.Result">
<summary>
Gets Result.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.Resampler.Execute">
<summary>
Method executed in parallel
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.Resampler.ResampleScan(System.Double[],ThermoFisher.CommonCore.Data.Business.SegmentedScan,System.Int32)">
<summary>
re-sample a scan.
</summary>
<param name="resampledMasses">
The re-sampled masses.
</param>
<param name="scanData">
The scan data.
</param>
<param name="scansAveraged">
The scans averaged.
</param>
<returns>
The set of resampled peaks, which must be merged into the final scan.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.SumUpSpectraResampledParallel2(ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.FindSegmentedScan,ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData,System.Int32,System.Int32)">
<summary>
Create the average profile spectrum.
Each scan is analyzed: Determining mass regions which contain non-zero data,
and re-sampling the intensity data aligned to a set of output bins.
After all scans have been re-sampled, the re-sampled data has to be merged into the final output.
</summary>
<param name="scanCreator">
tool to return scans
</param>
<param name="segmentList">
segment List
</param>
<param name="scans">
The number of scans to sum
</param>
<param name="taskBatching">
The minimum number of Resample tasks per thread.
Creating resampled data for profiles is a fairly fast task. It may be inefficient to queue workers to
created the merged data for each scan in the batch.
Setting this >1 will reduce threading overheads, when averaging small batches of scans with low intensity peaks.
This parameter only affects the re-sampling, as the final merge of the re-sampled data is single threaded.
</param>
<returns>
The re-sampled and summed up spectra.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.MergeData(ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.MergeActions,ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData)">
<summary>
The merge data.
</summary>
<param name="toMerge">
The to merge.
</param>
<param name="resampled">
The resampled.
</param>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.MergeActions">
<summary>
private class to hold an index/value pair.
This records the data which needs to be added to the re-sampled total.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.MergeActions.Indexes">
<summary>
Gets or sets Indexes.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.MergeActions.Values">
<summary>
Gets or sets Values.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.MergeActions.Filed">
<summary>
Gets or sets Filed.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.SubtractSpectraResampled(System.Collections.Generic.List{ThermoFisher.CommonCore.Data.Business.Scan},ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData)">
<summary>
Create the Subtracted profile spectrum.
</summary>
<param name="scanList">
The foreground and background scans
</param>
<param name="segmentList">The re-sampled mass and intensity arrays.
</param>
<returns>
The subtracted profile
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.SumSpectraResampled(System.Collections.Generic.List{ThermoFisher.CommonCore.Data.Business.Scan},ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData)">
<summary>
Create the Summed profile spectrum, for the "Add" method
</summary>
<param name="scanList">
The scans to add
</param>
<param name="segmentList">The re-sampled mass and intensity arrays.
</param>
<returns>
The subtracted profile
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CentroidizeProfileSpectrum(ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData)">
<summary>
Determines the centroids of all peaks in the given spectrum.
<para>
For the centroid the position, intensity and resolution are calculated.
The resolution is the calculated as the quotient of the position and the
width of the peak.
</para>
<para>
The following algorithm calculates the centroid as the vertex of a second
order parabola laid through the top three points of a peak. If the width
cannot be determined directly from the profile peak (e.g. because of
overlapping peaks), the full width at half height (FWHH) of the parabola
fitted to determine the centroid position is used (see below). This width
is usually smaller than the real peak width for FT data.
</para>
<para>
This algorithm simplifies the calculation by moving the x coordinate of the
top three points to -1, 0 and +1, respectively. This is only applicable if
the points are equidistant, which would be exactly true for the spectrum
in frequency domain, and is a valid approximation for the spectrum in mass
domain.
</para>
<code>
Parabola: y = a(x-xv)^2 + yv
1. Find maximum and two surrounding points:
Given p1(x1,y1); p2(x2,y2); p3(x3,y3)
if dx = x2 - x1 = x3 - x2
and x2 = n * dx
2. Map the three points to the unity interval [-1, 1]:
p1'(-1,y1);p2'(0,y2);p3'(1,y3) - This simplifies the calculations.
