ms_ms1quant_match Class Reference

A peptide that has been matched, in quantitation, to a protein hit. More...

#include <ms_ms1quant_match.hpp>

Inherits ms_handle.

Public Types
enum	chargeType {   CHARGETYPE_ORIGINAL ,   CHARGETYPE_ALL }
	Types of charge state used when matching. More...

Public Member Functions
	ms_ms1quant_match ()
	Default constructor; for standard library collections.
	ms_ms1quant_match (const ms_ms1quant_match_body &body)
	Populated constructor, linked to loaded data.
ms_ms1quant_match_component *	addComponent (const matrix_science::ms_ms1quant_match_component &component)
	Add a new component to the list. Must already have a component to base this one on.
ms_ms1quant_match_component *	addCreatedComponent (const matrix_science::ms_ms1quant_match_component &component)
	Add a new component to the list. Must already have a component to base this one on.
ms_ms1quant_match_component *	addCreatedComponent (const std::string &componentName)
bool	allComponentsIdentified () const
	Check if all the match components were identified by Mascot.
void	clearHitRatioExcluded (const std::string &ratioName, int hitId, int memberNumber)
	Clear the match ratio from being excluded from a hit.
void	clearHitRatioOutlier (const std::string &ratioName, int hitId, int memberNumber)
	Clear the match ratio from being an outlier for a hit.
int	getChargeState () const
	Get the ion charge state.
ms_ms1quant_charge_state	getChargeStateData () const
	Get the charge state data.
chargeType	getChargeType () const
	Get whether this charge state has been extrapolated from the charge state of a Mascot match.
ms_ms1quant_match_component	getComponent (int index) const
	Get a component associated with this match by its index (1..getNumComponents).
ms_ms1quant_match_component	getComponent (std::string componentName) const
	Get a component of the matched peptide.
std::string	getConciseLabelFreeVarMods () const
	Get the concise (un-numbered) readable variable modifications.
const ms_matrix &	getCorrectionMatrix () const
	Get the correction matrix A, product of J (averagine) and I (impurity).
int	getDataSourceId () const
	Get the data source identifier if processed independantly.
double	getDisplayIntensity () const
	Get the total intensity of fitted peaks across the XIC peak.
int	getFirstXicScanId () const
	Get the first scan of all the scans processed in the search for an XIC peak. Can be a wide region.
const ms_protein *	getHit (int index1) const
	Get a protein hit associated with this match by its index (1..getNumHits).
matrix_science::ms_peptide_quant_key	getKey () const
	Get a ms_peptide_quant_key code identifying the individual match.
std::string	getLabelFreeVarMods () const
	Get the variable modification identifiers, with the labels removed.
int	getLastXicScanId () const
	Get the last scan of all the scans processed in the search for an XIC peak. Can be a wide region..
int	getNumComponents () const
	Get the number of components associated with this match.
int	getNumHits () const
	Get the number of protein hits associated with this match.
int	getNumPeptideRatios () const
	Get the number of peptide ratios associated with this match.
ms_ms1quant_match_ratio	getPeptideRatio (const std::string &ratioName) const
	Get a peptide ratio value for the ratio name.
ms_ms1quant_match_ratio	getPeptideRatio (int index) const
	Get a peptide ratio associated with this match by its index (0..getNumPeptideRatios-1).
std::string	getPeptideString () const
	Get the peptide sequence in 1-letter code.
const ms_matrix &	getPerfectObservedMatrix () const
	Get the predicted stick spectrum for measured amounts of each component.
const ms_matrix &	getPredictionMatrix () const
	Get the predicted stick spectrum for equal amounts of each component.
std::string	getReadableLabelFreeVarMods () const
	Get the readable variable modifications.
std::string	getVarMods () const
	Get the variable modifications encoded as string of integers.
bool	hasComponent (std::string componentName) const
	Returns true if the matched peptide has the component.
bool	hasIdentifiedComponent () const
	Check if the match has any component that was identified by Mascot.
bool	hasPeptideRatio (const std::string &ratioName) const
	Returns true if the match has a peptide ratio value for the ratio name.
bool	isHitRatioExcluded (const std::string &ratioName, int hitId, int memberNumber) const
	Returns true if the match ratio is excluded from a hit.
bool	isHitRatioOutlier (const std::string &ratioName, int hitId, int memberNumber) const
	Returns true if the match ratio is an outlier for a hit.
bool	isHitRatioUsedForAverage (const std::string &ratioName, int hitId, int memberNumber) const
	Returns true if the match ratio is used in the average quantitation protocol for a hit.
bool	removeComponent (const std::string &componentName)
	Primarily for replicate where we want to remove components that are found in other files.
void	setHitRatioExcluded (const std::string &ratioName, int hitId, int memberNumber)
	Set the match ratio to be excluded from a hit.
void	setHitRatioOutlier (const std::string &ratioName, int hitId, int memberNumber)
	Set the match ratio to be an outlier for a hit.

