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 }
	Enumeration for specifying which side of the compomer to operate on. More...

typedef std::map< String, Adduct >	CompomerSide
	Type definition for one side of a compomer (maps adduct labels to Adduct objects) More...

typedef std::vector< CompomerSide >	CompomerComponents
	Container for both sides of a compomer. More...

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

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

	Compomer (const Compomer &p)
	Copy constructor. More...

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

void	add (const Adduct &a, UInt side)
	Add an adduct to a specific side of the compomer. More...

bool	isConflicting (const Compomer &cmp, UInt side_this, UInt side_other) const
	Determines if two compomers conflict with each other. More...

void	setID (const Size &id)
	Set a unique identifier for this compomer. More...

const Size &	getID () const
	Get the unique identifier of this compomer. More...

const CompomerComponents &	getComponent () const
	Get both sides (left and right) of this compomer. More...

const Int &	getNetCharge () const
	Get the net charge of this compomer. More...

const double &	getMass () const
	Get the total mass difference represented by this compomer. More...

const Int &	getPositiveCharges () const
	Get the sum of positive charges in this compomer. More...

const Int &	getNegativeCharges () const
	Get the sum of negative charges in this compomer. More...

const double &	getLogP () const
	Get the log probability of this adduct combination. More...

const double &	getRTShift () const
	Get the expected retention time shift caused by this compomer. More...

String	getAdductsAsString () const
	Get a string representation of all adducts in this compomer. More...

String	getAdductsAsString (UInt side) const
	Get a string representation of adducts on a specific side. More...

bool	isSingleAdduct (Adduct &a, const UInt side) const
	Check if the compomer contains only a single adduct on the specified 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)
	Add a complete set of adducts to a specific side of the 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_
	Sum of positive charges. More...

Int	neg_charges_
	Sum of negative charges. More...

double	log_p_
	Log probability of this adduct combination. More...

double	rt_shift_
	Expected net RT shift (-shift_leftside + shift_rightside) More...

Size	id_
	Unique identifier for this compomer. More...

Friends
bool	operator< (const Compomer &c1, const Compomer &c2)
	Comparison operator for sorting compomers. More...

std::ostream &	operator<< (std::ostream &os, const Compomer &cmp)
	Output stream operator for printing compomer contents. More...

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

Detailed Description

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

A Compomer represents the chemical composition difference between two mass spectrometry features. It stores information about the adducts (ions, molecules, or atoms) that explain the mass and charge differences between these features.

The Compomer has two sides:

LEFT side: adducts subtracted from the first feature
RIGHT side: adducts added to the first feature

This model allows representing the relationship between features that correspond to the same analyte but with different adduct compositions or charge states.

The Compomer maintains metadata such as:

Net charge (difference between right and left sides)
Total mass difference
Probability score of this adduct combination
Expected RT shift caused by the adducts

This class is used extensively in the feature decharging and adduct annotation processes.

Member Typedef Documentation

◆ CompomerComponents

typedef std::vector<CompomerSide> CompomerComponents

Container for both sides of a compomer.

Vector with exactly two elements:

[0] = left side (adducts subtracted)
[1] = right side (adducts added)

◆ CompomerSide

typedef std::map<String, Adduct> CompomerSide

Type definition for one side of a compomer (maps adduct labels to Adduct objects)

Member Enumeration Documentation

◆ SIDE

enum SIDE

Enumeration for specifying which side of the compomer to operate on.

LEFT: The left side (adducts subtracted from the first feature)
RIGHT: The right side (adducts added to the first feature)
BOTH: Both sides of the compomer

Enumerator
LEFT
RIGHT
BOTH

Constructor & Destructor Documentation

◆ Compomer() [1/3]

Compomer ( )

Default Constructor.

Initializes an empty compomer with zero net charge, mass, and probability.

◆ Compomer() [2/3]

Compomer	(	Int	net_charge,
		double	mass,
		double	log_p
	)

Constructor with net-charge, mass, and probability.

Parameters

net_charge	Net charge of the compomer (right side - left side)
mass	Mass difference represented by the compomer
log_p	Log probability of this adduct combination

◆ Compomer() [3/3]

Compomer ( const Compomer & p )

Copy constructor.

Parameters

p	Source compomer to copy from

Member Function Documentation

◆ add() [1/2]

void add	(	const Adduct &	a,
		UInt	side
	)

Add an adduct to a specific side of the compomer.

