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

#include <OpenMS/DATASTRUCTURES/Compomer.h>

Public Types
enum	SIDE { LEFT, RIGHT, BOTH }
	side of compomer (LEFT ^ substract; RIGHT ^ add) More...
typedef Map< String, Adduct >	CompomerSide
typedef std::vector< CompomerSide >	CompomerComponents
	adducts and their abundance etc
Public Member Functions
	Compomer ()
	container for the two sides [0]=left, [1]=right
	Compomer (Int net_charge, DoubleReal mass, DoubleReal log_p)
	Constructor with net-charge and mass.
	Compomer (const Compomer &p)
	Copy C'tor.
Compomer &	operator= (const Compomer &source)
	Assignment Operator.
void	add (const Adduct &a, UInt side)
	Add a.amount of Adduct.
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
const Size &	getID () const
	return Id which allows unique identification of this compomer
const CompomerComponents &	getComponent () const
	left and right adducts of this compomer
const Int &	getNetCharge () const
	net charge of compomer (i.e. difference between left and right side of compomer)
const DoubleReal &	getMass () const
	mass of all contained adducts
const Int &	getPositiveCharges () const
	summed positive charges of contained adducts
const Int &	getNegativeCharges () const
	summed negative charges of contained adducts
const DoubleReal &	getLogP () const
	return log probability
const DoubleReal &	getRTShift () const
	return log probability
String	getAdductsAsString () const
	get adducts with their abundance as compact string for both sides
String	getAdductsAsString (UInt side) const
bool	isSingleAdduct (Adduct &a, const UInt side) const
	check if Compomer only contains a single adduct on side `side`
Compomer	removeAdduct (const Adduct &a) const
	Remove all adducts of type `a`.
Compomer	removeAdduct (const Adduct &a, const UInt side) const
	Remove all adducts of type `a` from `side` (LEFT or RIGHT).
StringList	getLabels (const UInt side) const
	Returns the adduct labels from `side` (LEFT or RIGHT).
void	add (const CompomerSide &add_side, UInt side)
	Adds `add_side` to this compomer.
Private Attributes
CompomerComponents	cmp_
Int	net_charge_
DoubleReal	mass_
Int	pos_charges_
Int	neg_charges_
DoubleReal	log_p_
DoubleReal	rt_shift_
Size	id_
Friends
bool	operator< (const Compomer &c1, const Compomer &c2)
	Sort compomer by (in order of importance): net-charge, mass, probability.
std::ostream &	operator<< (std::ostream &os, const Compomer &cmp)
	Print the contents of a Compomer to a stream.
bool	operator== (const Compomer &a, const Compomer &b)
	Comparator.

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 egde (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

typedef std::vector<CompomerSide> CompomerComponents

adducts and their abundance etc

typedef Map<String, Adduct> CompomerSide

Member Enumeration Documentation

enum SIDE

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

Enumerator:

LEFT
RIGHT
BOTH

Constructor & Destructor Documentation

Compomer ( )

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

Default Constructor

Compomer	(	Int	net_charge,
		DoubleReal	mass,
		DoubleReal	log_p
	)

Constructor with net-charge and mass.

Compomer ( const Compomer & p )

Copy C'tor.

Member Function Documentation

void add	(	const Adduct &	a,
		UInt	side
	)

Add a.amount of Adduct.

Parameters:

	a	to Compomer's
	side	and update its properties

void add	(	const CompomerSide &	add_side,
		UInt	side
	)

Adds add_side to this compomer.

String getAdductsAsString ( ) const

get adducts with their abundance as compact string for both sides

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

const CompomerComponents& getComponent ( ) const

left and right adducts of this compomer

const Size& getID ( ) const

return Id which allows unique identification of this compomer

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).

const DoubleReal& getLogP ( ) const

return log probability

const DoubleReal& getMass ( ) const

mass of all contained adducts

const Int& getNegativeCharges ( ) const

summed negative charges of contained adducts

const Int& getNetCharge ( ) const

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

const Int& getPositiveCharges ( ) const

summed positive charges of contained adducts

const DoubleReal& getRTShift ( ) const

return log probability

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.

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

check if Compomer only contains a single adduct on side side

Compomer& operator= ( const Compomer & source )

Assignment Operator.

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

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

void setID ( const Size & id )

set an Id which allows unique identification of a compomer