Reads and parses the masses file with residue and atom masses. More...

#include <ms_masses.hpp>

Inheritance diagram for ms_masses:

Collaboration diagram for ms_masses:

[legend]

Public Member Functions
	ms_masses ()
	Default constructor.

	ms_masses (const char filename, const matrix_science::ms_connection_settings cs=0)
	Reads the file immediately after the construction.

	ms_masses (const ms_masses &src)
	Copying constructor.

	ms_masses (const ms_umod_configfile &src, bool addMissingResidueMasses=true)
	Copying constructor.

	ms_masses (const ms_umod_configfile &src, const ms_quant_component &quantComp)
	Constructor for prepared isotope-substituted version of masses.

	~ms_masses ()
	Destructor.

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

ms_modvector	applyFixedMods (const ms_modvector mods, ms_errs err)
	Change residue masses according to the list of fixed modifications.

void	applyIsotopes (const ms_umod_configfile umodFile, const ms_quant_component quantComp)
	Update masses of amino-acids with isotope substitution.

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.

void	copyFrom (const ms_masses *right)
	Copies masses from another instance.

void	copyFrom (const ms_umod_configfile *right, bool addMissingResidueMasses=true)
	Copies masses from a Unimod file.

void	defaultValues (bool useDefaultResidueMasses=true)
	Use this member to re-initialise internal members.

double	getCarbonMass (const matrix_science::MASS_TYPE massType) const
	Returns a carbon(C) atom mass for a given mass type (MONO or AVE).

matrix_science::ms_connection_settings	getConnectionSettings () const
	Returns the sessionID and proxy server for use with an HTTP transfer.

double	getCtermDelta (const matrix_science::MASS_TYPE massType) const
	Returns C-term modification delta if there is a correspondent fixed modification applied.

double	getCterminalMass (const matrix_science::MASS_TYPE massType) const
	Returns C-terminal group mass (i.e. fixed modification delta or OH-mass).

double	getCtermNeutralLoss (const matrix_science::MASS_TYPE massType) const
	Returns C-term neutral loss value if there is a correspondent fixed modification applied.

double	getElectronMass () const
	Returns an electron mass.

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

std::string	getFileName () const
	Returns a file name set before or by default.

double	getFragResidueMass (const matrix_science::MASS_TYPE massType, const char residue) const
	Returns a residue mass with neutral loss after applying fixed modifications.

double	getHydrogenMass (const matrix_science::MASS_TYPE massType) const
	Returns a hydrogen (H) atom mass for a given mass type (MONO or AVE).

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.

double	getNitrogenMass (const matrix_science::MASS_TYPE massType) const
	Returns a nitrogen (N) atom mass for a given mass type (MONO or AVE).

double	getNtermDelta (const matrix_science::MASS_TYPE massType) const
	Returns N-term modification delta if there is a correspondent fixed modification applied.

double	getNterminalMass (const matrix_science::MASS_TYPE massType) const
	Returns N-terminal group mass (i.e. fixed modification delta or H-mass).

double	getNtermNeutralLoss (const matrix_science::MASS_TYPE massType) const
	Returns N-term neutral loss value if there is a correspondent fixed modification applied.

double	getOxygenMass (const matrix_science::MASS_TYPE massType) const
	Returns a oxygen (O) atom mass for a given mass type (MONO or AVE).

double	getResidueMass (const matrix_science::MASS_TYPE massType, const char residue) const
	Returns a mass for a given amino acid.

bool	isResidueModified (const char residue) const
	Returns true for residues modified by fixed modifications.

bool	isSame (const ms_masses &other, const MASS_TYPE massType) const
	Return true if other ms_masses is the same as this one.

