Helper routines for peptide quantitation. More...

#include <ms_quant_helper.hpp>

Inheritance diagram for ms_quant_helper:

Collaboration diagram for ms_quant_helper:

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Public Types
enum	PEPTIDE_QUALITY { PEPTIDE_QUALITY_IS_OK = 0x0000 , PEPTIDE_CHARGE_BELOW_PRECURSOR_MIN = 0x0001 , PEPTIDE_SCORE_BELOW_SCORE_THR = 0x0002 , PEPTIDE_EXPECT_ABOVE_THRESHOLD = 0x0003 , PEPTIDE_SCORE_BELOW_IDENTITY_THR = 0x0004 , PEPTIDE_SCORE_BELOW_IDENTITY_THR_NOHOM = 0x0005 , PEPTIDE_SCORE_BELOW_HOMOLOGY_THR = 0x0006 , PEPTIDE_NOT_UNIQUE = 0x0007 , PEPTIDE_QUALITY_UNAVAILABLE = 0xf000 }
	Possible reasons why a peptide does not pass quality tests using a given quantitation method. More...

enum	PEPTIDE_QUANTIFIABILITY { PEPTIDE_IS_QUANTIFIABLE = 0x0000 , PEPTIDE_HAS_NO_REQUIRED_FIXEDMOD = 0x0001 , PEPTIDE_HAS_NO_REQUIRED_VARMOD = 0x0002 , PEPTIDE_HAS_EXCLUDED_FIXEDMOD = 0x0010 , PEPTIDE_HAS_EXCLUDED_LOCAL_FIXEDMOD = 0x0011 , PEPTIDE_HAS_EXCLUDED_VARMOD = 0x0012 , PEPTIDE_HAS_UNMODIFIED_SITE = 0x0013 , PEPTIDE_HAS_EXCLUDED_LOCAL_VARMOD = 0x0014 , PEPTIDE_HAS_NO_EXCLUSIVE_MODS = 0x0015 , PEPTIDE_QUANTIFIABILITY_UNAVAILABLE = 0xf000 }
	Possible reasons a peptide is not quantifiable using a given quantitation method. More...

Public Member Functions
	ms_quant_helper (const ms_peptidesummary &pepsum, const ms_quant_method &qm, const ms_umod_configfile &umodfile, const int file_index=ms_quant_file_index::file_index_value_not_set)
	Default constructor.

	~ms_quant_helper ()
	Destructor.

void	appendErrors (const ms_errors &src)
	Copies all errors from another instance and appends them at the end of own list.

void	clearAllErrors ()
	Remove all errors from the current list of errors.

void	copyFrom (const ms_errors *right)
	Use this member to make a copy of another instance.

int	createMissingComponents (matrix_science::ms_ms1quant_match *match) const
	Create any missing components and return the number of new components created.

const ms_errs *	getErrorHandler () const
	Retrive the error object using this function to get access to all errors and error parameters.

int	getFraction (const int file_index) const

int	getLastError () const
	Return the error description of the last error that occurred.

std::string	getLastErrorString () const
	Return the error description of the last error that occurred.

int	isPeptideQualityOK (int q, int p, std::string &reasonStrRef) const
	Given a peptide, test whether it passes the quality thresholds.

int	isPeptideQuantifiable (int q, int p, const ms_protein *protein, int peptideIndex, std::string &reasonStrRef) const
	Given a peptide and the residues before and after, test whether it is quantifiable.

bool	isValid () const
	Call this function to determine if there have been any errors.

Detailed Description

Helper routines for peptide quantitation.

Member Enumeration Documentation

◆ PEPTIDE_QUALITY

enum PEPTIDE_QUALITY

Possible reasons why a peptide does not pass quality tests using a given quantitation method.

Enumerator
PEPTIDE_QUALITY_IS_OK	Peptide passes quality thresholds.
PEPTIDE_CHARGE_BELOW_PRECURSOR_MIN	Peptide charge is less than minimum precursor charge.
PEPTIDE_SCORE_BELOW_SCORE_THR	Peptide score is below threshold.
PEPTIDE_EXPECT_ABOVE_THRESHOLD	Peptide expect value exceeds threshold.
PEPTIDE_SCORE_BELOW_IDENTITY_THR	Peptide score is below identity threshold.
PEPTIDE_SCORE_BELOW_IDENTITY_THR_NOHOM	Peptide score is below identity threshold (no homology threshold available).
PEPTIDE_SCORE_BELOW_HOMOLOGY_THR	Peptide score is below homology threshold.
PEPTIDE_NOT_UNIQUE	Peptide is not unique.
PEPTIDE_QUALITY_UNAVAILABLE	Quality cannot be determined.

