MassExplainer Class Reference

computes empirical formulas for given mass differences using a set of allowed elements More...

#include <OpenMS/DATASTRUCTURES/MassExplainer.h>

Public Types
typedef Adduct::AdductsType	AdductsType
typedef std::vector< Compomer >::const_iterator	CompomerIterator

Public Member Functions
void	compute ()
	fill map with possible mass-differences along with their explanation More...
SignedSize	query (const Int net_charge, const float mass_to_explain, const float mass_delta, const float thresh_log_p, std::vector< Compomer >::const_iterator &firstExplanation, std::vector< Compomer >::const_iterator &lastExplanation) const
void	setAdductBase (AdductsType adduct_base)
	Sets the set of possible adducts. More...
AdductsType	getAdductBase () const
	Returns the set of adducts. More...
const Compomer &	getCompomerById (Size id) const
	return a compomer by its Id (useful after a query() ). More...

Protected Member Functions
bool	compomerValid_ (const Compomer &cmp)
	check if the generated compomer is valid judged by its probability, charges etc More...
Adduct	createAdduct_ (const String &formula, const Int charge, const double p) const
	create a proper adduct from formula and charge and probability More...

Protected Attributes
std::vector< Compomer >	explanations_
	store possible explanations (as formula) for a certain ChargeDifference and MassDifference More...
AdductsType	adduct_base_
	all allowed adducts, whose combination explains the mass difference More...
Int	q_min_
	minimal expected charge More...
Int	q_max_
	maximal expected charge More...
Int	max_span_
	maximal span (in terms of charge) for co-features, e.g. a cluster with q={3,6} has span=4 More...
double	thresh_p_
	minimum required probability of a compound (all other compounds are discarded) More...
Size	max_neutrals_
	Maximum number of neutral(q=0) adducts. More...

Constructors and destructor
	MassExplainer ()
	Default constructor. More...
	MassExplainer (AdductsType adduct_base)
	Constructor. More...
	MassExplainer (Int q_min, Int q_max, Int max_span, double thresh_logp)
	Constructor. More...
	MassExplainer (AdductsType adduct_base, Int q_min, Int q_max, Int max_span, double thresh_logp, Size max_neutrals)
	Constructor. More...
MassExplainer &	operator= (const MassExplainer &rhs)
	Assignment operator. More...
virtual	~MassExplainer ()
	Destructor. More...
void	init_ (bool init_thresh_p)

Detailed Description

computes empirical formulas for given mass differences using a set of allowed elements

Member Typedef Documentation

AdductsType

typedef Adduct::AdductsType AdductsType

CompomerIterator

typedef std::vector<Compomer>::const_iterator CompomerIterator

Constructor & Destructor Documentation

MassExplainer() [1/4]

MassExplainer

(

)

Default constructor.

MassExplainer() [2/4]

MassExplainer

(

AdductsType

adduct_base

)

Constructor.

MassExplainer() [3/4]

MassExplainer	(	Int	q_min,
		Int	q_max,
		Int	max_span,
		double	thresh_logp
	)

Constructor.

MassExplainer() [4/4]

MassExplainer	(	AdductsType	adduct_base,
		Int	q_min,
		Int	q_max,
		Int	max_span,
		double	thresh_logp,
		Size	max_neutrals
	)

Constructor.

~MassExplainer()

virtual ~MassExplainer ( )

virtual

Destructor.

Member Function Documentation

compomerValid_()

bool compomerValid_ ( const Compomer &  cmp )

protected

check if the generated compomer is valid judged by its probability, charges etc

compute()

void compute

(

)

fill map with possible mass-differences along with their explanation

createAdduct_()

Adduct createAdduct_ ( const String &  formula, const Int  charge, const double  p  ) const

protected

create a proper adduct from formula and charge and probability

getAdductBase()

AdductsType getAdductBase

(

)

const

Returns the set of adducts.

getCompomerById()

const Compomer& getCompomerById

(

Size

id

)

const

return a compomer by its Id (useful after a query() ).

init_()

void init_ ( bool  init_thresh_p )

private

check consistency of input

Parameters

init_thresh_p

set default threshold (set to "false" to keep current value)

operator=()

MassExplainer& operator=

(

const MassExplainer &

rhs

)

Assignment operator.

query()

SignedSize query	(	const Int	net_charge,
		const float	mass_to_explain,
		const float	mass_delta,
		const float	thresh_log_p,
		std::vector< Compomer >::const_iterator &	firstExplanation,
		std::vector< Compomer >::const_iterator &	lastExplanation
	)		const

search the mass database for explanations

Parameters

net_charge	net charge of compomer seeked
mass_to_explain	mass in Da that needs explanation
mass_delta	allowed deviation from exact mass
thresh_log_p	minimal log probability required
firstExplanation	begin range with candidates according to net_charge and mass
lastExplanation	end range

setAdductBase()

void setAdductBase

(

AdductsType

adduct_base

)

Sets the set of possible adducts.

Member Data Documentation

adduct_base_

AdductsType adduct_base_

protected

all allowed adducts, whose combination explains the mass difference

explanations_

std::vector<Compomer> explanations_

protected

store possible explanations (as formula) for a certain ChargeDifference and MassDifference

max_neutrals_

Size max_neutrals_

protected

Maximum number of neutral(q=0) adducts.

max_span_

Int max_span_

protected

maximal span (in terms of charge) for co-features, e.g. a cluster with q={3,6} has span=4

q_max_

Int q_max_

protected

maximal expected charge

q_min_

Int q_min_

protected

minimal expected charge

thresh_p_

double thresh_p_

protected

minimum required probability of a compound (all other compounds are discarded)