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

ms_masses &	operator= (const ms_masses &right)
	C++ style assignment operator.

void	read_file ()
	Reads the configuration file, parses it and fill the mass arrays.

void	save_file ()
	Saves the information back to the file.

void	saveToString (std::string &modfileAsStr)
	Stores masses information in the string supplied.

void	setCarbonMass (const double massMono, const double massAve)
	Changes carbon mass values.

void	setConnectionSettings (const matrix_science::ms_connection_settings &cs)
	Sets the sessionID and proxy server for use with an HTTP transfer.

void	setCtermModification (const double monoDelta, const double aveDelta, const double monoNeutralLoss=0.0, const double aveNeutralLoss=0.0)
	Set C-term modification.

void	setElectronMass (const double mass)
	Changes oxygen mass values.

void	setFileName (const char *name)
	Set a custom file name instead of `../config/masses`.

void	setHydrogenMass (const double massMono, const double massAve)
	Changes hydrogen mass values.

void	setNitrogenMass (const double massMono, const double massAve)
	Changes nitrogen mass values.

void	setNtermModification (const double monoDelta, const double aveDelta, const double monoNeutralLoss=0.0, const double aveNeutralLoss=0.0)
	Set N-term modification.

void	setOxygenMass (const double massMono, const double massAve)
	Changes oxygen mass values.

void	setResidueMasses (const char residue, const double massMono, const double massAve)
	Changes mass values for a single residue.

void	setResidueModification (const double monoDelta, const double aveDelta, const double monoNeutralLoss, const double aveNeutralLoss, const char *residues)
	Applies a single residue modification.

Detailed Description

Reads and parses the masses file with residue and atom masses.

After reading a file and before using the object, check its validity by calling isValid() and retrieve error descriptions with getLastErrorString() if not valid.

A class instance can be used even if the configuration file has been read with problems or not read at all. Default values will be given to all members in that case.

Examples: config_masses.cpp, config_modfile.cpp, and tools_aahelper.cpp.

Constructor & Destructor Documentation

◆ ms_masses() [1/5]

ms_masses ( )

Default constructor.

Sets default mass values for all residues

◆ ms_masses() [2/5]

ms_masses ( const ms_masses & src )

Copying constructor.

Parameters

src	is the source object to copy masses from

◆ ms_masses() [3/5]

ms_masses	(	const ms_umod_configfile &	src,
		bool	addMissingResidueMasses = `true`
	)

Copying constructor.

Implemented by calling copyFrom(const ms_umod_configfile *, bool)

Parameters

src	has the residue and elemental masses that are used to initialise the masses
addMissingResidueMasses	is used to specify whether residue masses missing from the src should be set to zero or set to the default masses. If true, then default masses are used and if false, then any missing masses are just set to zero.

◆ ms_masses() [4/5]

ms_masses	(	const ms_umod_configfile &	src,
		const ms_quant_component &	quantComp
	)

Constructor for prepared isotope-substituted version of masses.

Masses of amino-acids are re-calculated with a different isotope applied (for example, 13C instead of C).

Parameters

src	a Unimod file object containing the composition of amino acids and original masses.
quantComp	a quantitation component containing isotope substitutions used in the quantitation experiment. This object can be created from scratch without reading its content from a file, but normally it should be taken from the quantitation method selected by a user. An alternative way to apply isotope substition is to use applyIsotopes() method.

◆ ms_masses() [5/5]

ms_masses	(	const char *	filename,
		const matrix_science::ms_connection_settings *	cs = `0`
	)

Reads the file immediately after the construction.

Parameters

filename	can be either a local file path or a Mascot server URL, it cannot be an empty string or NULL pointer. If it is a URL it should be of the form `http://your-server/mascot/cgi` .
cs	is a pointer to the connection settings. This should contain a sessionID and optionally the proxy server settings.

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.

◆ applyFixedMods()

ms_modvector applyFixedMods	(	const ms_modvector *	mods,
		ms_errs *	err
	)

Change residue masses according to the list of fixed modifications.

If you want to get the original (unmodified) masses of amino acids, load them from a file or obtain from another instance of the class.

Fixed modifications can also be applied separately using setNtermModification(), setCtermModification() and setResidueModification().

Parameters

mods	is the vector of modifications to apply
err	is used to collect the errors. To add any errors to the ms_masses object, pass this->getErrorHandler()

Returns: the new list of modifications

◆ applyIsotopes()

void applyIsotopes	(	const ms_umod_configfile *	umodFile,
		const ms_quant_component *	quantComp
	)

Update masses of amino-acids with isotope substitution.

