A result from a charge state calculation. More...

#include <ms_ms1quant_charge_state.hpp>

Inherits ms_handle.

Public Member Functions
	ms_ms1quant_charge_state ()
	Default constructor.

	ms_ms1quant_charge_state (const double correctSppWidthMin, const double correctSppWidthMax, const double correctSppWidth, const double bucketWidth, const double maxAlignment, const double matchedRho, const double matchedFraction, const double totalIntensity, const std::map< int, std::map< int, double > > &bucketAreas, const std::vector< double > &calcMzVar, const std::vector< int > &idx2Comp)

	ms_ms1quant_charge_state (const ms_ms1quant_charge_state_body &body)
	Populated constructor.

bool	getBucket (const int file_index, int index, unsigned &scanId, double &area) const
	Get a bucket scan number and intensity by its index (1..n).

bool	getBucket (int index, unsigned &scanId, double &area) const
	Get a bucket scan number and intensity by its index (1..n).

double	getBucketWidth () const
	Get the width of buckets used to collect peak area.

double	getCorrectedMaxSPPwidth () const
	Get the maximum peak width used for final stage of peak detection.

double	getCorrectedMinSPPwidth () const
	Get the minimum peak width used for final stage of peak detection.

double	getCorrectedSPPwidth () const
	Get the expected peak width used for final stage of peak detection.

double	getMatchedFraction () const
	Get the fitted peak area as a fraction of total peak area in XIC region. Value of 1.0 is perfect.

double	getMatchedRho () const
	Get the correlation coefficient between calculated and experimental spectrum in XIC region. A value of 1.0 indicates a perfect fit.

double	getMaxAlignment () const
	Get the offset required for optimum alignment of buckets with spectrum.

int	getNumberOfBuckets (const int file_index=ms_quant_file_index::file_index_value_not_set) const
	Get the number of bucket scan areas.

double	getTotalIntensity () const
	Get the peak area falling in all buckets summed over all scans in XIC peak.

Detailed Description

A result from a charge state calculation.

This is stored in XML in a "chargeStateData" entity.

Constructor & Destructor Documentation

◆ ms_ms1quant_charge_state() [1/3]

ms_ms1quant_charge_state ( )

Default constructor.

Assigns reasonable default values to all internal members.

◆ ms_ms1quant_charge_state() [2/3]

ms_ms1quant_charge_state ( const ms_ms1quant_charge_state_body & body )

Populated constructor.

Parameters

body	The data loaded from the result file.

◆ ms_ms1quant_charge_state() [3/3]

ms_ms1quant_charge_state	(	const double	correctSppWidthMin,
		const double	correctSppWidthMax,
		const double	correctSppWidth,
		const double	bucketWidth,
		const double	maxAlignment,
		const double	matchedRho,
		const double	matchedFraction,
		const double	totalIntensity,
		const std::map< int, std::map< int, double > > &	bucketAreas,
		const std::vector< double > &	calcMzVar,
		const std::vector< int > &	idx2Comp
	)

Parameters

correctSppWidthMin	see getCorrectedMinSPPwidth()
correctSppWidthMax	see getCorrectedMaxSPPwidth()
correctSppWidth	see getCorrectedSPPwidth()
bucketWidth	see getBucketWidth()
maxAlignment	see getMaxAlignment()
matchedRho	see getMatchedRho()
matchedFraction	see getMatchedFraction()
totalIntensity	see getTotalIntensity()
bucketAreas	is a std::map of scanIDs to area
calcMzVar	is a vector of calculated m/z values for each scan??
idx2Comp	is a vector of index to component values

Member Function Documentation

◆ getBucket() [1/2]

bool getBucket	(	const int	file_index,
		int	index,
		unsigned &	scanId,
		double &	area
	)		const

Get a bucket scan number and intensity by its index (1..n).

See Multiple return values in Perl, Java, Python and C#.

Peak area falling in a bucket for each scan in XIC peak.

