The class represents a single modification-entry in mod_file. More...

#include <ms_modfile.hpp>

Inheritance diagram for ms_modification:

Collaboration diagram for ms_modification:

Public Member Functions
	ms_modification (const ms_masses *massFile=NULL)
	Default constructor.
	ms_modification (const ms_modification &src)
	Copying constructor.
	~ms_modification ()
	Destructor.
void	appendIgnoreMass (const double massMono, const double massAve)
	Appends a new ignore mass pair.
void	appendModifiedResidue (const char residue, const double massMono, const double massAve)
	Adds one more residue that can be modified together with its new mass.
void	clearIgnoreMasses ()
	Deletes all ignore-masses.
void	clearModifiedResidues ()
	Deletes all residues modified together with their masses and deltas.
void	copyFrom (const ms_modification *src)
	Copies modification configuration from another instance.
void	copyMassFile (const ms_masses *massFile)
void	defaultValues ()
	Re-initialises the object.
std::string	getCode () const
	Return the monolink code.
double	getCTerminusMass (const MASS_TYPE massType) const
	Returns the mass of modified C-terminus.
double	getDelta (const MASS_TYPE massType) const
	Returns delta (in Da) value for the given mass type.
bool	getFromUnimod (const char modName, const ms_umod_configfile umod_file)
	Retrieves modification from the Unimod file object by its mod_file-style name.
double	getIgnoreMass (const MASS_TYPE massType, const int idx) const
	Returns the value of the i^th ignore mass. See getNumberOfIgnoreMasses() for more explanations.
const ms_masses *	getMassFile () const
	Returns a pointer to ms_masses instance held internally.
int	getModificationType () const
	Returns the type (or class) of modification.
char	getModifiedResidue (const int n) const
	Traverse the modified residues list.
std::string	getMonoLinkTitle () const
	Return the modification title with monolink code appended.
ms_vectorDouble	getNeutralLoss (const MASS_TYPE massType) const
	Return neutral loss delta.
ms_vectorBool	getNeutralLossRequired () const
	Returns a vector of boolean values (required/not required) for each neutral loss value.
double	getNTerminusMass (const MASS_TYPE massType) const
	Returns the mass of modified N-terminus.
int	getNumberOfIgnoreMasses () const
	Returns the number of masses to be ignored.
int	getNumberOfModifiedResidues () const
	Returns a total number of modified residue for a residue-specific modification.
std::string	getPairsWith () const
	Return the monolink codes this monolink pairs with.
ms_vectorDouble	getPepNeutralLoss (const MASS_TYPE massType) const
	Returns a vector of PepNeutralLoss-values.
std::string	getPreceedingComments () const
	Returns any comments preceeding the section.
ms_vectorDouble	getReqPepNeutralLoss (const MASS_TYPE massType) const
	Returns a vector of RepPepNeutralLoss-values.
double	getResidueMass (const MASS_TYPE massType, const char residue) const
	Returns a mass of modified residue.
std::string	getTitle () const
	Returns the modification title.
bool	inErrorTolerant () const
	Returns whether this modification should be used in error tolerant searches.
bool	inLongList () const
	Returns whether this modification is flagged to appear in the search form long list.
bool	inShortList () const
	Returns whether this modification is flagged to appear in the search form short list.
bool	isGeneratedMonoLinker () const
	Return true if this is a monolink modification.
bool	isHidden () const
	Returns value of the Hidden parameter.
bool	isLoopLinker () const
	Return true if this is a monolink modification whose delta corresponds to the intact link mass.
bool	isResidueModified (const char residue) const
	Check a single residue.
bool	isSubstitution () const
	Returns TRUE if the modification is derived from the `substitutions` file.
ms_modification &	operator= (const ms_modification &right)
	C++ style assignment operator.
void	setCTerminusMass (const double massMono, const double massAve)
	Sets the mass of modified C-terminus.
void	setDelta (const double massMono, const double massAve)
	Changes delta value for the given mass type.
void	setHidden (const bool value)
	Sets the value of Hidden parameter.
void	setInErrorTolerant (const bool value)
	Sets whether this modification should be used in error tolerant searches.
void	setInLongList (const bool value)
	Sets whether this modification is flagged to appear in the search form long list.
void	setInShortList (const bool value)
	Sets whether this modification is flagged to appear in the search form short list.
void	setMassFile (const ms_masses *massFile)
	Stores pointer to the external ms_masses object to refer later.
void	setModificationType (const int type)
	Sets the modification type parameter into the supplied value.
void	setNeutralLoss (const ms_vectorDouble massMono, const ms_vectorDouble massAve, const ms_vectorBool required)
	Returns a vector of corresponding frequencies for each neutral loss value.
void	setNTerminusMass (const double massMono, const double massAve)
	Sets the mass of modified N-terminus.
void	setPepNeutralLoss (const ms_vectorDouble valuesMono, const ms_vectorDouble valuesAve)
	Set the vector of PepNeutralLoss-values.
void	setPreceedingComments (const std::string &comments)
	Sets any comments preceeding the section.
void	setReqPepNeutralLoss (const ms_vectorDouble valuesMono, const ms_vectorDouble valuesAve)
	Set the vector of RepPepNeutralLoss-values.
void	setTitle (const char *value)
	Change the title for the modification.
void	setTitleSource (const char unimodName, const char specString)