Static Public Member Functions
static chargeType	getCodeFromXml (std::string text)
	Get the charge type code for an XML attribute value.
static std::string	getXmlCode (chargeType code)
	Get the XML attribute value for a charge type code.

Detailed Description

A peptide that has been matched, in quantitation, to a protein hit.

Each protein can be matched to a number of peptides. The quantitation ratios of these peptides are used to determine the quantitaion ratio of the protein.

A peptide match can have a number of labelled components (such as 'heavy' and 'light') that are determined by the modifications.

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

Member Enumeration Documentation

chargeType

enum chargeType

Types of charge state used when matching.

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

Enumerator
CHARGETYPE_ORIGINAL	Charge state found in result file.
CHARGETYPE_ALL	Match created in all charge states.

Constructor & Destructor Documentation

ms_ms1quant_match() [1/2]

ms_ms1quant_match

(

)

Default constructor; for standard library collections.

Assigns reasonable default values to all internal members.

ms_ms1quant_match() [2/2]

ms_ms1quant_match

(

const ms_ms1quant_match_body &

body

)

Populated constructor, linked to loaded data.

Parameters

body	The data loaded from the result file.

Member Function Documentation

addComponent()

ms_ms1quant_match_component * addComponent

(

const matrix_science::ms_ms1quant_match_component &

component

)

Add a new component to the list. Must already have a component to base this one on.

Primarily for replicate. Take the first component for this match, make a copy of it and add it to the match, leving the it's origin unaltered

Parameters

component

is the new component to be added

Returns

a pointer to the newly created component

addCreatedComponent() [1/2]

ms_ms1quant_match_component * addCreatedComponent

(

const matrix_science::ms_ms1quant_match_component &

component

)

Add a new component to the list. Must already have a component to base this one on.

Primarily for replicate. Take the first component for this match, make a copy of it and add it to the match, and set it's origin to be 'created'

Parameters

component

is the new component to be added

Returns

a pointer to the newly created component

addCreatedComponent() [2/2]

ms_ms1quant_match_component * addCreatedComponent

(

const std::string &

componentName

)

Primarily for replicate. Take the first component for this match, make a copy of it and add it to the match

Parameters

componentName

is the name of the new component to be added

Returns

a pointer to the newly created component

allComponentsIdentified()

bool allComponentsIdentified

(

)

const

Check if all the match components were identified by Mascot.

Tests to see if all the components were identified by Mascot. This method can return false event if hasIdentifiedComponent() returns true, as that method only requires one of the components to have been identified

See also

hasIdentifiedComponent()

Returns

True if all the components were identified by Mascot matches, false if not

clearHitRatioExcluded()

void clearHitRatioExcluded	(	const std::string &	ratioName,
		int	hitId,
		int	memberNumber
	)

Clear the match ratio from being excluded from a hit.

Clears any excluded status for the match in the specified protein ratio.

See also

setHitRatioExcluded()

Parameters

ratioName	The name of the ratio.
hitId	One based protein hit number.
memberNumber	One based family member number.

clearHitRatioOutlier()

void clearHitRatioOutlier	(	const std::string &	ratioName,
		int	hitId,
		int	memberNumber
	)

Clear the match ratio from being an outlier for a hit.

Data for a protein hit to which the peptide match is assigned.

Parameters

ratioName	The name of the ratio.
hitId	Protein hit number.
memberNumber	Family member number.

getChargeState()

int getChargeState

(

)

const

Get the ion charge state.

Returns

The ion charge state.

getChargeStateData()

matrix_science::ms_ms1quant_charge_state getChargeStateData

(

)

const

Get the charge state data.

Returns

The charge state data.

getChargeType()

ms_ms1quant_match::chargeType getChargeType

(

)

const

Get whether this charge state has been extrapolated from the charge state of a Mascot match.