◆ PEPTIDE_QUANTIFIABILITY

enum PEPTIDE_QUANTIFIABILITY

Possible reasons a peptide is not quantifiable using a given quantitation method.

Enumerator
PEPTIDE_IS_QUANTIFIABLE	Peptide is quantifiable using the given quantitation method.
PEPTIDE_HAS_NO_REQUIRED_FIXEDMOD	Peptide is missing a required fixed modification.
PEPTIDE_HAS_NO_REQUIRED_VARMOD	Peptide is missing a required variable modification.
PEPTIDE_HAS_EXCLUDED_FIXEDMOD	Peptide has an excluded fixed modification.
PEPTIDE_HAS_EXCLUDED_LOCAL_FIXEDMOD	Peptide has an excluded fixed modification, defined in the local modification definitions.
PEPTIDE_HAS_EXCLUDED_VARMOD	Peptide has an excluded variable modification.
PEPTIDE_HAS_UNMODIFIED_SITE	Peptide has an unmodified site where required modification should be.
PEPTIDE_HAS_EXCLUDED_LOCAL_VARMOD	Peptide has an excluded variable modification, defined in the local modification definitions.
PEPTIDE_HAS_NO_EXCLUSIVE_MODS	Peptide has none of the exclusive modifications (only tested when constrain search is disabled).
PEPTIDE_QUANTIFIABILITY_UNAVAILABLE	Quantifiability cannot be determined.

Constructor & Destructor Documentation

◆ ms_quant_helper()

ms_quant_helper	(	const ms_peptidesummary &	pepsum,
		const ms_quant_method &	qm,
		const ms_umod_configfile &	umodfile,
		const int	file_index = `ms_quant_file_index::file_index_value_not_set`
	)

Default constructor.

The object should receive the full quantitation method, including, in particular, component definitions and peptide quality settings. If the quantitation method is missing either set of settings, the corresponding methods will return the status "unavailable".

The constructor creates a copy of the relevant bits of the quantitation method and stores those internally. If you change the quantitation method later, you must create a new ms_quant_helper object.

Parameters

pepsum	Mascot results file whose peptide matches are to be tested.
qm	Quantitation method with component definitions, peptide quality settings and report ratio definitions.
umodfile	Unimod configuration file for looking up modification specificities.
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.

Member Function Documentation

◆ appendErrors()

void appendErrors ( const ms_errors & src )

inherited

Copies all errors from another instance and appends them at the end of own list.

Parameters

src	The object to copy the errors across from. See Maintaining object references: two rules of thumb.

◆ clearAllErrors()

void clearAllErrors ( )

inherited

Remove all errors from the current list of errors.

The list of 'errors' can include fatal errors, warning messages, information messages and different levels of debugging messages.

All messages are accumulated into a list in this object, until clearAllErrors() is called.

See Error Handling.

See also: isValid(), getLastError(), getLastErrorString(), getErrorHandler()

Examples: common_error.cpp, resfile_error.cpp, and resfile_summary.cpp.

◆ copyFrom()

void copyFrom ( const ms_errors * right )

inherited

Use this member to make a copy of another instance.

Parameters

right is the source to initialise from

◆ createMissingComponents()

int createMissingComponents ( matrix_science::ms_ms1quant_match * match ) const

Create any missing components and return the number of new components created.

Only supports the "precursor" protocol. Other protocols do nothing and return 0

For precursor, this will add the 'derived' matches. For example, if there is a peptide match to the light component, it will add an expected heavy match, even though there is no search ID for the heavy match.

Parameters

match contains the peptide match to which new 'components' are to be added.

Returns: the number of new components added to the match

◆ getErrorHandler()

const ms_errs * getErrorHandler ( ) const

inherited

Retrive the error object using this function to get access to all errors and error parameters.

See Error Handling.

Returns: Constant pointer to the error handler

See also: isValid(), getLastError(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, and http_helper_getstring.cpp.

◆ getFraction()

int getFraction ( const int file_index ) const

Parameters

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.

Returns: the fraction, if one has been specified in the method, otherwise return matrix_science::ms_quant_file_index::file_index_value_not_set

◆ getLastError()

int getLastError ( ) const

inherited

Return the error description of the last error that occurred.

All errors are accumulated into a list in this object, until clearAllErrors() is called. This function returns the last error that occurred.

See Error Handling.

See also: isValid(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Returns: the error number of the last error, or 0 if there have been no errors.

◆ getLastErrorString()

std::string getLastErrorString ( ) const

inherited

Return the error description of the last error that occurred.