Detailed Description

The class represents a single modification-entry in mod_file.

Instances of this class are created in ms_modfile when parsing mod_file. It should be used in read-only mode. But if you really want to create a custom modification from scratch then specify modification type and supply the mass file object first and set residue masses or deltas second.

Modifications that only apply to a specific residue at a specific terminus need to be handled with care. An example is the conversion of Methionine to Homoserine lactone. This is defined in mod_file as follows:

   Title:Hse_lact (C-term M)
   ResiduesCterm:M -31.000631 -31.1002

These mods are always processed as variable mods, even if they were originally specified as fixed mods. Mascot Parser implicitly treats them as terminal group mods, so that the return values from Mascot Parser for this modification are as follows:

     ms_modification::getResidueMass(matrix_science::MASS_TYPE_MONO, "M") returns 0
     ms_modification::getDelta(matrix_science::MASS_TYPE_MONO) returns -48.003370665
     ms_modification::isResidueModified("M") returns TRUE
     ms_modification::getCTerminusMass(matrix_science::MASS_TYPE_MONO) returns -31.000631
     ms_masses::getResidueMass(matrix_science::MASS_TYPE_MONO, "M") returns 131.04048
     ms_masses::isResidueModified("M") returns FALSE
     ms_masses::getCtermDelta(matrix_science::MASS_TYPE_MONO) returns 0
     ms_masses::getCterminalMass(matrix_science::MASS_TYPE_MONO) returns 17.002739665

When writing code, you may wish to categorise such cases as residue mods. If so, in the case of Hse_lact, the mass of the modified residue would be the sum of the return values from ms_modification::getDelta() and ms_masses::getResidueMass().

Also get yourselves acquainted with the base class ms_customproperty. It facilitates the following tasks:

Retrieving an unsupported property.
Retrieving a raw/text/XML property representation.
Checking for existence of a certain property rather than dealing with its default value.
Accessing commented lines in a section.

More functionality is described in the documentation for ms_customproperty.

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

Constructor & Destructor Documentation

ms_modification ( const ms_masses * massFile = NULL )

Default constructor.

Not normally called from client applications.

Parameters:

massFile Optional parameter to specify the source file for this modification.

ms_modification ( const ms_modification & src )

Copying constructor.

Not normally called from client applications.

Parameters:

src	reference to an ms_modification object

Member Function Documentation

void appendIgnoreMass	(	const double	massMono,
		const double	massAve
	)

Appends a new ignore mass pair.

