ms_ms1quant_time_align_limits Class Reference

Limits for m/z and retention time. More...

#include <ms_ms1quant_time_align_limits.hpp>

Inherits ms_handle.

Public Types
typedef int	combinedRT_t
	At the moment, when creating a common grid, integer retention times are used.

Public Member Functions
	ms_ms1quant_time_align_limits ()
	Constructor.
int	getCombinedMaxBinNum () const
	Get the maximum bin number.
combinedRT_t	getCombinedMaxRT () const
	Get the maximum retention time to be used for the common grid.
int	getCombinedMinBinNum () const
	Get the minimum bin number.
combinedRT_t	getCombinedMinRT () const
	Get the minimum retention time to be used for the common grid.
double	getMaxMZ () const
	Get the maximum m/z value found.
double	getMaxRT () const
	Get the maximum retention time found.
double	getMinMZ () const
	Get the minimum m/z value found.
double	getMinRT () const
	Get the minimum retention time found.
int	getNumQueries () const
	Get the number of queries found.
int	getNumQueriesAboveThreshold () const
	Get the number of queries with scores above threshold found.
void	setMaxBinNum (const int value)
	Set the maximum bin number.
void	setMaxMZ (const double value)
	Set the maximum m/z value found.
void	setMaxRT (const double value)
	Set the maximum retention time found.
void	setMinBinNum (const int value)
	Set the minimum bin number.
void	setMinMZ (const double value)
	Set the minimum m/z value found.
void	setMinRT (const double value)
	Set the minimum retention time found.
void	setNumQueries (const int value)
	Set the number of queries found.
void	setNumQueriesAboveThreshold (const int value)
	Set the number of queries with scores above threshold found.

Static Public Attributes
static const combinedRT_t	combinedRTinterval = 1
	At the moment, when creating a common grid, integer retention times are used.

Detailed Description

Limits for m/z and retention time.

Contains the m/z and retention time limits used for time alignment.

See ms_ms1quant_time_align::getCombinedLimits() and ms_ms1quantitation::getTimeAlignmentData() for details of how to get this object from the ms1 quantitation data

Constructor & Destructor Documentation

ms_ms1quant_time_align_limits()

ms_ms1quant_time_align_limits

(

)

Constructor.

Constructor for the m/z and retention time limits used for time alignment.

See ms_ms1quant_time_align::getCombinedLimits() and ms_ms1quantitation::getTimeAlignmentData() for details of how to get this object from the ms1 quantitation data

Member Function Documentation

getCombinedMaxBinNum()

int getCombinedMaxBinNum

(

)

const

Get the maximum bin number.

Returns

the maximum bin number required for the common grid

getCombinedMaxRT()

ms_ms1quant_time_align_limits::combinedRT_t getCombinedMaxRT

(

)

const

Get the maximum retention time to be used for the common grid.

When the common grid is created for looking up the retention times, the start, end and step size need to be determined. These are currently integer values.

Currently calculated by calling round( getMaxRT() ) and casting to the return type

Returns

the maximum retention time used for the common grid

getCombinedMinBinNum()

int getCombinedMinBinNum

(

)

const

Get the minimum bin number.

Returns

the minimum bin number required for the common grid

getCombinedMinRT()

ms_ms1quant_time_align_limits::combinedRT_t getCombinedMinRT

(

)

const

Get the minimum retention time to be used for the common grid.

When the common grid is created for looking up the retention times, the start, end and step size need to be determined. These are currently integer values.

Currently calculated by calling round( getMinRT() ) and casting to the return type

Returns

the minimum retention time used for the common grid

getMaxMZ()

double getMaxMZ

(

)

const

Get the maximum m/z value found.

The constructor initialises this value to zero

See also

setMaxMZ()

Returns

the maximum m/z value.

getMaxRT()

double getMaxRT

(

)

const

Get the maximum retention time found.

The constructor initialises this value to zero

See also

setMaxRT()

getCombinedMaxRT()

Returns

the maximum retention time.

getMinMZ()

double getMinMZ

(

)

const

Get the minimum m/z value found.

The constructor initialises this value to the maximum possible double value

See also

setMinMZ()

Returns

the minimum m/z value.

getMinRT()

double getMinRT

(

)

const

Get the minimum retention time found.

The constructor initialises this value to the maximum possible double value

See also

setMinRT()

getCombinedMinRT()

Returns

the minimum retention time.

getNumQueries()

int getNumQueries

(

)

const

Get the number of queries found.

The constructor initialises this value to zero

Not strictly part of the limits, but this is the number of queries from the Mascot database search(es) that were used when determining the limits

See also

setNumQueries()

getNumQueriesAboveThreshold()

Returns

the number of queries

getNumQueriesAboveThreshold()

int getNumQueriesAboveThreshold

(

)

const

Get the number of queries with scores above threshold found.

The constructor initialises this value to zero

Not strictly part of the limits, but this is the number of queries above the specified threshold from the Mascot database search(es) that were used when determining the limits

See also

setNumQueriesAboveThreshold()

getNumQueries()

Returns

the number of queries above the threshold

setMaxBinNum()

void setMaxBinNum

(

const int

value

)

Set the maximum bin number.

The constructor initialises this value to zero

Not strictly part of the limits. It is calculated from int(round(getMaxMZ())) / binSize

See also

getCombinedMaxBinNum()

Parameters

value

is the new maximum bin number

setMaxMZ()

void setMaxMZ

(

const double

value

)

Set the maximum m/z value found.

The constructor initialises this value to zero

See also

getMaxMZ()

Parameters

value

is the new maximum m/z value.

setMaxRT()

void setMaxRT

(

const double

value

)

Set the maximum retention time found.

The constructor initialises this value to zero

See also

getMaxRT()

getCombinedMaxRT()

Parameters

value

is the new maximum retention time.

setMinBinNum()

void setMinBinNum

(

const int

value

)

Set the minimum bin number.

The constructor initialises this value to zero

Not strictly part of the limits. It is calculated from int(round(getMinMZ())) / binSize

See also

getCombinedMinBinNum()

Parameters

value

is the new minimum bin number

setMinMZ()

void setMinMZ

(

const double

value

)

Set the minimum m/z value found.

The constructor initialises this value to the maximum possible double value

See also

getMinMZ()

Parameters

value

is the new minimum m/z value.

setMinRT()

void setMinRT

(

const double

value

)

Set the minimum retention time found.

The constructor initialises this value to the maximum possible double value

See also

getMinRT()

getCombinedMinRT()

Parameters

value

is the new minimum retention time.

setNumQueries()

void setNumQueries

(

const int

value

)

Set the number of queries found.

The constructor initialises this value to zero

Not strictly part of the limits, but this is the number of queries from the Mascot database search(es) that were used when determining the limits

See also

getNumQueries()

Parameters

value

is the new number of queries

setNumQueriesAboveThreshold()

void setNumQueriesAboveThreshold

(

const int

value

)

Set the number of queries with scores above threshold found.

The constructor initialises this value to zero

Not strictly part of the limits, but this is the number of queries above the specified threshold from the Mascot database search(es) that were used when determining the limits

See also

setNumQueriesAboveThreshold()

getNumQueries()

Parameters

value

is the new number of queries above the threshold

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

• ms_ms1quant_time_align_limits.hpp
• ms_ms1quant_time_align_limits.cpp