Adds the specified amount of the adduct to the given side and updates the compomer's properties (net charge, mass, etc.).

Parameters

a	The adduct to add
side	Which side to add the adduct to (0=LEFT, 1=RIGHT)

◆ add() [2/2]

void add	(	const CompomerSide &	add_side,
		UInt	side
	)

Add a complete set of adducts to a specific side of the compomer.

Parameters

add_side	The set of adducts to add
side	Which side to add the adducts to (LEFT or RIGHT)

◆ getAdductsAsString() [1/2]

String getAdductsAsString ( ) const

Get a string representation of all adducts in this compomer.

Returns: String representation of adducts on both sides

◆ getAdductsAsString() [2/2]

String getAdductsAsString ( UInt side ) const

Get a string representation of adducts on a specific side.

Parameters

side	Which side to get adducts for (LEFT, RIGHT, or BOTH)

Returns: String representation of adducts on the specified side

◆ getComponent()

const CompomerComponents& getComponent ( ) const

Get both sides (left and right) of this compomer.

Returns: Reference to the compomer components (left and right sides)

◆ getID()

const Size& getID ( ) const

Get the unique identifier of this compomer.

Returns: The unique ID 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

Get the log probability of this adduct combination.

Higher values indicate more likely combinations.

Returns: Log probability value

◆ getMass()

const double& getMass ( ) const

Get the total mass difference represented by this compomer.

Returns: Mass difference in Da

◆ getNegativeCharges()

const Int& getNegativeCharges ( ) const

Get the sum of negative charges in this compomer.

Returns: Total negative charges

◆ getNetCharge()

const Int& getNetCharge ( ) const

Get the net charge of this compomer.

The net charge is calculated as the difference between the right and left sides.

Returns: Net charge value

◆ getPositiveCharges()

const Int& getPositiveCharges ( ) const

Get the sum of positive charges in this compomer.

Returns: Total positive charges

◆ getRTShift()

const double& getRTShift ( ) const

Get the expected retention time shift caused by this compomer.

Returns: Expected RT shift value

◆ isConflicting()

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

Determines if two compomers conflict with each other.

Checks if these two compomers can coexist for one feature by examining if they have conflicting adduct compositions on the specified sides.

Parameters

cmp	The other Compomer to compare against
side_this	Which side of this compomer to check (0=LEFT, 1=RIGHT)
side_other	Which side of the other compomer to check (0=LEFT, 1=RIGHT)

Returns: True if the compomers conflict (cannot coexist), false otherwise

◆ isSingleAdduct()

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

Check if the compomer contains only a single adduct on the specified side.

Parameters

a	Output parameter that will contain the adduct if found
side	Which side to check (LEFT or RIGHT)

Returns: True if only a single adduct is present on the specified side

◆ operator=()

Compomer& operator= ( const Compomer & source )

Assignment Operator.

Parameters

source Source compomer to assign from

Returns: Reference to this object

◆ 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 a unique identifier for this compomer.

Parameters

id	The unique ID to assign

Friends And Related Function Documentation

◆ operator<

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

friend

Comparison operator for sorting compomers.

Sorts compomers by (in order of importance):

Net charge
Mass
Probability

Parameters

c1	First compomer to compare
c2	Second compomer to compare

Returns: True if c1 should be ordered before c2

◆ operator<<

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

friend

Output stream operator for printing compomer contents.

Parameters

os	Output stream to write to
cmp	Compomer to print

Returns: Reference to the output stream

◆ operator==

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

friend

Equality comparison operator.

Parameters

a	First compomer to compare
b	Second compomer to compare

Returns: True if the compomers are equal

Member Data Documentation

◆ cmp_

CompomerComponents cmp_

private

Adducts of left and right side.

◆ id_

Size id_

private

Unique identifier for this compomer.

◆ log_p_

double log_p_

private

Log probability of this adduct combination.

◆ mass_

double mass_

private

Net mass (right - left)

◆ neg_charges_

Int neg_charges_

private

Sum of negative charges.

◆ net_charge_

Int net_charge_

private

Net charge (right - left)

◆ pos_charges_

Int pos_charges_

private

Sum of positive charges.

◆ rt_shift_

double rt_shift_

private

Expected net RT shift (-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_