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

#include <OpenMS/DATASTRUCTURES/MassExplainer.h>

Collaboration diagram for MassExplainer:

Public Types
typedef Adduct::AdductsType	AdductsType
	Type definition for a vector of Adduct objects. More...

typedef std::vector< Compomer >::const_iterator	CompomerIterator
	Type definition for an iterator over Compomer objects. More...

Constructors and destructor
std::vector< Compomer >	explanations_
	Vector storing all possible explanations for mass differences. More...

AdductsType	adduct_base_
	Set of allowed adducts that can be combined to explain mass differences. More...

Int	q_min_
	Minimum charge state to consider in explanations. More...

Int	q_max_
	Maximum charge state to consider in explanations. More...

Int	max_span_
	Maximum allowed charge span between related features (e.g., a cluster with q={3,6} has span=4) More...

double	thresh_p_
	Minimum required probability threshold for accepting explanations. More...

Size	max_neutrals_
	Maximum number of neutral (q=0) adducts allowed in an explanation. More...

	MassExplainer ()
	Default constructor. More...

	MassExplainer (AdductsType adduct_base)
	Constructor with custom adduct base. More...

	MassExplainer (Int q_min, Int q_max, Int max_span, double thresh_logp)
	Constructor with custom charge parameters. More...

	MassExplainer (AdductsType adduct_base, Int q_min, Int q_max, Int max_span, double thresh_logp, Size max_neutrals)
	Constructor with all custom parameters. More...

MassExplainer &	operator= (const MassExplainer &rhs)
	Assignment operator. More...

virtual	~MassExplainer ()
	Destructor. More...

void	compute ()
	Compute all possible mass differences and their explanations. More...

void	setAdductBase (AdductsType adduct_base)
	Set the base set of allowed adducts. More...

AdductsType	getAdductBase () const
	Get the current set of allowed adducts. More...

const Compomer &	getCompomerById (Size id) const
	Get a specific compomer by its ID. 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
	Search for explanations of a given mass difference. More...

void	init_ (bool init_thresh_p)
	Check consistency of input parameters and initialize internal data structures. More...

bool	compomerValid_ (const Compomer &cmp) const
	Check if a generated compomer is valid based on its probability, charges, etc. More...

Adduct	createAdduct_ (const String &formula, const Int charge, const double p) const
	Create a proper adduct from formula, charge, and probability. More...

Detailed Description

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

MassExplainer is used to explain observed mass differences between features by determining the most likely combination of adducts that could cause such differences.

The class works by:

Taking a set of allowed adducts (elements, molecules, or ions)
Computing all possible combinations of these adducts that could explain observed mass differences
Providing a query interface to search for explanations for specific mass differences

This is particularly useful in mass spectrometry data analysis for identifying related features that represent the same analyte but with different adducts or charge states.

Member Typedef Documentation

◆ AdductsType

typedef Adduct::AdductsType AdductsType

Type definition for a vector of Adduct objects.

◆ CompomerIterator

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

Type definition for an iterator over Compomer objects.

Constructor & Destructor Documentation

◆ MassExplainer() [1/4]

MassExplainer ( )

Default constructor.

Initializes with default parameters:

No adducts
Charge range from -2 to +4
Maximum charge span of 4
Log probability threshold of -5.0
Maximum number of neutral adducts of 2

◆ MassExplainer() [2/4]

MassExplainer ( AdductsType adduct_base )

Constructor with custom adduct base.

Parameters

adduct_base Set of allowed adducts to use for mass difference explanations

◆ MassExplainer() [3/4]

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

Constructor with custom charge parameters.

Parameters

q_min	Minimum charge state to consider
q_max	Maximum charge state to consider
max_span	Maximum allowed charge span between related features
thresh_logp	Minimum log probability threshold for accepting explanations

◆ MassExplainer() [4/4]

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

Constructor with all custom parameters.

Parameters

adduct_base	Set of allowed adducts to use for mass difference explanations
q_min	Minimum charge state to consider
q_max	Maximum charge state to consider
max_span	Maximum allowed charge span between related features
thresh_logp	Minimum log probability threshold for accepting explanations
max_neutrals	Maximum number of neutral adducts allowed in an explanation

◆ ~MassExplainer()

virtual ~MassExplainer ( )

virtual

Destructor.