3. Calculate center offset dxc', height yc, and width w'
(dxc' and w' are in unity units):
a = 0.5 * (y1+y3) - y2;
dxc' = (y1-y3) / 4a
yc = y2 - a * dxc'^2
w' = 2.0 * sqrt(yc/2|a|)
4. Calculate center and width:
xc = x2 + dxc' * dx
w = w' * dx
</code>
</summary>
<param name="segmentScan">
List of segments to be converted to centroids
</param>
<returns>
The centroids detected.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CalculateNoiseInfo(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReaderBase,ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.FindCentroids,System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},System.Collections.Generic.List{System.Int32},System.Boolean)">
<summary>
Recalculates the baseline and noise information for the averaged spectrum.
</summary>
<param name="rawData">Raw file reader</param>
<param name="scanCreator">
The scan Creator.
</param>
<param name="centroidStream">
The centroid Stream.
</param>
<param name="scanNumbers">
The scans.
</param>
<param name="useOriginalNoiseAlgorithm">If true, use noise algorithm from Xcalibur</param>
<returns>
The calculated noise packets.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CalculateNoiseInfo(ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.FindCentroids,System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},System.Collections.Generic.List{System.Int32})">
<summary>
Recalculates the baseline and noise information for the averaged spectrum.
</summary>
<param name="scanCreator">
The scan Creator.
</param>
<param name="centroidStream">
The centroid Stream.
</param>
<param name="scanNumbers">
The scans.
</param>
<returns>
The calculated noise packets.
</returns>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.NoiseInformation">
<summary>
The noise information.
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.NoiseInformation.ScanAlignedNoise">
<summary>
Gets or sets the scan aligned noise.
This is data for each mass in the centroid scan
</summary>
</member>
<member name="P:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.NoiseInformation.RawFileNoise">
<summary>
Gets or sets the noise data as recorded in a raw file.
This data need not be aligned with the scan masses.
Values for each mass can be interpolated from this table.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CalculateNoiseInfoUsingNoiseTable(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReaderPlus,System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},System.Collections.Generic.List{System.Int32})">
<summary>
Recalculates the baseline and noise information for the averaged spectrum.
</summary>
<param name="filePlus">Tool to read noise data</param>
<param name="centroidStream">
The centroid Stream.
</param>
<param name="scanNumbers">
The scans.
</param>
<returns>
The calculated noise packets.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.BuildNoiseDataForScan(System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},ThermoFisher.CommonCore.Data.Business.NoiseAndBaseline[])">
<summary>
build noise data for scan.
Applies the noise and baseline data to a scan, making a noise table.
</summary>
<param name="centroidStream">
The centroid stream.
</param>
<param name="noiseAndBaselines">
The noise and baselines (input).
</param>
<returns>
The <see cref="T:ThermoFisher.CommonCore.BackgroundSubtraction.NoisePackets"/>.
</returns>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.NoiseFromScans">
<summary>
Class to obtain noise from a 2 scan: foreground (0) or background (1).
Designed to create a function delegate, needed by
the noise generation algorithm.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.NoiseFromScans.#ctor(ThermoFisher.CommonCore.Data.Business.Scan,ThermoFisher.CommonCore.Data.Business.Scan)">
<summary>
Initializes a new instance of the <see cref="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.NoiseFromScans"/> class.
</summary>
<param name="foreground">
The scan to subtract from.
</param>
<param name="background">
The (background) scan to be subtracted.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.NoiseFromScans.NoiseAndBaselinesFromScan(System.Int32)">
<summary>
Get The noise and baselines from a file.
</summary>
<param name="index">
The index.
</param>
<returns>
The Noise data based on the index
</returns>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.NoiseFromFile">
<summary>
Class to obtain noise from a file.
Designed to create a function delegate, needed by
the noise generation algorithm.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.NoiseFromFile.#ctor(ThermoFisher.CommonCore.Data.Interfaces.IDetectorReaderPlus,System.Collections.Generic.List{System.Int32})">
<summary>
Initializes a new instance of the <see cref="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.NoiseFromFile"/> class.
