ms_ms1quant_peptide_status Class Reference [Quantitation analysis for Mascot Server and Distiller]

An individual peptide's quantitation status. More...

#include <ms_ms1quant_peptide_status.hpp>

Inherits matrix_science::ms_handle.

List of all members.

Public Types
enum	peptideStatus {   PS_OK = 0,   PS_EXPECTGREATERTHAN = 1,   PS_LESSTHANIDENTITY = 2,   PS_MINCHARGE = 3,   PS_NOTUNIQUE = 4,   PS_SCORELESSHOMOLOGY = 5,   PS_SCORELESSIDENTITY_NOHOMO = 6,   PS_SCORELESSTHRESHOLD = 7,   PS_EXCLUDE_LOCALDEF = 8,   PS_EXCLUDE_MODFILE = 9,   PS_EXCLUDE_UNMODIFIED = 10,   PS_NOTPARTOFQUANTITATION = 11,   PS_DUPLICATESAMEQUERY = 12,   PS_MAX = 13 }
	Status codes from fitting peptides. More...
Public Member Functions
	ms_ms1quant_peptide_status ()
	Default constructor.
	ms_ms1quant_peptide_status (const ms_ms1quant_peptide_status_body &body)
	Populated constructor, linked to loaded data.
std::string	getComponent () const
	Get the component for the peptide hit.
int	getQuery () const
	Get the query for the peptide.
int	getRank () const
	Get the rank for the peptide.
peptideStatus	getStatus () const
	Get the status for the peptide hit.
Static Public Member Functions
static peptideStatus	getCodeFromXml (std::string str)
	Get the status code for an XML attribute value.
static std::string	getXmlCode (peptideStatus code)
	Get the XML attribute value for a status code.

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Detailed Description

An individual peptide's quantitation status.

This is the status determined for the peptide during quantitation.

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Member Enumeration Documentation

enum peptideStatus

Status codes from fitting peptides.

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

Enumerator:

PS_OK	No problem.
PS_EXPECTGREATERTHAN	The expectation is greater then 1.
PS_LESSTHANIDENTITY	The score is less than that required for identity.
PS_MINCHARGE	The charge state is less than the minimum required.
PS_NOTUNIQUE	The peptide is not unique.
PS_SCORELESSHOMOLOGY	The score is less than that required for homology.
PS_SCORELESSIDENTITY_NOHOMO	The score is less than that required for identity and there is no homology.
PS_SCORELESSTHRESHOLD	The score is less than the required threshold.
PS_EXCLUDE_LOCALDEF	The peptide is excluded due to a local definition.
PS_EXCLUDE_MODFILE	The peptide is excluded due to a modification file.
PS_EXCLUDE_UNMODIFIED	The peptide is excluded due to it being unmodified.
PS_NOTPARTOFQUANTITATION	The peptide is excluded because it is not part of quantitation.
PS_DUPLICATESAMEQUERY	The peptide is excluded because it is a duplicate in the same query.
PS_MAX	The number of values in this enumeration.

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Constructor & Destructor Documentation

ms_ms1quant_peptide_status

(

)

Default constructor.

Assigns reasonable default values to all internal members. The status is set to PS_NOTPARTOFQUANTITATION.

ms_ms1quant_peptide_status

(

const ms_ms1quant_peptide_status_body &

body )

Populated constructor, linked to loaded data.

Parameters:

body	The data loaded from the result file.

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Member Function Documentation

ms_ms1quant_peptide_status::peptideStatus getCodeFromXml

(

std::string

str )

[static]

Get the status code for an XML attribute value.

Some of the returned values include a substitution string of "%s" or "%d". The text is decoded based on the value up until the first substitution position.

Parameters:

str	The string used to encode the status value in the XML file.

Returns:

The peptide status corresponding to the XML encoded string.

std::string getComponent

(

)

const

Get the component for the peptide hit.

Returns:

The component (e.g. "Heavy") for the peptide component.

int getQuery

(

)

const

Get the query for the peptide.

Returns:

The query number.

int getRank

(

)

const

Get the rank for the peptide.

Returns:

The rank within the query.

matrix_science::ms_ms1quant_peptide_status::peptideStatus getStatus

(

)

const

Get the status for the peptide hit.

Returns:

The status for the peptide hit.

std::string getXmlCode

(

ms_ms1quant_peptide_status::peptideStatus

code )

[static]

Get the XML attribute value for a status 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 peptide status to get the XML excoding string for.

Returns:

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

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

• ms_ms1quant_peptide_status.hpp
• ms_ms1quant_peptide_status.cpp