Returns

CHARGETYPE_ORIGINAL if this charge state was found in the result file, otherwise CHARGETYPE_ALL as it has been extrapolated from the charge state of a Mascot match.

getCodeFromXml()

ms_ms1quant_match::chargeType getCodeFromXml ( std::string  text )

static

Get the charge type code for an XML attribute value.

Parameters

text	The string used to encode the charge type in the XML file.

Returns

The charge type corresponding to the XML encoded string.

getComponent() [1/2]

ms_ms1quant_match_component getComponent

(

int

index

)

const

Get a component associated with this match by its index (1..getNumComponents).

Parameters

index

An index (1..getNumComponents()) into the components associated with the peptide match.

Returns

The component.

getComponent() [2/2]

ms_ms1quant_match_component getComponent

(

std::string

componentName

)

const

Get a component of the matched peptide.

Parameters

componentName

The name of component to be retrieved, e.g. "Heavy".

Returns

The component.

getConciseLabelFreeVarMods()

std::string getConciseLabelFreeVarMods

(

)

const

Get the concise (un-numbered) readable variable modifications.

For example: "Dimethyl (KR); Acetyl (K); Methyl (KR)".

Returns

A semi-colon separated text string.

getCorrectionMatrix()

const matrix_science::ms_matrix & getCorrectionMatrix

(

)

const

Get the correction matrix A, product of J (averagine) and I (impurity).

Returns

The correction matrix

getDataSourceId()

int getDataSourceId

(

)

const

Get the data source identifier if processed independantly.

Returns

The data source identifier, if processed independantly.

getDisplayIntensity()

double getDisplayIntensity

(

)

const

Get the total intensity of fitted peaks across the XIC peak.

Returns

The total intensity of fitted peaks across the XIC peak.

getFirstXicScanId()

int getFirstXicScanId

(

)

const

Get the first scan of all the scans processed in the search for an XIC peak. Can be a wide region.

Returns

The identifier of the first scan of all the scans processed in the search for an XIC peak. Can be a wide region.

getHit()

const matrix_science::ms_protein * getHit

(

int

index1

)

const

Get a protein hit associated with this match by its index (1..getNumHits).

Parameters

index1

An index (1..getNumHits()) into the protein hits associated with the peptide match.

Returns

A protein hit, or null if the index is out of range.

getKey()

matrix_science::ms_peptide_quant_key getKey

(

)

const

Get a ms_peptide_quant_key code identifying the individual match.

Returns

The identifier for the match within the quantitation results.

getLabelFreeVarMods()

std::string getLabelFreeVarMods

(

)

const

Get the variable modification identifiers, with the labels removed.

For example: "00000100000043000009a2000".

Returns

A string of letters representing the modifications.

getLastXicScanId()

int getLastXicScanId

(

)

const

Get the last scan of all the scans processed in the search for an XIC peak. Can be a wide region..

Returns

The identifier of the last scan of all the scans processed in the search for an XIC peak. Can be a wide region.

getNumComponents()

int getNumComponents

(

)

const

Get the number of components associated with this match.

Returns

The number of components associated with the match.

getNumHits()

int getNumHits

(

)

const

Get the number of protein hits associated with this match.

Not all peptide matches are associated with every protein. This returns the number of proteins that are matched to this particular peptide and is typically less than the number of proteins in the peptide summary.

Returns

The number of protein hits associated with the match.

getNumPeptideRatios()

int getNumPeptideRatios

(

)

const

Get the number of peptide ratios associated with this match.

Returns

The number of peptide ratios associated with the match.

getPeptideRatio() [1/2]

matrix_science::ms_ms1quant_match_ratio getPeptideRatio

(

const std::string &

ratioName

)

const

Get a peptide ratio value for the ratio name.

Peptide ratio data that is independent of the assigned protein hit. To find out whether a match has been accepted or rejected under a particular protein hit, need to look under isHitRatioExcluded().

Parameters

ratioName

The name of ratio to be searched for, e.g. "H/L".

Returns

The peptide match.

getPeptideRatio() [2/2]

matrix_science::ms_ms1quant_match_ratio getPeptideRatio

(

int

index

)

const

Get a peptide ratio associated with this match by its index (0..getNumPeptideRatios-1).

Parameters

index

An index (0..getNumPeptideRatios()-1) into the peptide ratios associated with the match.