Member Function Documentation

◆ compomerValid_()

bool compomerValid_ ( const Compomer & cmp ) const

protected

Check if a generated compomer is valid based on its probability, charges, etc.

Parameters

cmp	The compomer to validate

Returns: True if the compomer is valid, false otherwise

◆ compute()

void compute ( )

Compute all possible mass differences and their explanations.

This method generates all possible combinations of adducts from the adduct base and stores them internally for later querying. This must be called after changing any parameters and before performing queries.

◆ createAdduct_()

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

protected

Create a proper adduct from formula, charge, and probability.

Parameters

formula	Chemical formula of the adduct
charge	Charge of the adduct
p	Probability of the adduct

Returns: Adduct object with the specified properties

◆ getAdductBase()

AdductsType getAdductBase ( ) const

Get the current set of allowed adducts.

Returns: Vector of adducts currently used for explanations

◆ getCompomerById()

const Compomer& getCompomerById ( Size id ) const

Get a specific compomer by its ID.

This is typically used after a query() to retrieve detailed information about a specific explanation.

Parameters

id	ID of the compomer to retrieve

Returns: Reference to the requested compomer

◆ init_()

void init_ ( bool init_thresh_p )

private

Check consistency of input parameters and initialize internal data structures.

This method validates the input parameters and sets default values where needed.

Parameters

init_thresh_p Whether to initialize the probability threshold with default value (set to "false" to keep current value)

◆ operator=()

MassExplainer& operator= ( const MassExplainer & rhs )

Assignment operator.

Parameters

rhs	Source object to assign from

Returns: Reference to this object

◆ 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 for explanations of a given mass difference.

This method searches the precomputed explanations for those that match the given mass difference within the specified tolerance and have the required net charge.

Parameters

net_charge	Net charge of the compomer being sought
mass_to_explain	Mass difference in Da that needs explanation
mass_delta	Allowed deviation from exact mass (tolerance)
thresh_log_p	Minimum log probability required for explanations
firstExplanation	Output iterator to the beginning of matching explanations
lastExplanation	Output iterator to the end of matching explanations

Returns: Number of explanations found, or negative value if no explanations found

◆ setAdductBase()

void setAdductBase ( AdductsType adduct_base )

Set the base set of allowed adducts.

Parameters

adduct_base Vector of adducts to use for explanations

Member Data Documentation

◆ adduct_base_

AdductsType adduct_base_

protected

Set of allowed adducts that can be combined to explain mass differences.

◆ explanations_

std::vector<Compomer> explanations_

protected

Vector storing all possible explanations for mass differences.

◆ max_neutrals_

Size max_neutrals_

protected

Maximum number of neutral (q=0) adducts allowed in an explanation.

◆ max_span_

Int max_span_

protected

Maximum allowed charge span between related features (e.g., a cluster with q={3,6} has span=4)

◆ q_max_

Int q_max_

protected

Maximum charge state to consider in explanations.

◆ q_min_

Int q_min_

protected

Minimum charge state to consider in explanations.

◆ thresh_p_

double thresh_p_

protected

Minimum required probability threshold for accepting explanations.

Public Types

Constructors and destructor

Detailed Description

Member Typedef Documentation

◆ AdductsType

◆ CompomerIterator

Constructor & Destructor Documentation

◆ MassExplainer() [1/4]

◆ MassExplainer() [2/4]

◆ MassExplainer() [3/4]

◆ MassExplainer() [4/4]

◆ ~MassExplainer()

Member Function Documentation

◆ compomerValid_()

◆ compute()

◆ createAdduct_()

◆ getAdductBase()

◆ getCompomerById()

◆ init_()

◆ operator=()

◆ query()

◆ setAdductBase()

Member Data Documentation

◆ adduct_base_

◆ explanations_

◆ max_neutrals_

◆ max_span_

◆ q_max_

◆ q_min_

◆ thresh_p_