ms_modvector Class Reference [Mascot configuration files module]

General usage class for creating lists of modifications to be passed as parameters. More...

#include <ms_modfile.hpp>

List of all members.

Public Member Functions
	ms_modvector ()
	Default constructor.
	ms_modvector (const ms_modvector &src)
	Copying constructor.
	ms_modvector (const ms_umod_modification &src, const ms_umod_configfile &umod_file)
	Copying constructor that takes a Unimod file object as a source.
	~ms_modvector ()
	Destructor.
void	appendModification (const ms_modification *item)
	Adds a new modification at the end of the vector.
void	appendModifications (ms_modvector &right)
	Adds copies of modifications at the end of the vector.
void	clearModifications ()
	Deletes all modifications from the vector.
void	copyFrom (const ms_modvector *right)
	Copies all content from another instance.
void	copyFrom (const ms_umod_modification *right, const ms_umod_configfile *umod_file)
	Copies all content from a Unimod modification object.
const ms_modification *	getModificationByName (const std::string &name) const
	Returns a modification object by its name.
const ms_modification *	getModificationByNumber (const int numMod) const
	Returns a modification object by its number.
int	getNumberOfModifications () const
	Returns the number of modifications currently held in the vector.
ms_modvector &	operator= (const ms_modvector &right)
	C++ style assignment operator.

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Detailed Description

General usage class for creating lists of modifications to be passed as parameters.

Examples:

tools_aahelper.cpp.

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Constructor & Destructor Documentation

ms_modvector	(	const ms_umod_modification &	src,
		const ms_umod_configfile &	umod_file
	)

Copying constructor that takes a Unimod file object as a source.

Each modificationbelement in Unimod consists of one or more specificities that can be grouped by their specGroup value. Therefore, each modification element can be converted to one or more mod_file style modifications.

Parameters:

src	a Unimod object to copy the content from.
umod_file	an instance of a Unimod file object from which to extract element masses.

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Member Function Documentation

void copyFrom	(	const ms_umod_modification *	right,
		const ms_umod_configfile *	umod_file
	)

Copies all content from a Unimod modification object.

Every modification object in a Unimod file consits of one or more specificities. Specificities can be grouped or merged by their specificity group ID. Therefore, we can potentially obtain a vector of specificity groups out of any modification in a Unimod file. Such specificity groups can be converted into mod_file style modifications directly.

Parameters:

right	a Unimod style modification object to copy the content from.
umod_file	Unimod file object from which to get masses of elements and amino-acids.

const ms_modification * getModificationByName

(

const std::string &

nameMod )

const

Returns a modification object by its name.

Parameters:

nameMod

is the modification name to match.

Returns:

The modification object, or a null value if a non-existent nameMod value is passed.

const ms_modification * getModificationByNumber

(

const int

numMod )

const

Returns a modification object by its number.

Parameters:

numMod

is the modification number greater than or equal to zero and less than getNumberOfModifications().

Returns:

The modification object, or a null value if an invalid numMod value is passed. See Maintaining object references: two rules of thumb.

Examples:

tools_aahelper.cpp.

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

• ms_modfile.hpp
• ms_modfile.cpp