See also:: getNumberOfIgnoreMasses(), getIgnoreMass(), clearIgnoreMasses()

Parameters:

massMono	is the mono-isotopic mass of the fragment to be ignored.
massAve	is the average mass of the fragment to be ignored.

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

Adds one more residue that can be modified together with its new mass.

If you call this method for terminal residue modifications, the supplied masses are ignored, only the modified flag for the residue will be set and the total number of residues will be increased. However, if you need to set modified terminal masses for terminal modifications (residue-specific or not) use setNTerminusMass() and setCTerminusMass().

Parameters:

residue	needs to be a residue A-Z (or a-z).
massMono	is the mono-isotopic mass of the modified residue.
massAve	is the average mass of the modified residue.

void clearIgnoreMasses ( )

Deletes all ignore-masses.

See also:: getNumberOfIgnoreMasses(), getIgnoreMass(), appendIgnoreMass()

void clearModifiedResidues ( )

Deletes all residues modified together with their masses and deltas.

Values returned by getDelta() and getNeutralLoss() are not cleared.

void copyFrom ( const ms_modification * src )

Copies modification configuration from another instance.

Parameters:

src	is the source modification to be copied.

void copyMassFile ( const ms_masses * massFile )

Deprecated:: Do not use.

Parameters:

massFile pointer to a ms_masses object

void defaultValues ( )

Re-initialises the object.

Call this member if you want to re-use the instance by resetting all values to defaults.

Reimplemented from ms_customproperty.

std::string getCode ( ) const

Return the monolink code.

The monolink code is a single letter identifier, like A or W.

See also:: ms_mascotresfile::getMonoLinkModification

Returns:: Empty string if no code is defined, or a string containing one letter.

double getCTerminusMass ( const MASS_TYPE massType ) const

Returns the mass of modified C-terminus.

Call this method only for terminal modifications (irrespective of whether it is residue-specific or not). Residue modifications will always return zero.

Parameters:

massType should be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.

Returns:: mass of C-Terminus

double getDelta ( const MASS_TYPE massType ) const

Returns delta (in Da) value for the given mass type.

By default all values are equal to zero.

Parameters:

massType should be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.

Returns:: difference between unmodified and modified mass.

bool getFromUnimod	(	const char *	modName,
		const ms_umod_configfile *	umod_file
	)

Retrieves modification from the Unimod file object by its mod_file-style name.

Parameters:

modName	modification name in a mod_file style, such as "Acetyl (C)".
umod_file	a pointer to a Unimod file object where the modification is retrieved from.

Returns:: TRUE if the modification is successfully retrieved and FALSE if it is not found in the the Unimod file.

double getIgnoreMass	(	const MASS_TYPE	massType,
		const int	idx
	)		const

Returns the value of the i^th ignore mass. See getNumberOfIgnoreMasses() for more explanations.

See also:: getNumberOfIgnoreMasses(), clearIgnoreMasses(), appendIgnoreMass()

Parameters:

massType	should be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.
idx	index of the mass to be ignored and can be one of 0..(getNumberOfIgnoreMasses()-1).

Returns:: The mass in Daltons.

const ms_masses * getMassFile ( ) const

Returns a pointer to ms_masses instance held internally.

See also:: setMassFile()

Returns:: A pointer to the ms_masses object used. See Maintaining object references: two rules of thumb.

int getModificationType ( ) const

Returns the type (or class) of modification.

By default this is a residue modification.

Returns:: One of the enumeration MOD_TYPES values.

char getModifiedResidue ( const int n ) const

Traverse the modified residues list.

Parameters:

n	residue number that can be one of 0..(getNumberOfModifiedResidues()-1).

Returns:: a letter encoding an amino acid.

std::string getMonoLinkTitle ( ) const

Return the modification title with monolink code appended.

The monolink title consists of the Unimod name followed by the monolink code in square brackets. For example, the W monolink of Xlink:DSS (K) has monolink title "Xlink:DSS[W] (K)".

If this object is not a monolink (isGeneratedMonoLink() returns false), or if the modification was not generated from a Unimod entry, the monolink title is the same as ms_modification::getTitle().

