Holds information on an edge connecting two features from a (putative) charge ladder. More...

#include <OpenMS/DATASTRUCTURES/Compomer.h>

Collaboration diagram for Compomer:

Public Types
enum	SIDE { LEFT, RIGHT, BOTH }
	side of compomer (LEFT ^ subtract; RIGHT ^ add) More...

typedef std::map< String, Adduct >	CompomerSide
	adducts and their abundance etc More...

typedef std::vector< CompomerSide >	CompomerComponents
	container for the two sides [0]=left, [1]=right More...

Public Member Functions
	Compomer ()
	Default Constructor. More...

	Compomer (Int net_charge, double mass, double log_p)
	Constructor with net-charge and mass. More...

	Compomer (const Compomer &p)
	Copy C'tor. More...

Compomer &	operator= (const Compomer &source)
	Assignment Operator. More...

void	add (const Adduct &a, UInt side)
	Add a.amount of Adduct. More...

bool	isConflicting (const Compomer &cmp, UInt side_this, UInt side_other) const

void	setID (const Size &id)
	set an Id which allows unique identification of a compomer More...

const Size &	getID () const
	return Id which allows unique identification of this compomer More...

const CompomerComponents &	getComponent () const
	left and right adducts of this compomer More...

const Int &	getNetCharge () const
	net charge of compomer (i.e. difference between left and right side of compomer) More...

const double &	getMass () const
	mass of all contained adducts More...

const Int &	getPositiveCharges () const
	summed positive charges of contained adducts More...

const Int &	getNegativeCharges () const
	summed negative charges of contained adducts More...

const double &	getLogP () const
	return log probability More...

const double &	getRTShift () const
	return log probability More...

String	getAdductsAsString () const
	get adducts with their abundance as compact string for both sides More...

String	getAdductsAsString (UInt side) const

bool	isSingleAdduct (Adduct &a, const UInt side) const
	check if Compomer only contains a single adduct on side `side` More...

Compomer	removeAdduct (const Adduct &a) const
	Remove all adducts of type `a`. More...

Compomer	removeAdduct (const Adduct &a, const UInt side) const
	Remove all adducts of type `a` from `side` (LEFT or RIGHT) More...

StringList	getLabels (const UInt side) const
	Returns the adduct labels from `side` (LEFT or RIGHT) More...

void	add (const CompomerSide &add_side, UInt side)
	Adds `add_side` to this compomer. More...

Private Attributes
CompomerComponents	cmp_
	adducts of left and right side More...

Int	net_charge_
	net charge (right - left) More...

double	mass_
	net mass (right - left) More...

Int	pos_charges_
	net charges on the right More...

Int	neg_charges_
	net charges on the left More...

double	log_p_
	log probability of compomer More...

double	rt_shift_
	expected net RT shift of compomer (-shift_leftside + shift_rightside) More...

Size	id_

Friends
bool	operator< (const Compomer &c1, const Compomer &c2)
	Sort compomer by (in order of importance): net-charge, mass, probability. More...

std::ostream &	operator<< (std::ostream &os, const Compomer &cmp)
	Print the contents of a Compomer to a stream. More...

bool	operator== (const Compomer &a, const Compomer &b)
	Comparator. More...

Detailed Description

Holds information on an edge connecting two features from a (putative) charge ladder.

A compomer is storing information on the adducts used on LEFT and RIGHT nodes (Features) that are connected by the edge (i.e. ChargePair) holding the compomer. Additionally meta information on the edge (net_charge, edge score, id) which is kept up-to-date when adducts are added to either side is stored.

Member Typedef Documentation

◆ CompomerComponents

typedef std::vector<CompomerSide> CompomerComponents

container for the two sides [0]=left, [1]=right

◆ CompomerSide

typedef std::map<String, Adduct> CompomerSide

adducts and their abundance etc

Member Enumeration Documentation

◆ SIDE

enum SIDE

side of compomer (LEFT ^ subtract; RIGHT ^ add)

Enumerator
LEFT
RIGHT
BOTH

Constructor & Destructor Documentation

◆ Compomer() [1/3]

Compomer ( )

Default Constructor.

◆ Compomer() [2/3]

Compomer	(	Int	net_charge,
		double	mass,
		double	log_p
	)

Constructor with net-charge and mass.

◆ Compomer() [3/3]

Compomer ( const Compomer & p )

Copy C'tor.

Member Function Documentation

◆ add() [1/2]

void add	(	const Adduct &	a,
		UInt	side
	)

Add a.amount of Adduct.

Parameters

a	to Compomer's
side	and update its properties

◆ add() [2/2]

void add	(	const CompomerSide &	add_side,
		UInt	side
	)

Adds add_side to this compomer.