All errors are accumulated into a list in this object, until clearAllErrors() is called. This function returns the last error that occurred.

Returns: Most recent error, warning, information or debug message

See Error Handling.

See also: isValid(), getLastError(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, config_enzymes.cpp, config_fragrules.cpp, config_license.cpp, config_mascotdat.cpp, config_masses.cpp, config_modfile.cpp, config_procs.cpp, config_quantitation.cpp, config_taxonomy.cpp, http_helper_getstring.cpp, and tools_aahelper.cpp.

◆ isPeptideQualityOK()

int isPeptideQualityOK	(	int	q,
		int	p,
		std::string &	reasonStrRef
	)		const

Given a peptide, test whether it passes the quality thresholds.

The peptide identified by query q and rank p is tested against peptide quality settings in the quantitation method. If it does not pass all of the quality tests (e.g. score thresholds), the corresponding status is returned; see PEPTIDE_QUALITY for details.

The method defers loading the full peptide object until it is really needed, if at all. Significance tests and score and expect value thresholds can be conducted without loading the peptide object in its entirety. This means the method is fast both when caching is in use and without caching.

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

Thread safe: This method is safe to use from multiple threads. See also Using Parser in multithreaded applications.

Parameters

[in]	q	Peptide query.
[in]	p	Peptide rank.
[out]	reasonStrRef	is a free-text description of the return status is assigned to the variable. If status is `PEPTIDE_QUALITY_IS_OK`, reasonStrRef will be the empty string. If status is `PEPTIDE_QUALITY_UNAVAILABLE`, reasonStrRef will not be changed by this method.

Returns: Status describing whether the peptide meets all the requirements to be quantifiable using the quantitation method.

◆ isPeptideQuantifiable()

int isPeptideQuantifiable	(	int	q,
		int	p,
		const ms_protein *	protein,
		int	peptideIndex,
		std::string &	reasonStrRef
	)		const

Given a peptide and the residues before and after, test whether it is quantifiable.

The method first loads the peptide with query q and rank p. The peptide is tested against component definitions in the quantitation method. If it is missing required modifications, or if it contains excluded modifications, the corresponding status is returned; see PEPTIDE_QUANTIFIABILITY for details.

If the quantitation method does not contain suitable component definitions, the return status is PEPTIDE_QUANTIFIABILITY_UNAVAILABLE.

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

Parameters

[in]	q	Peptide query.
[in]	p	Peptide rank.
[in]	protein	Protein hit to which the peptide match is assigned. This is only needed in the case where a quality parameter is specified to exclude an unmodified protein N- or C-terminus residue. In this case, this code needs to know if the flanking residue is the corresponding protein terminus. The same peptide may appear in multiple proteins, and may be at the terminus of just one of them, so if you need all peptides that may be quantifiable, pass 0 or NULL.
[in]	peptideIndex	Integer index of the peptide match in the protein hit, between 1 and `protein->getNumPeptides()`. If protein is null, use 0.
[out]	reasonStrRef	is a free-text description of the return status is assigned to the variable. If status is `PEPTIDE_IS_QUANTIFIABLE`, reasonStrRef will be the empty string. If status is `PEPTIDE_QUANTIFIABILITY_UNAVAILABLE`, reasonStrRef will not be changed by this method.

Returns: Status describing whether the peptide meets all the requirements to be quantifiable using the quantitation method.

◆ isValid()

bool isValid ( ) const

inherited

Call this function to determine if there have been any errors.

This will return true unless there have been any fatal errors.

See Error Handling.

Returns: True if no fatal error occured

See also: getLastError(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, config_enzymes.cpp, config_fragrules.cpp, config_license.cpp, config_mascotdat.cpp, config_masses.cpp, config_modfile.cpp, config_procs.cpp, config_quantitation.cpp, config_taxonomy.cpp, http_helper_getstring.cpp, peptide_list.cpp, repeat_search.cpp, resfile_error.cpp, resfile_info.cpp, resfile_input.cpp, resfile_params.cpp, resfile_summary.cpp, and tools_aahelper.cpp.

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

ms_quant_helper.hpp
ms_quant_helper.cpp

Public Types

Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ PEPTIDE_QUALITY

◆ PEPTIDE_QUANTIFIABILITY

Constructor & Destructor Documentation

◆ ms_quant_helper()

Member Function Documentation

◆ appendErrors()

◆ clearAllErrors()

◆ copyFrom()

◆ createMissingComponents()

◆ getErrorHandler()

◆ getFraction()

◆ getLastError()

◆ getLastErrorString()

◆ isPeptideQualityOK()

◆ isPeptideQuantifiable()

◆ isValid()