</summary>
<param name="rawDataReaderPlus">
The file.
</param>
<param name="scanNumbers">
The scan numbers.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.NoiseFromFile.NoiseAndBaselinesFromFile(System.Int32)">
<summary>
Get The noise and baselines from a file.
</summary>
<param name="index">
The index.
</param>
<returns>
The Noise data based on the index
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CreateNoiseAndBaselines(System.Func{System.Int32,ThermoFisher.CommonCore.Data.Business.NoiseAndBaseline[]},System.Int32)">
<summary>
create noise and baselines.
</summary>
<param name="noiseReader">
The noise Reader.
</param>
<param name="scans">
The scans.
</param>
<returns>
The noise and baselines (averaged)
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.InterpolateValues(System.Double,System.Double,System.Double,System.Double,System.Double@)">
<summary>
Interpolate noise or baseline value.
</summary>
<param name="currentValue">
The current value.
</param>
<param name="previousValue">
The previous value.
</param>
<param name="currentMass">
The current mass.
</param>
<param name="previousMass">
The previous mass.
</param>
<param name="slope">
The slope.
</param>
<returns>
The interpolated value.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CalculateAndAssignChargeStates(ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData,System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint})">
<summary>
The function determines the charge state of the peaks in
the spectrum and assign the calculated charge to the
centroids of the corresponding isotopic cluster.
<para>
The functions tries to determine the charge states of the peaks in the
spectrum and to assign the calculated charges to the centroids of the
corresponding isotopic clusters in the spectrum.
The algorithm tries to determine charges for the top peaks in the spectrum.
The algorithm tries at most MaxChargeDeterminations, or until the peak
intensity falls below a calculated noise level in the spectrum, whichever
comes first.
</para>
<para>
The charge determination is done by going through the spectrum starting with
the most intense peak. The calculation is done on a small interval around the
peak centroid ([centroid - 1.5 Da/1200.0, centroid + 1.5 Da]).
Two independent approaches are used for the charge calculation:
</para>
<code>
1. Calculation of an FFT on the profile points, and
2. Calculation by considering the centroid distances (Patterson charge
calculations).
</code>
<para>
The two charge calculation algorithms fill a charge histogram map. This
histogram is then analyzed for exhibiting a top scored charge that has a
clear separation from the second best hit.
If there is a clear best hit for the charge, this charge is assigned to the
corresponding isotopic cluster. This is the most difficult part of the charge
assignment. For details how the isotopic cluster is identified see the
description on the charge assignment routine (-> AssignCharge()).
</para>
</summary>
<param name="segmentList">
The profile for the scan.
</param>
<param name="massSortedCentroidList">
List of centroids to assign charges to
</param>
<returns>
The points with charge states.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.AssignCharge(ThermoFisher.CommonCore.BackgroundSubtraction.ChargeResult,System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint})">
<summary>
assign charge.
</summary>
<param name="result">
The result of charge calculation.
</param>
<param name="massSortedCentroidList">
The mass sorted centroid list.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CompressProfileSpectrum(ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData)">
<summary>
Compress the averaged profile spectrum to reduce its memory footprint.
The sampling rate of the FT instruments is very high. Due to the very high
resolution of these instruments, the spectra are often quite empty. i.e.
that there are large areas of zero intensities between the two peaks.
It is sufficient that we keep only a small number of consecutive zero intensity
points. We do not remove them entirely because this will have strange effects
on smoothing routines (currently we keep at most eight consecutive zero
intensity points. This is sufficient to enable 15-point smoothing over the
spectrum).
</summary>
<param name="segmentList">
The segment list.
</param>
<returns>
The compressed data.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.FillAverageScan(ThermoFisher.CommonCore.Data.Business.Scan,ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData,System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.NoiseInformation,ThermoFisher.CommonCore.Data.Business.MassToFrequencyConverter)">
<summary>
Fill the target raw scan provided by the caller with the result of the average calculation.
