ms_ms1quant_match_ratio Class Reference [Quantitation analysis for Mascot Server and Distiller]

The status resulting ratio for a peptide found in a match. More...

#include <ms_ms1quant_match_ratio.hpp>

Inherits matrix_science::ms_handle.

List of all members.

Public Types
enum	ratioStatusCode {   RS_EMPTY = 0,   RS_OK = 1,   RS_ISOLATEDPRECURSORFAILED = 2,   RS_INTEFERENCEFAILED = 4,   RS_NODATA = 8,   RS_FITEXYSIGMA = 16,   RS_NEGATIVERATIO = 32,   RS_INFINITERATIO = 64,   RS_ZERORATIO = 128,   RS_DO_NOT_USE = 256,   RS_TOTALINTENSITYFAILED = 512 }
	Status codes from fitting ratios. More...
Public Member Functions
	ms_ms1quant_match_ratio ()
	Default constructor.
	ms_ms1quant_match_ratio (const ms_ms1quant_match_ratio_body &body)
	Populated constructor, linked to loaded data.
bool	getFitexy (ms_fitexy_result &value) const
	Get the fitexy value. Returns true if a fitexy value is set.
double	getQuality () const
	Get the quality of the match.
std::string	getRatioName () const
	Returns the ratio name.
int	getStatus () const
	Get the status composite value.
std::vector< ratioStatusCode >	getStatusList () const
	Get the status values. Each status in the list is a single bit.
double	getValue () const
	Return the numerical value of the ratio.
bool	isIncluded () const
	Returns true if the item should be included in calculations.
bool	isSet () const
	Returns true if the item has a value set.
bool	isUsedForAverage () const
	Returns true if the item is used in the average protocol for quantitation.
bool	isValid () const
	Returns true if the item has a valid value.
Static Public Member Functions
static ratioStatusCode	getCodeFromXml (std::string text)
	Get the status code for an XML attribute value.
static bool	getCodeInfo (ratioStatusCode code, const ms_quant_method &method, double &info)
	Return true if the status is associated with further information.
static std::string	getXmlCode (ratioStatusCode code)
	Get the XML attribute value for a status code.

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Detailed Description

The status resulting ratio for a peptide found in a match.

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

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Member Enumeration Documentation

enum ratioStatusCode

Status codes from fitting ratios.

See Using enumerated values and static const ints in Perl, Java, Python and C#.

Note that RS_FITEXYSIGMA maps to "StdErrAboveTreshold" which has always been misspelt.

The "XML text" is returned by matrix_science::ms_ms1quant_match_ratio::getXmlCode

The statuses get set by matrix_science::ms_ms1quant_match::applyThresholds()

Enumerator:

RS_EMPTY	XML text: "". No status set.
RS_OK	XML text: "ok". OK.
RS_ISOLATEDPRECURSORFAILED	XML text: "AreaFractionBelowThreshold". Isolated precursor failed [extra information is option value 'isolated precursor threshold'].
RS_INTEFERENCEFAILED	XML text: "PeakCorrBelowThreshold". Inteference failed [extra information is option value 'matched rho'].
RS_NODATA	XML text: "RatioUndefined". No data.
RS_FITEXYSIGMA	XML text: "StdErrAboveTreshold". fitexy sigma [extra information is option value 'elution profile correlation threshold'].
RS_NEGATIVERATIO	XML text: "NegativeRatio". Negative ratio.
RS_INFINITERATIO	XML text: "InfiniteRatio". Infinite ratio.
RS_ZERORATIO	XML text: "ZeroRatio". Zero ratio.
RS_DO_NOT_USE	XML text: "". Do not use (outlier)
RS_TOTALINTENSITYFAILED	XML text: "TotalIntensityBelowThreshold" Total intensity failed [extra information is option value 'total intensity threshold'].

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Constructor & Destructor Documentation

ms_ms1quant_match_ratio

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_ms1quant_match_ratio

(

const ms_ms1quant_match_ratio_body &

body )

Populated constructor, linked to loaded data.

Parameters:

body	The data loaded from the result file.

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Member Function Documentation

matrix_science::ms_ms1quant_match_ratio::ratioStatusCode getCodeFromXml

(

std::string

text )

[static]

Get the status code for an XML attribute value.

Parameters:

text	The string used to encode the ratio status in the XML file.

Returns:

The ratio status corresponding to the XML encoded string.

bool getCodeInfo	(	ratioStatusCode	code,
		const ms_quant_method &	method,
		double &	info
	)		[static]

Return true if the status is associated with further information.

Four status codes have further information associated with them:

• RS_ISOLATEDPRECURSORFAILED: isolated precursor threshold.
• RS_INTEFERENCEFAILED: matched rho.
• RS_FITEXYSIGMA: elution profile correlation threshold.
• RS_TOTALINTENSITYFAILED: total intensity threshold.

Parameters:

code	The ratio status for which extra information is wanted.
method	The quantitation method.
info	Filled in with the value of the extra information.

Returns:

True if there is extra information for this ratio status.

bool getFitexy

(

matrix_science::ms_fitexy_result &

value )

const

Get the fitexy value. Returns true if a fitexy value is set.

Parameters:

value

Filled in with the ms_fitexy_result, if any.

Returns:

True if a fitexy value is set.

double getQuality

(

)

const

Get the quality of the match.

Std. Err. = sigb / abs(b) from fitexy. Perfect fit is 0.0.

Returns:

The quality of the ratio.

std::string getRatioName

(

)

const

Returns the ratio name.

Returns:

The ratio name.

int getStatus

(

)

const

Get the status composite value.

Whether a peptide ratio is included or rejected when calculating a protein ratio.

These can be retrieved as a collection of separate values with getStatusList().

Returns:

A bitwise OR of any number of ratioStatusCode values.

std::vector< ms_ms1quant_match_ratio::ratioStatusCode > getStatusList

(

)

const

Get the status values. Each status in the list is a single bit.

These can be retrieved as a single composite value with getStatus().

Returns:

A collection of the individual status values.

double getValue

(

)

const

Return the numerical value of the ratio.

Returns:

The value of the ratio.

std::string getXmlCode

(

ratioStatusCode

code )

[static]

Get the XML attribute value for a status code.

Parameters:

code	The ratio status to get the XML excoding string for.

Returns:

The string used to encode the ratio status in the XML file.

bool isIncluded

(

)

const

Returns true if the item should be included in calculations.

Returns:

True if the item should be included in calculations.

bool isSet

(

)

const

Returns true if the item has a value set.

Returns:

True if the item has a value set.

bool isUsedForAverage

(

)

const

Returns true if the item is used in the average protocol for quantitation.

The Average protocol only uses a number of the the most intense peptides.

Returns:

True if the item has been used in the Average protocol calculations.

bool isValid

(

)

const

Returns true if the item has a valid value.

Returns:

True if the item has a valid value.

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

• ms_ms1quant_match_ratio.hpp
• ms_ms1quant_match_ratio.cpp