◆ getAdductsAsString() [1/2]

String getAdductsAsString ( ) const

get adducts with their abundance as compact string for both sides

◆ getAdductsAsString() [2/2]

String getAdductsAsString ( UInt side ) const

get adducts with their abundance as compact string (amounts are absolute unless side=BOTH)

Parameters

side	Use LEFT for left, RIGHT for right

◆ getComponent()

const CompomerComponents& getComponent ( ) const

left and right adducts of this compomer

◆ getID()

const Size& getID ( ) const

return Id which allows unique identification of this compomer

◆ getLabels()

StringList getLabels ( const UInt side ) const

Returns the adduct labels from side (LEFT or RIGHT)

Get a list of labels for the side (useful for assigning channels (light, heavy etc) to features).

◆ getLogP()

const double& getLogP ( ) const

return log probability

◆ getMass()

const double& getMass ( ) const

mass of all contained adducts

◆ getNegativeCharges()

const Int& getNegativeCharges ( ) const

summed negative charges of contained adducts

◆ getNetCharge()

const Int& getNetCharge ( ) const

net charge of compomer (i.e. difference between left and right side of compomer)

◆ getPositiveCharges()

const Int& getPositiveCharges ( ) const

summed positive charges of contained adducts

◆ getRTShift()

const double& getRTShift ( ) const

return log probability

◆ isConflicting()

bool isConflicting	(	const Compomer &	cmp,
		UInt	side_this,
		UInt	side_other
	)		const

indicates if these two compomers can coexist for one feature

Parameters

cmp	The other Compomer we compare to
side_this	Indicates which "side"(negative or positive adducts) we are looking at. Negative adducts belong to the left side of the ChargePair.
side_other	See above.

◆ isSingleAdduct()

bool isSingleAdduct	(	Adduct &	a,
		const UInt	side
	)		const

check if Compomer only contains a single adduct on side side

◆ operator=()

Compomer& operator= ( const Compomer & source )

Assignment Operator.

◆ removeAdduct() [1/2]

Compomer removeAdduct ( const Adduct & a ) const

Remove all adducts of type a.

Remove ALL instances of the given adduct, BUT use the given adducts parameters (charge, logp, mass etc) to update the compomers members

◆ removeAdduct() [2/2]

Compomer removeAdduct	(	const Adduct &	a,
		const UInt	side
	)		const

Remove all adducts of type a from side (LEFT or RIGHT)

remove ALL instances of the given adduct from the given side (LEFT or RIGHT), BUT use the given adducts parameters (charge, logp, mass etc) to update the compomers members

◆ setID()

void setID ( const Size & id )

set an Id which allows unique identification of a compomer

Friends And Related Function Documentation

◆ operator<

bool operator<	(	const Compomer &	c1,
		const Compomer &	c2
	)

friend

Sort compomer by (in order of importance): net-charge, mass, probability.

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		const Compomer &	cmp
	)

friend

Print the contents of a Compomer to a stream.

◆ operator==

bool operator==	(	const Compomer &	a,
		const Compomer &	b
	)

friend

Comparator.

Member Data Documentation

◆ cmp_

CompomerComponents cmp_

private

adducts of left and right side

◆ id_

Size id_

private

◆ log_p_

double log_p_

private

log probability of compomer

◆ mass_

double mass_

private

net mass (right - left)

◆ neg_charges_

Int neg_charges_

private

net charges on the left

◆ net_charge_

Int net_charge_

private

net charge (right - left)

◆ pos_charges_

Int pos_charges_

private

net charges on the right

◆ rt_shift_

double rt_shift_

private

expected net RT shift of compomer (-shift_leftside + shift_rightside)

Public Types

Public Member Functions

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ CompomerComponents

◆ CompomerSide

Member Enumeration Documentation

◆ SIDE

Constructor & Destructor Documentation

◆ Compomer() [1/3]

◆ Compomer() [2/3]

◆ Compomer() [3/3]

Member Function Documentation

◆ add() [1/2]

◆ add() [2/2]

◆ getAdductsAsString() [1/2]

◆ getAdductsAsString() [2/2]

◆ getComponent()

◆ getID()

◆ getLabels()

◆ getLogP()

◆ getMass()

◆ getNegativeCharges()

◆ getNetCharge()

◆ getPositiveCharges()

◆ getRTShift()

◆ isConflicting()

◆ isSingleAdduct()

◆ operator=()

◆ removeAdduct() [1/2]

◆ removeAdduct() [2/2]

◆ setID()

Friends And Related Function Documentation

◆ operator<

◆ operator<<

◆ operator==

Member Data Documentation

◆ cmp_

◆ id_

◆ log_p_

◆ mass_

◆ neg_charges_

◆ net_charge_

◆ pos_charges_

◆ rt_shift_