Call this method explictly in order to re-calculate all amino acid masses according to a selected quantitation method. However, the quantitation component object can also be created on the fly with any custom isotope substitution. All applied fixed modifications are cancelled and should be re-applied if necessary with applyFixedMods() method.

Parameters

umodFile	a Unimod file object containing chemical composition of amino acids and element masses.
quantComp	a quantitation component object with isotope substitution information. If the object doesn't have any isotope elements in it no action will be taken.

◆ 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() [1/3]

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

◆ copyFrom() [2/3]

void copyFrom ( const ms_masses * right )

Copies masses from another instance.

Parameters

right is the source masses object

◆ copyFrom() [3/3]

void copyFrom	(	const ms_umod_configfile *	right,
		bool	addMissingResidueMasses = `true`
	)

Copies masses from a Unimod file.

Parameters

right	a pointer to unimod file object to copy the masses from.
addMissingResidueMasses	is used to specify whether residue masses missing from right should be set to zero or set to the default masses. If true, then default masses are used and if false, then any missing masses are just set to zero.

◆ defaultValues()

void defaultValues ( bool useDefaultResidueMasses = true )

Use this member to re-initialise internal members.

Called internally, but may also be used by other applications

Parameters

useDefaultResidueMasses should be set to true if the residue masses are to be initialised with default values. Otherwise they will all be set to mass zero.

◆ getCarbonMass()

double getCarbonMass ( const matrix_science::MASS_TYPE massType ) const

Returns a carbon(C) atom mass for a given mass type (MONO or AVE).

Parameters

massType one of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).

Returns: the mass of carbon

◆ getConnectionSettings()

matrix_science::ms_connection_settings getConnectionSettings ( ) const

Returns the sessionID and proxy server for use with an HTTP transfer.

See also the constructor documentation and setConnectionSettings().

Returns: The current connection settings.

◆ getCtermDelta()

double getCtermDelta ( const matrix_science::MASS_TYPE massType ) const

Returns C-term modification delta if there is a correspondent fixed modification applied.

See also: getCterminalMass()

Parameters

massType one of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).

Returns: the delta compared to an unmodified C terminus mass

◆ getCterminalMass()

double getCterminalMass ( const matrix_science::MASS_TYPE massType ) const

Returns C-terminal group mass (i.e. fixed modification delta or OH-mass).

See also: getCtermDelta()

Parameters

massType one of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).

Returns: the C terminus mass, including any applied modification

◆ getCtermNeutralLoss()

double getCtermNeutralLoss ( const matrix_science::MASS_TYPE massType ) const

Returns C-term neutral loss value if there is a correspondent fixed modification applied.

See also: getCterminalMass()

Parameters

massType one of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).

Returns: the delta compared to an unmodified C terminus mass

◆ getElectronMass()

double getElectronMass ( ) const

Returns an electron mass.

Returns: the mass of an electron

◆ 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.

◆ getFileName()

std::string getFileName ( ) const

Returns a file name set before or by default.

See also: setFileName()

Returns: the name of the masses file

◆ getFragResidueMass()

double getFragResidueMass	(	const matrix_science::MASS_TYPE	massType,
		const char	residue
	)		const

Returns a residue mass with neutral loss after applying fixed modifications.

Parameters

massType	one of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).
residue	a single letter encoding an amino acid in the range a..z or A..Z.

Returns: an absolute fragment for the amino acid.

◆ getHydrogenMass()

double getHydrogenMass ( const matrix_science::MASS_TYPE massType ) const

Returns a hydrogen (H) atom mass for a given mass type (MONO or AVE).

Parameters

massType one of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).

Returns: the mass of hydrogen

◆ 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.

◆ getNitrogenMass()

double getNitrogenMass ( const matrix_science::MASS_TYPE massType ) const

Returns a nitrogen (N) atom mass for a given mass type (MONO or AVE).

Parameters

massType one of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).

Returns: the mass of nitrogen

◆ getNtermDelta()

double getNtermDelta ( const matrix_science::MASS_TYPE massType ) const

Returns N-term modification delta if there is a correspondent fixed modification applied.

