ModifierRep Class Reference

Implements modification for suffix arrays. More...

#include <OpenMS/CHEMISTRY/ModifierRep.h>

List of all members.

Public Member Functions
	ModifierRep ()
	Constructor.
	ModifierRep (const ModifierRep &source)
	copy constructor
virtual	~ModifierRep ()
	destructor
void	setNumberOfModifications (Size i)
	setter for number of modifications
Size	getNumberOfModifications () const
	getter for number of modifications
const std::vector< std::vector < double > > &	getModificationTable ()
	getter for the modification table
void	refreshModificationList (std::map< double, SignedSize > &mod_map, const char &c)
	updates the modifications list if with the modifications of a new amino acid
Size	getMaxModificationMasses ()
	calculates the maximal number unique masses of combinations of modifications (maximal possible size of the modification map)
std::vector< String >	getModificationsForMass (double &m)
	gets all modification possibilities for a given mass
std::vector< String >	getModificationsForMass (double &m, const String &seq)
	gets all modification possibilities for a given mass and for the given peptide
Protected Attributes
std::vector< std::vector < double > >	modification_table_
	all possible modifications
Size	number_of_modifications_
	number of maximal modifications
std::map< String, std::vector < String > >	mass_mapping_
	maps a mass to the combination of modifications

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Detailed Description

Implements modification for suffix arrays.

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Constructor & Destructor Documentation

ModifierRep

(

)

Constructor.

ModifierRep

(

const ModifierRep &

source

)

copy constructor

virtual ~ModifierRep

(

)

[virtual]

destructor

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Member Function Documentation

Size getMaxModificationMasses

(

)

calculates the maximal number unique masses of combinations of modifications (maximal possible size of the modification map)

Returns:

Size

std::vector<String> getModificationsForMass	(	double &	m,
		const String &	seq
	)

gets all modification possibilities for a given mass and for the given peptide

Parameters:

	m	masse
	seq	peptide sequence

Returns:

vector of strings the getModificationsForMass (double & m) will be used. then a chacater histogramm of the sequence is created as well as for every possible combination of modifications. Then only modifications that are possible are returned.

std::vector<String> getModificationsForMass

(

double &

m

)

gets all modification possibilities for a given mass

Parameters:

m

masse

Returns:

vector of strings therefor at first the massmapping is calculated. This massmapping will be saved as private member mass_mapping_ so that it has to be calculated only once.

const std::vector<std::vector<double> >& getModificationTable

(

)

getter for the modification table

Returns:

const reference to the modofication table

Size getNumberOfModifications

(

)

const

getter for number of modifications

Returns:

number of modifications

void refreshModificationList	(	std::map< double, SignedSize > &	mod_map,
		const char &	c
	)

updates the modifications list if with the modifications of a new amino acid

Parameters:

	mod_map	reference to the map holding the possible modifications
	c	const character for the amino acid

all modification for the given amino acid are added to the map. The key is the mass, the value is the number of modifications for that mass. So the advantage of using a map is that a value will occure only once. the mass of the modification is added to all elements in the map whose number of modifications is smaller than the maximal number of modifications.

void setNumberOfModifications

(

Size

i

)

setter for number of modifications

Parameters:

i

number of modifications

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Member Data Documentation

std::map<String, std::vector<String> > mass_mapping_ [protected]

maps a mass to the combination of modifications

std::vector<std::vector<double> > modification_table_ [protected]

all possible modifications

Size number_of_modifications_ [protected]

number of maximal modifications