LightTransition Struct Reference

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

Collaboration diagram for LightTransition:

Public Member Functions
bool	getDecoy () const
void	setDecoy (bool d)
std::string	getFragmentType () const
void	setFragmentType (const std::string &s)
std::string	getAnnotation () const
int	getProductChargeState () const
bool	isProductChargeStateSet () const
bool	isPrecursorImSet () const
std::string	getNativeID () const
std::string	getPeptideRef () const
std::string	getCompoundRef () const
double	getLibraryIntensity () const
void	setLibraryIntensity (double l)
double	getProductMZ () const
double	getPrecursorMZ () const
double	getPrecursorIM () const
void	setDetectingTransition (bool d)
bool	isDetectingTransition () const
void	setQuantifyingTransition (bool q)
bool	isQuantifyingTransition () const
void	setIdentifyingTransition (bool i)
bool	isIdentifyingTransition () const
bool	operator== (const LightTransition &rhs) const
	Equality operator - compares transition_name (consistent with hash)
bool	operator!= (const LightTransition &rhs) const

Public Attributes
std::string	transition_name
std::string	peptide_ref
double	library_intensity {}
double	product_mz {}
double	precursor_mz {}
double	precursor_im {-1}
int8_t	fragment_charge {}
	Fragment charge (compact: range typically 1-8)
TransitionFlags	flags {}
	Packed boolean flags.
int16_t	fragment_nr {-1}
	Fragment ion ordinal (e.g. 7 for y7)
FragmentIonType	fragment_type {FragmentIonType::Empty}
	Fragment ion type enum.
std::vector< std::string >	peptidoforms
	Peptidoforms for IPF.

Member Function Documentation

getAnnotation()

std::string getAnnotation ( ) const

inline

Reconstruct annotation from fragment_type, fragment_nr, and fragment_charge Returns string like "b8", "y6^2", "prec", or empty if no fragment info set

References OpenSwath::Empty, LightTransition::fragment_charge, LightTransition::fragment_nr, LightTransition::fragment_type, OpenSwath::fragmentIonTypeToString(), and OpenSwath::Precursor.

getCompoundRef()

std::string getCompoundRef ( ) const

inline

References LightTransition::peptide_ref.

getDecoy()

bool getDecoy ( ) const

inline

References TransitionFlags::decoy, and LightTransition::flags.

getFragmentType()

std::string getFragmentType ( ) const

inline

References LightTransition::fragment_type, and OpenSwath::fragmentIonTypeToString().

getLibraryIntensity()

double getLibraryIntensity ( ) const

inline

References LightTransition::library_intensity.

getNativeID()

std::string getNativeID ( ) const

inline

References LightTransition::transition_name.

getPeptideRef()

std::string getPeptideRef ( ) const

inline

References LightTransition::peptide_ref.

getPrecursorIM()

double getPrecursorIM ( ) const

inline

References LightTransition::precursor_im.

getPrecursorMZ()

double getPrecursorMZ ( ) const

inline

References LightTransition::precursor_mz.

getProductChargeState()

int getProductChargeState ( ) const

inline

References LightTransition::fragment_charge.

getProductMZ()

double getProductMZ ( ) const

inline

References LightTransition::product_mz.

isDetectingTransition()

bool isDetectingTransition ( ) const

inline

References TransitionFlags::detecting, and LightTransition::flags.

isIdentifyingTransition()

bool isIdentifyingTransition ( ) const

inline

References LightTransition::flags, and TransitionFlags::identifying.

isPrecursorImSet()

bool isPrecursorImSet ( ) const

inline

References LightTransition::precursor_im.

isProductChargeStateSet()

bool isProductChargeStateSet ( ) const

inline

References LightTransition::fragment_charge.

isQuantifyingTransition()

bool isQuantifyingTransition ( ) const

inline

References LightTransition::flags, and TransitionFlags::quantifying.

operator!=()

bool operator!= ( const LightTransition &  rhs ) const

inline

operator==()

bool operator== ( const LightTransition &  rhs ) const

inline

Equality operator - compares transition_name (consistent with hash)

References LightTransition::transition_name.

setDecoy()

void setDecoy ( bool  d )

inline

References TransitionFlags::decoy, and LightTransition::flags.

setDetectingTransition()

void setDetectingTransition ( bool  d )

inline

References TransitionFlags::detecting, and LightTransition::flags.

setFragmentType()

void setFragmentType ( const std::string &  s )

inline

References LightTransition::fragment_type, and OpenSwath::stringToFragmentIonType().

setIdentifyingTransition()

void setIdentifyingTransition ( bool  i )

inline

References LightTransition::flags, and TransitionFlags::identifying.

setLibraryIntensity()

void setLibraryIntensity ( double  l )

inline

References LightTransition::library_intensity.

setQuantifyingTransition()

void setQuantifyingTransition ( bool  q )

inline

References LightTransition::flags, and TransitionFlags::quantifying.

Member Data Documentation

flags

TransitionFlags flags {}

Packed boolean flags.

Referenced by LightTransition::getDecoy(), LightTransition::isDetectingTransition(), LightTransition::isIdentifyingTransition(), LightTransition::isQuantifyingTransition(), LightTransition::setDecoy(), LightTransition::setDetectingTransition(), LightTransition::setIdentifyingTransition(), and LightTransition::setQuantifyingTransition().

fragment_charge

int8_t fragment_charge {}

Fragment charge (compact: range typically 1-8)

Referenced by LightTransition::getAnnotation(), LightTransition::getProductChargeState(), and LightTransition::isProductChargeStateSet().

fragment_nr

int16_t fragment_nr {-1}

Fragment ion ordinal (e.g. 7 for y7)

Referenced by LightTransition::getAnnotation().

fragment_type

FragmentIonType fragment_type {FragmentIonType::Empty}

Fragment ion type enum.

Referenced by LightTransition::getAnnotation(), LightTransition::getFragmentType(), and LightTransition::setFragmentType().

library_intensity

double library_intensity {}

Referenced by LightTransition::getLibraryIntensity(), and LightTransition::setLibraryIntensity().

peptide_ref

std::string peptide_ref

Referenced by LightTransition::getCompoundRef(), and LightTransition::getPeptideRef().

peptidoforms

std::vector<std::string> peptidoforms

Peptidoforms for IPF.

precursor_im

double precursor_im {-1}

Referenced by LightTransition::getPrecursorIM(), and LightTransition::isPrecursorImSet().

precursor_mz

double precursor_mz {}

Referenced by LightTransition::getPrecursorMZ().

product_mz

double product_mz {}

Referenced by LightTransition::getProductMZ().

transition_name

std::string transition_name

Referenced by LightTransition::getNativeID(), and LightTransition::operator==().