See also: getNterminalMass()

Parameters

massType one of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).

Returns: the delta compared to an unmodified N terminus mass

◆ getNterminalMass()

double getNterminalMass ( const matrix_science::MASS_TYPE massType ) const

Returns N-terminal group mass (i.e. fixed modification delta or H-mass).

See also: getNtermDelta()

Parameters

massType one of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).

Returns: the N terminus mass, including any applied modification

◆ getNtermNeutralLoss()

double getNtermNeutralLoss ( const matrix_science::MASS_TYPE massType ) const

Returns N-term neutral loss value if there is a correspondent fixed modification applied.

Parameters

massType one of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).

Returns: any neutral loss on the N terminus

◆ getOxygenMass()

double getOxygenMass ( const matrix_science::MASS_TYPE massType ) const

Returns a oxygen (O) atom mass for a given mass type (MONO or AVE).

Parameters

massType one of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).

Returns: the mass of oxygen

◆ getResidueMass()

double getResidueMass	(	const matrix_science::MASS_TYPE	massType,
		const char	residue
	)		const

Returns a mass for a given amino acid.

Parameters

massType	one of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).
residue	a single letter encoding an amino acid in the range a..z or A..Z.

Returns: an absolute mass for the amino acid.

Examples: config_masses.cpp.

◆ isResidueModified()

bool isResidueModified ( const char residue ) const

Returns true for residues modified by fixed modifications.

Parameters

residue a single letter encoding an amino acid in the range a..z or A..Z.

Returns: true for residues modified by fixed modifications.

◆ isSame()

bool isSame	(	const ms_masses &	right,
		const MASS_TYPE	massType
	)		const

Return true if other ms_masses is the same as this one.

Parameters

right	is the object to test against
massType	specifies whether to compare monoisotopic or average masses.

Returns: true if all the masses are the same

◆ 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.

◆ operator=()

ms_masses & operator= ( const ms_masses & right )

C++ style assignment operator.

Only available for C++

Parameters

right is the source object

Returns: a reference to 'this'

◆ read_file()

void read_file ( )

Reads the configuration file, parses it and fill the mass arrays.

Called from the constructor: ms_masses(const char*, const ms_connection_settings*)

◆ save_file()

void save_file ( )

Saves the information back to the file.

See also: setFileName() If the file cannot be opened for writing, an ms_errs::ERR_MSP_FAILED_TO_OPEN_FILE error is added.

Other errors in saving the file use ms_errs::ERR_MSP_FAILED_TO_WRITE_FILE

◆ saveToString()

void saveToString ( std::string & asStr )

Stores masses information in the string supplied.

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

Parameters

[out] asStr is the complete file as a string

◆ setCarbonMass()

void setCarbonMass	(	const double	massMono,
		const double	massAve
	)

Changes carbon mass values.

Parameters

massMono	is the new monoisotopic mass of carbon
massAve	is the new average mass of carbon

◆ setConnectionSettings()

void setConnectionSettings ( const matrix_science::ms_connection_settings & cs )

Sets the sessionID and proxy server for use with an HTTP transfer.

This value would normally be passed in the constructor.

Parameters

cs	is the new connection settings.

◆ setCtermModification()

void setCtermModification	(	const double	monoDelta,
		const double	aveDelta,
		const double	monoNeutralLoss = `0.0`,
		const double	aveNeutralLoss = `0.0`
	)

Set C-term modification.

Warning: The name of this function and the name of the first two parameters are potentially misleading.

Parameters

monoDelta	is the mass of the CTerminus. If there is no fixed modification, the value passed should be the monoisotopic mass of hydrogen plus the monoisotopic mass of oxygen.
aveDelta	is the mass of the CTerminus. If there is no fixed modification, the value passed should be the average mass of hydrogen plus the average mass of oxygen.
monoNeutralLoss	is the neutral loss of any fixed C terminus modification.
aveNeutralLoss	is the neutral loss of any fixed C terminusmodification.

◆ setElectronMass()

void setElectronMass ( const double mass )

Changes oxygen mass values.

Parameters

mass	is the new monoisotopic mass of an electron

◆ setFileName()

void setFileName ( const char * name )

Set a custom file name instead of ../config/masses.