</summary>
<param name="firstScan">
the first scan in the set to average
</param>
<param name="segmentScan">
List holding the averaged segmented scan
</param>
<param name="centroidStream">
Holding the averaged centroid stream
</param>
<param name="noiseInformation">
Noise and baseline data
</param>
<param name="massToFrequencyConverter">
Mass calibration for target scan
</param>
<returns>
The filled average scan.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.GetTic(ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.ProfileData,System.Double[])">
<summary>
get tic.
</summary>
<param name="segmentScan">
The segment scan.
</param>
<param name="resampledIntensities">
The re-sampled intensities.
</param>
<returns>
The Tic of the intensities
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.FindMaxElement(System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint})">
<summary>
find max element.
</summary>
<param name="centroids">
The centroids.
</param>
<returns>
The CentroidStreamPoint object which has the largest intensity
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CalculateTargetSpectrumParameters(ThermoFisher.CommonCore.Data.Business.Scan,ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.FindSegmentedScan,System.Int32)">
<summary>
Calculates and retrieves the necessary parameters for creating
the averaged scan from the the given set of raw scans to average.
</summary>
<param name="firstScan">
The first Scan.
</param>
<param name="findSegmentedScan">
The find Segmented Scan.
</param>
<param name="scans">
The scans.
</param>
<returns>
The calculated target spectrum parameters.
</returns>
</member>
<member name="T:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CentroidPositionComparer">
<summary>
The centroid position comparer.
</summary>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CentroidPositionComparer.Compare(ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint,ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint)">
<summary>
Compares two objects and returns a value indicating whether one is less than, equal to, or greater than the other.
</summary>
<returns>
Value Condition
Less than zero <paramref name="x"/> is less than <paramref name="y"/>.
Zero <paramref name="x"/> equals <paramref name="y"/>.
Greater than zero <paramref name="x"/> is greater than <paramref name="y"/>.
</returns>
<param name="x">
The first object to compare.
</param>
<param name="y">
The second object to compare.
</param>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CompareIntenisities(ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint,ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint)">
<summary>
Compare intensities.
</summary>
<param name="left">
The left point.
</param>
<param name="right">
The right point.
</param>
<returns>
1 if left less than right
-1 if left greater than right
0 if left and right are equal
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.FindMaxElement(System.Collections.Generic.List{ThermoFisher.CommonCore.BackgroundSubtraction.CentroidStreamPoint},System.Int32,System.Int32)">
<summary>
Finds the CentroidStreamPoint object which contains the maximum Intensity
</summary>
<param name="centroids">
List of Centroids
</param>
<param name="startIndex">
Start of array slice to analyze
</param>
<param name="endIndex">
End of array slice to analyze
</param>
<returns>
The CentroidStreamPoint object which has the largest intensity
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CalculateDeltaFrequency(ThermoFisher.CommonCore.Data.Business.SegmentedScan,ThermoFisher.CommonCore.Data.Business.MassToFrequencyConverter)">
<summary>
Calculates the delta frequency for the given DataPeaks.
</summary>
<param name="scan">
Segmented Scan
</param>
<param name="massToFrequencyConverter">
Calibration data for target scan
</param>
<returns>
The calculated delta frequency.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CreateCentroidStream(System.Int32)">
<summary>
Create the CentroidStream object with the given size.
</summary>
<param name="size">The number of peaks in this stream.
</param>
<returns>
An empty centroid stream, with arrays allocated to the indicated size.
</returns>
</member>
<member name="M:ThermoFisher.CommonCore.BackgroundSubtraction.SpectrumAverager.CreateSegmentedScan(System.Int32,System.Double[],System.Double[],ThermoFisher.CommonCore.Data.Interfaces.IRangeAccess)">
<summary>
Create the <see cref="T:ThermoFisher.CommonCore.Data.Business.SegmentedScan"/> object withe given size, and attach the mass and intensity arrays.
</summary>
<param name="size">The number of mass/intensity pairs.
</param>
<param name="masses">
Mass data for scan
</param>
<param name="intensities">
Intensity data for scan
</param>
<param name="segmentRange">Mass range of the scan.</param>
<returns>
An scan with the mass and intensity data attached.
</returns>
</member>
</members>
</doc>