ModifierRep Class Reference

Implements modification for suffix arrays. More...

#include <OpenMS/CHEMISTRY/ModifierRep.h>

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

Protected Attributes
std::vector< std::vector< double > >	modification_table_
	all possible modifications More...
Size	number_of_modifications_
	number of maximal modifications More...
std::map< String, std::vector< String > >	mass_mapping_
	maps a mass to the combination of modifications More...

Detailed Description

Implements modification for suffix arrays.

Constructor & Destructor Documentation

ModifierRep() [1/2]

ModifierRep

(

)

Constructor.

ModifierRep() [2/2]

ModifierRep

(

const ModifierRep &

source

)

copy constructor

~ModifierRep()

virtual ~ModifierRep ( )

virtual

destructor

Member Function Documentation

getMaxModificationMasses()

Size getMaxModificationMasses

(

)

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

Returns

Size

getModificationsForMass() [1/2]

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.

getModificationsForMass() [2/2]

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

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

Parameters

m	mass
seq	peptide sequence

Returns

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

getModificationTable()

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

(

)

getter for the modification table

Returns

const reference to the modofication table

getNumberOfModifications()

Size getNumberOfModifications

(

)

const

getter for number of modifications

Returns

number of modifications

refreshModificationList()

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 occur 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.

setNumberOfModifications()

void setNumberOfModifications

(

Size

i

)

setter for number of modifications

Parameters

i	number of modifications

Member Data Documentation

mass_mapping_

std::map<String, std::vector<String> > mass_mapping_

protected

maps a mass to the combination of modifications

modification_table_

std::vector<std::vector<double> > modification_table_

protected

all possible modifications

number_of_modifications_

Size number_of_modifications_

protected

number of maximal modifications