Does not re-read the file, just saves the new name

See also: getFileName(); read_file()

Parameters

name	is the new file name

◆ setHydrogenMass()

void setHydrogenMass	(	const double	massMono,
		const double	massAve
	)

Changes hydrogen mass values.

Parameters

massMono	is the new monoisotopic mass of hydrogen
massAve	is the new average mass of hydrogen

◆ setNitrogenMass()

void setNitrogenMass	(	const double	massMono,
		const double	massAve
	)

Changes nitrogen mass values.

Parameters

massMono	is the new monoisotopic mass of nitrogen
massAve	is the new average mass of nitrogen

◆ setNtermModification()

void setNtermModification	(	const double	monoDelta,
		const double	aveDelta,
		const double	monoNeutralLoss = `0.0`,
		const double	aveNeutralLoss = `0.0`
	)

Set N-term modification.

Warning: The name of this function and the name of the first two parameters are potentially misleading.

Parameters

monoDelta	is the mass of the NTerminus. If there is no fixed modification, the value passed should be the monoisotopic mass of hydrogen.
aveDelta	is the mass of the NTerminus. If there is no fixed modification, the value passed should be the average mass of hydrogen.
monoNeutralLoss	is the neutral loss of any fixed N terminus modification.
aveNeutralLoss	is the neutral loss of any fixed N terminus modification.

◆ setOxygenMass()

void setOxygenMass	(	const double	massMono,
		const double	massAve
	)

Changes oxygen mass values.

Parameters

massMono	is the new monoisotopic mass of oxygen
massAve	is the new average mass of oxygen

◆ setResidueMasses()

void setResidueMasses	(	const char	residue,
		const double	massMono,
		const double	massAve
	)

Changes mass values for a single residue.

Parameters

residue	a single letter encoding an amino acid in the range a..z or A..Z.
massMono	is the new monoisotopic mass for the residue
massAve	is the new average mass for the residue

◆ setResidueModification()

void setResidueModification	(	const double	monoDelta,
		const double	aveDelta,
		const double	monoNeutralLoss,
		const double	aveNeutralLoss,
		const char *	residues
	)

Applies a single residue modification.

Parameters

monoDelta	is the delta in daltons for monoisotopic masses
aveDelta	is the delta in daltons for average masses
monoNeutralLoss	is the neutral loss for monoisotopic masses (typically zero)
aveNeutralLoss	is the neutral loss for average masses (typically zero)
residues	is a null terminated string with one or more letters which encoding amino acids in the range a..z or A..Z.

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

ms_masses.hpp
ms_masses.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ms_masses() [1/5]

◆ ms_masses() [2/5]

◆ ms_masses() [3/5]

◆ ms_masses() [4/5]

◆ ms_masses() [5/5]

Member Function Documentation

◆ appendErrors()

◆ applyFixedMods()

◆ applyIsotopes()

◆ clearAllErrors()

◆ copyFrom() [1/3]

◆ copyFrom() [2/3]

◆ copyFrom() [3/3]

◆ defaultValues()

◆ getCarbonMass()

◆ getConnectionSettings()

◆ getCtermDelta()

◆ getCterminalMass()

◆ getCtermNeutralLoss()

◆ getElectronMass()

◆ getErrorHandler()

◆ getFileName()

◆ getFragResidueMass()

◆ getHydrogenMass()

◆ getLastError()

◆ getLastErrorString()

◆ getNitrogenMass()

◆ getNtermDelta()

◆ getNterminalMass()

◆ getNtermNeutralLoss()

◆ getOxygenMass()

◆ getResidueMass()

◆ isResidueModified()

◆ isSame()

◆ isValid()

◆ operator=()

◆ read_file()

◆ save_file()

◆ saveToString()

◆ setCarbonMass()

◆ setConnectionSettings()

◆ setCtermModification()

◆ setElectronMass()

◆ setFileName()

◆ setHydrogenMass()

◆ setNitrogenMass()

◆ setNtermModification()

◆ setOxygenMass()

◆ setResidueMasses()

◆ setResidueModification()