LightCompound Struct Reference

#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>

Collaboration diagram for LightCompound:

Public Member Functions
	LightCompound ()
bool	isPeptide () const
void	setChargeState (int ch)
int	getChargeState () const
void	setDriftTime (double d)
double	getDriftTime () const
bool	operator== (const LightCompound &rhs) const
	Equality operator - compares id (consistent with hash)
bool	operator!= (const LightCompound &rhs) const

Public Attributes
double	drift_time
double	rt
double	rt_start
double	rt_end
int	charge
std::string	sequence
std::vector< std::string >	protein_refs
std::string	peptide_group_label
std::string	gene_name
std::string	id
std::string	sum_formula
std::string	compound_name
std::string	label_type
	Label type (e.g. "heavy" or "light")
std::string	smiles
	SMILES representation (metabolomics)
std::string	adducts
	Adducts (metabolomics)
std::vector< LightModification >	modifications

Constructor & Destructor Documentation

LightCompound()

LightCompound ( )

inline

Member Function Documentation

getChargeState()

int getChargeState ( ) const

inline

References LightCompound::charge.

getDriftTime()

double getDriftTime ( ) const

inline

References LightCompound::drift_time.

isPeptide()

bool isPeptide ( ) const

inline

References LightCompound::compound_name.

operator!=()

bool operator!= ( const LightCompound &  rhs ) const

inline

operator==()

bool operator== ( const LightCompound &  rhs ) const

inline

Equality operator - compares id (consistent with hash)

References LightCompound::id.

setChargeState()

void setChargeState ( int  ch )

inline

References LightCompound::charge.

setDriftTime()

void setDriftTime ( double  d )

inline

References LightCompound::drift_time.

Member Data Documentation

adducts

std::string adducts

Adducts (metabolomics)

charge

int charge

Referenced by OpenMS::ChromatogramExtractor::extract_id_< OpenSwath::LightTargetedExperiment >(), LightCompound::getChargeState(), and LightCompound::setChargeState().

compound_name

std::string compound_name

Referenced by OpenMS::ChromatogramExtractor::extract_id_< OpenSwath::LightTargetedExperiment >(), and LightCompound::isPeptide().

drift_time

double drift_time

Referenced by LightCompound::getDriftTime(), and LightCompound::setDriftTime().

gene_name

std::string gene_name

id

std::string id

Referenced by LightCompound::operator==().

label_type

std::string label_type

Label type (e.g. "heavy" or "light")

modifications

std::vector<LightModification> modifications

peptide_group_label

std::string peptide_group_label

protein_refs

std::vector<std::string> protein_refs

rt

double rt

Retention time (seconds). NaN if unset — ChromatogramExtractor::prepare_coordinates throws if a non-negative rt_extraction_window is requested but rt is NaN.

rt_end

double rt_end

rt_start

double rt_start

Optional retention time range, used by ChromatogramExtractor::prepare_coordinates when called with rt_extraction_window=NaN. Both NaN means "no range encoded"; otherwise rt_start..rt_end define the per-compound extraction window. Populated by OpenSwathDataAccessHelper::convertTargetedExp from a heavyweight TargetedExperiment::Peptide that has two retention-time entries.

sequence

std::string sequence

Referenced by OpenMS::ChromatogramExtractor::extract_id_< OpenSwath::LightTargetedExperiment >().

smiles

std::string smiles

SMILES representation (metabolomics)

sum_formula

std::string sum_formula