Returns:: modification title containing the monolink code, in modfile-style format.

ms_vectorDouble getNeutralLoss ( const MASS_TYPE massType ) const

Return neutral loss delta.

By default there is no neutral loss for the modification (zero).

Parameters:

massType should be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.

Returns:: A vector of neutral loss values. For example, for phosphorylation three different netutral loss values may be specified.

ms_vectorBool getNeutralLossRequired ( ) const

Returns a vector of boolean values (required/not required) for each neutral loss value.

Returns:: The values in the vector have a one to one correspondence with the values returned by in getNeutralLoss().

double getNTerminusMass ( const MASS_TYPE massType ) const

Returns the mass of modified N-terminus.

Call this method only for terminal modifications (irrespective of whether it is residue-specific or not). Residue modifications will always return zero.

Parameters:

massType should be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.

Returns:: mass of N-Terminus

int getNumberOfIgnoreMasses ( ) const

Returns the number of masses to be ignored.

If a modification gives rise to intense, predictable non-sequence ion peaks, Mascot can be instructed to ignore these artefacts by means of "ignore masses". Initially, there is no ignore-masses in the list.

Returns:: The number of masses in the 'ignore' list.

int getNumberOfModifiedResidues ( ) const

Returns a total number of modified residue for a residue-specific modification.

By default the internal list of residues is empty.

Returns:: The number of modified residues.

std::string getPairsWith ( ) const

Return the monolink codes this monolink pairs with.

The pairsWith attribute is a string of single letter identifiers. These are typically used when pairing up peptide matches with MS-cleavable linkers.

See also:: ms_mascotresfile::getMonoLinkModification

Returns:: Empty string if no codes are defined, or a string containing one or more letters.

ms_vectorDouble getPepNeutralLoss ( const MASS_TYPE massType ) const

Returns a vector of PepNeutralLoss-values.

Parameters:

massType should be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.

Returns:: vector of PepNeutralLoss values

std::string getPreceedingComments ( ) const [inherited]

Returns any comments preceeding the section.

Sections in the mascot.dat file may have comments preceeding them. In most cases, these comments need to stay 'attached' to the section.

Multiple line comments are supported by having a single string with newline characters

See also:: setPreceedingComments()

Returns:: any comments preceeding the section

ms_vectorDouble getReqPepNeutralLoss ( const MASS_TYPE massType ) const

Returns a vector of RepPepNeutralLoss-values.

Parameters:

massType should be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.

Returns:: vector of RepPepNeutralLoss values

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

Returns a mass of modified residue.

Only modified residues will have non-zero mass. So, the default value returned by this function is zero.

Parameters:

massType	should be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.
residue	a letter encoding an amino acid.

Returns:: modification delta + absolute mass of the residue, in Daltons, or 0 if the residue is not modified.

std::string getTitle ( ) const

Returns the modification title.

A text string that is used to identify the modification in forms and reports. By default this is empty.

Returns:: The title.

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

bool isGeneratedMonoLinker ( ) const

Return true if this is a monolink modification.

A Unimod linker definition encodes monolinks as neutral losses. A monolink modification has the same title as the linker, but the delta is (linker mass - monolink NL).

See also:: ms_mascotresfile::getMonoLinkModification

Returns:: whether this modification is a monolink generated from a linker definition.

bool isHidden ( ) const

Returns value of the Hidden parameter.

If you wish to include modifications in mod_file without having them appear in a search form, the property Hidden should be set to TRUE.

By default this is not hidden.

Returns:: TRUE is the modification is hidden.

bool isLoopLinker ( ) const

Return true if this is a monolink modification whose delta corresponds to the intact link mass.

A Unimod linker definition encodes monolinks as neutral losses. A looplink modification is like a monolink modification, except its delta is the same as the intact linker mass.

See also:: ms_mascotresfile::getMonoLinkModification

Returns:: whether this modification is a looplink generated from a linker definition.

bool isResidueModified ( const char residue ) const

Check a single residue.