Returns

The peptide ratio.

getPeptideString()

std::string getPeptideString

(

)

const

Get the peptide sequence in 1-letter code.

Returns

The peptide sequence as a series of 1-letter codes.

getPerfectObservedMatrix()

const matrix_science::ms_matrix & getPerfectObservedMatrix

(

)

const

Get the predicted stick spectrum for measured amounts of each component.

Returns

The perfect observed matrix.

getPredictionMatrix()

const matrix_science::ms_matrix & getPredictionMatrix

(

)

const

Get the predicted stick spectrum for equal amounts of each component.

Returns

The prediction matrix

getReadableLabelFreeVarMods()

std::string getReadableLabelFreeVarMods

(

)

const

Get the readable variable modifications.

For example: "(1) Dimethyl (KR); (6) Acetyl (K); (9) Methyl (KR)".

Returns

A semi-colon separated text string.

getVarMods()

std::string getVarMods

(

)

const

Get the variable modifications encoded as string of integers.

Returns

The variable modifications encoded as string of integers.

getXmlCode()

std::string getXmlCode ( ms_ms1quant_match::chargeType  code )

static

Get the XML attribute value for a charge type code.

Some of the returned values include a substitution string of "%s" or "%d". These are replaced with a specific value in the created XML.

Parameters

code	The charge type to get the XML excoding string for.

Returns

The string used to encode the charge type in the XML file.

hasComponent()

bool hasComponent

(

std::string

componentName

)

const

Returns true if the matched peptide has the component.

Parameters

componentName

The name of component to be searched for, e.g. "Heavy".

Returns

True if the match has the component.

hasIdentifiedComponent()

bool hasIdentifiedComponent

(

)

const

Check if the match has any component that was identified by Mascot.

Returns

True if any component of the match has been identified.

hasPeptideRatio()

bool hasPeptideRatio

(

const std::string &

ratioName

)

const

Returns true if the match has a peptide ratio value for the ratio name.

Parameters

ratioName

The name of ratio to be searched for, e.g. "H/L".

Returns

True if the ratio exists for the peptide match.

isHitRatioExcluded()

bool isHitRatioExcluded	(	const std::string &	ratioName,
		int	hitId,
		int	memberNumber
	)		const

Returns true if the match ratio is excluded from a hit.

Data for a protein hit to which the peptide match is assigned.

Parameters

ratioName	The name of the ratio.
hitId	Protein hit number.
memberNumber	Family member number.

Returns

True if the match ratio is excluded from this hit.

isHitRatioOutlier()

bool isHitRatioOutlier	(	const std::string &	ratioName,
		int	hitId,
		int	memberNumber
	)		const

Returns true if the match ratio is an outlier for a hit.

Data for a protein hit to which the peptide match is assigned.

Parameters

ratioName	The name of the ratio.
hitId	Protein hit number.
memberNumber	Family member number.

Returns

True if the match ratio is an outlier for the hit.

isHitRatioUsedForAverage()

bool isHitRatioUsedForAverage	(	const std::string &	ratioName,
		int	hitId,
		int	memberNumber
	)		const

Returns true if the match ratio is used in the average quantitation protocol for a hit.

Data for a protein hit to which the peptide match is assigned.

Parameters

ratioName	The name of the ratio.
hitId	Protein hit number.
memberNumber	Family member number.

Returns

True if the match ratio is used in the average protocol for this hit.

removeComponent()

bool removeComponent

(

const std::string &

componentName

)

Primarily for replicate where we want to remove components that are found in other files.

Parameters

componentName

is the name of the new component to be added

Returns

true if the component was removed

setHitRatioExcluded()

void setHitRatioExcluded	(	const std::string &	ratioName,
		int	hitId,
		int	memberNumber
	)

Set the match ratio to be excluded from a hit.

Data for a protein hit to which the peptide match is assigned.

See also

clearHitRatioExcluded()

Parameters

ratioName	The name of the ratio.
hitId	One based protein hit number.
memberNumber	One based family member number.

setHitRatioOutlier()

void setHitRatioOutlier	(	const std::string &	ratioName,
		int	hitId,
		int	memberNumber
	)

Set the match ratio to be an outlier for a hit.

Data for a protein hit to which the peptide match is assigned.

Parameters

ratioName	The name of the ratio.
hitId	Protein hit number.
memberNumber	Family member number.

---

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

• ms_ms1quant_match.hpp
• ms_ms1quant_match.cpp