Parameters

[in]	file_index	is used for replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file. Old files didn't store the file_index for the bucket areas, so these will be set to ms_quant_file_index::file_index_value_not_set . So, try and cope with this intelligently. If the request is for a specific file_index, but the only one here is for ms_quant_file_index::file_index_value_not_set then return that one.
[in]	index	The bucket scan identifier and area by its index (1..getNumberOfBuckets()).
[out]	scanId	Filled in with the scan identifier of the bucket.
[out]	area	Filled in with the area of the bucket.

Returns: True if the index is in range and refers to a bucket.

◆ getBucket() [2/2]

bool getBucket	(	int	index,
		unsigned &	scanId,
		double &	area
	)		const

Get a bucket scan number and intensity by its index (1..n).

See Multiple return values in Perl, Java, Python and C#.

Peak area falling in a bucket for each scan in XIC peak.

Deprecated:: see getBucket(const int, int, unsigned &, double &)

Parameters

[in]	index	The bucket scan identifier and area by its index (1..getNumberOfBuckets()).
[out]	scanId	Filled in with the scan identifier of the bucket.
[out]	area	Filled in with the area of the bucket.

Returns: True if the index is in range and refers to a bucket.

◆ getBucketWidth()

double getBucketWidth ( ) const

Get the width of buckets used to collect peak area.

Returns: The bucket width.

◆ getCorrectedMaxSPPwidth()

double getCorrectedMaxSPPwidth ( ) const

Get the maximum peak width used for final stage of peak detection.

Returns: The corrected maximum SPP width.

◆ getCorrectedMinSPPwidth()

double getCorrectedMinSPPwidth ( ) const

Get the minimum peak width used for final stage of peak detection.

Returns: The corrected minimum SPP width.

◆ getCorrectedSPPwidth()

double getCorrectedSPPwidth ( ) const

Get the expected peak width used for final stage of peak detection.

Returns: The corrected SPP width.

◆ getMatchedFraction()

double getMatchedFraction ( ) const

Get the fitted peak area as a fraction of total peak area in XIC region. Value of 1.0 is perfect.

Returns: The matched fraction value.

◆ getMatchedRho()

double getMatchedRho ( ) const

Get the correlation coefficient between calculated and experimental spectrum in XIC region. A value of 1.0 indicates a perfect fit.

Returns: The matched rho value.

◆ getMaxAlignment()

double getMaxAlignment ( ) const

Get the offset required for optimum alignment of buckets with spectrum.

Returns: The maximum alignment value.

◆ getNumberOfBuckets()

int getNumberOfBuckets ( const int file_index = ms_quant_file_index::file_index_value_not_set ) const

Get the number of bucket scan areas.

Parameters

[in] file_index is used for replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file. Old files didn't store the file_index for the bucket areas, so these will be set to ms_quant_file_index::file_index_value_not_set . So, try and cope with this intelligently. If the request is for a specific file_index, but the only one here is for ms_quant_file_index::file_index_value_not_set then return that one.

Returns: The number of bucket scan areas.

◆ getTotalIntensity()

double getTotalIntensity ( ) const

Get the peak area falling in all buckets summed over all scans in XIC peak.

Returns: The total intensity.

The documentation for this class was generated from the following files:

ms_ms1quant_charge_state.hpp
ms_ms1quant_charge_state.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ms_ms1quant_charge_state() [1/3]

◆ ms_ms1quant_charge_state() [2/3]

◆ ms_ms1quant_charge_state() [3/3]

Member Function Documentation

◆ getBucket() [1/2]

◆ getBucket() [2/2]

◆ getBucketWidth()

◆ getCorrectedMaxSPPwidth()

◆ getCorrectedMinSPPwidth()

◆ getCorrectedSPPwidth()

◆ getMatchedFraction()

◆ getMatchedRho()

◆ getMaxAlignment()

◆ getNumberOfBuckets()

◆ getTotalIntensity()