By default FALSE is returned for each residue, meaning "residue not modified".

Parameters:

residue a letter encoding an amino acid.

Returns:: TRUE if the residue is modified.

bool isSubstitution ( ) const

Returns TRUE if the modification is derived from the substitutions file.

If the modification is AA-substitution then this method will return TRUE.

Returns:: true if the modification is from substitution

ms_modification & operator= ( const ms_modification & right )

C++ style assignment operator.

Parameters:

right is the source modification to be copied.

Returns:: reference to the current object

void setCTerminusMass	(	const double	massMono,
		const double	massAve
	)

Sets the mass of modified C-terminus.

The method only has an effect for c-terminus modifications. This method will also override the delta value depending on the terminus mass supplied with the mass file object. However, if the mass file object has some fixed modifications applied, the delta will reflect this fact (not the terminus mass itself).

Parameters:

massMono	mass mono-isotopic
massAve	average mass

void setDelta	(	const double	massMono,
		const double	massAve
	)

Changes delta value for the given mass type.

By default all values are equal to zero.

Parameters:

massMono	is the delta using 12C monoisotopic masses.
massAve	is the delta using average masses.

void setHidden ( const bool value )

Sets the value of Hidden parameter.

If you wish to include modifications in mod_file without having them appear in a search form, the property Hidden should be set to TRUE.

By default this is not hidden.

Parameters:

value should be set to TRUE if the modification is to be hidden.

Examples:: config_modfile.cpp.

void setMassFile ( const ms_masses * massFile )

Stores pointer to the external ms_masses object to refer later.

If no external ms_masses instance is supplied, then the modification object will create an internal ms_masses instance filled with default values. Create an instance of ms_masses class, call its ms_masses::read_file() member and then call this function to supply the instance as a parameter. Alternatively, you can use copyMassFile() for content copying instead of pointer-copying.

Remember to keep massFile in memory for as long as you use this class object. See Memory management conventions.

Parameters:

massFile must be a valid pointer to an ms_masses object. See Maintaining object references: two rules of thumb.

void setModificationType ( const int type )

Sets the modification type parameter into the supplied value.

Parameters:

type	should be one of the MOD_TYPES values.

void setNeutralLoss	(	const ms_vectorDouble	massMono,
		const ms_vectorDouble	massAve,
		const ms_vectorBool	required
	)

Returns a vector of corresponding frequencies for each neutral loss value.

Change neutral loss delta.

All three arrays must be the same length or the function will fail.

Parameters:

massMono	is an array of mono-isotopic mass neutral losses.
massAve	is an array of average mass neutral losses.
required	is an array of booleans to specify if fragments with the loss must be seen for the series to be scored.

void setNTerminusMass	(	const double	massMono,
		const double	massAve
	)

Sets the mass of modified N-terminus.

The method only has an effect for n-terminus modifications. This method will also override the delta value depending on the terminus mass supplied with the mass file object. However, if the mass file object has some fixed modifications applied, the delta will reflect this fact (not the terminus mass itself).

Parameters:

massMono	mass mono-isotopic
massAve	average mass

void setPreceedingComments ( const std::string & comments ) [inherited]

Sets any comments preceeding the section.

Sections in the mascot.dat file may have comments preceeding them. In most cases, these comments need to stay 'attached' to the section.

Multiple line comments are supported by having a single string with newline characters

See also:: getPreceedingComments()

Parameters:

comments any comments preceeding the section

void setTitle ( const char * value )

Change the title for the modification.

See getTitle() for more information.

Parameters:

value is a string value for the new title.

void setTitleSource	(	const char *	unimodName,
		const char *	specString
	)

Parameters:

unimodName	is the Unimod name of the source definition.
specString	is the specification string with a leading space, e.g. " (K)".

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

ms_modfile.hpp
ms_modfile.cpp

ms_modification Class Reference [Mascot configuration files module]

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

ms_modification Class Reference
[Mascot configuration files module]