MassExplainer Class Reference [Datastructures]

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

#include <OpenMS/DATASTRUCTURES/MassExplainer.h>

List of all members.

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
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.
AdductsType	getAdductBase () const
	Returns the set of adducts.
const Compomer &	getCompomerById (Size id) const
	return a compomer by its Id (useful after a query() ).
Protected Member Functions
bool	compomerValid_ (const Compomer &cmp)
	check if the generated compomer is valid judged by its probability, charges etc
Adduct	createAdduct_ (const String &formula, const Int charge, const DoubleReal p) const
	create a proper adduct from formula and charge and probability
Protected Attributes
std::vector< Compomer >	explanations_
	store possible explanations (as formula) for a certain ChargeDifference and MassDifference
AdductsType	adduct_base_
	all allowed adducts, whose combination explains the mass difference
Int	q_min_
	minimal expected charge
Int	q_max_
	maximal expected charge
Int	max_span_
	maximal span (in terms of charge) for co-features, e.g. a cluster with q={3,6} has span=4
DoubleReal	thresh_p_
	minimum required probability of a compound (all other compounds are discarded)
Size	max_neutrals_
	Maximum number of neutral(q=0) adducts.
Constructors and destructor
	MassExplainer ()
	Default constructor.
	MassExplainer (AdductsType adduct_base)
	Constructor.
	MassExplainer (Int q_min, Int q_max, Int max_span, DoubleReal thresh_logp)
	Constructor.
	MassExplainer (AdductsType adduct_base, Int q_min, Int q_max, Int max_span, DoubleReal thresh_logp, Size max_neutrals)
	Constructor.
MassExplainer &	operator= (const MassExplainer &rhs)
	Assignment operator.
virtual	~MassExplainer ()
	Destructor.
void	init_ (bool init_thresh_p)

---

Detailed Description

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

---

Member Typedef Documentation

typedef Adduct::AdductsType AdductsType

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

---

Constructor & Destructor Documentation

MassExplainer

(

)

Default constructor.

MassExplainer

(

AdductsType

adduct_base

)

Constructor.

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

Constructor.

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

Constructor.

virtual ~MassExplainer

(

)

[virtual]

Destructor.

---

Member Function Documentation

bool compomerValid_

(

const Compomer &

cmp

)

[protected]

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

void compute

(

)

fill map with possible mass-differences along with their explanation

Adduct createAdduct_	(	const String &	formula,
		const Int	charge,
		const DoubleReal	p
	)			const [protected]

create a proper adduct from formula and charge and probability

AdductsType getAdductBase

(

)

const

Returns the set of adducts.

const Compomer& getCompomerById

(

Size

id

)

const

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

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)

MassExplainer& operator=

(

const MassExplainer &

rhs

)

Assignment operator.

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

void setAdductBase

(

AdductsType

adduct_base

)

Sets the set of possible adducts.

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Member Data Documentation

AdductsType adduct_base_ [protected]

all allowed adducts, whose combination explains the mass difference

std::vector<Compomer> explanations_ [protected]

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

Size max_neutrals_ [protected]

Maximum number of neutral(q=0) adducts.

Int max_span_ [protected]

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

Int q_max_ [protected]

maximal expected charge

Int q_min_ [protected]

minimal expected charge

DoubleReal thresh_p_ [protected]

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