LCMS Class Reference

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/LCMS.h>

List of all members.

Classes
struct	OPERATOR_FeatureCompare
struct	OPERATOR_MZ
Public Member Functions
	~LCMS ()
	LCMS (std::string)
	LCMS ()
	LCMS (const LCMS *)
	LCMS (const LCMS &)
void	show_info ()
LCMS &	operator= (const LCMS &)
void	order_by_mass ()
float	compare_feature_mass (const void *, const void *)
void	tag_peaks_with_spectrum_ID ()
int	get_nb_common_peaks (int)
void	clear_feature_list ()
std::vector< SHFeature >	get_feature_list ()
std::vector< SHFeature > *	get_feature_list_reference ()
bool	check_feature_list_empty ()
std::vector< SHFeature >::iterator	get_feature_list_begin ()
std::vector< SHFeature >::iterator	get_feature_list_end ()
void	add_feature (SHFeature *IN)
void	remove_feature_by_ID (SHFeature *)
void	remove_feature_by_ID (int)
void	remove_feature (SHFeature *)
void	remove_feature (int i)
std::vector< SHFeature >::iterator	remove_feature_from_list (std::vector< SHFeature >::iterator IN)
unsigned int	get_nb_features ()
std::string	get_spec_name ()
void	set_spec_name (std::string IN)
int	get_spectrum_ID ()
void	set_spectrum_ID (int IN)
void	setFeatureLCMSID ()
SHFeature *	find_feature_by_ID (int)
void	remove_raw_spec_name (int ID)
void	add_raw_spec_name (int ID, std::string name)
bool	check_raw_spec_name_empty ()
std::map< int, std::string > ::iterator	get_raw_spec_name_start ()
std::map< int, std::string > ::iterator	get_raw_spec_name_end ()
std::map< int, std::string >	get_raw_spec_name_map ()
int	get_nb_raw_specs ()
std::string	get_raw_spec_name (int ID)
bool	check_LCMS_name (std::string)
bool	find_LC_MS_by_ID (int)
void	add_raw_spec_name_map (std::map< int, std::string > IN)
int	get_nb_identified_features ()
int	get_nb_identified_features (double PepProb_T)
void	add_alignment_error (double TR, double ERROR_UP, double ERROR_DOWN)
void	get_alignment_error (double, double *, double *)
void	set_MASTER_ID (int IN)
int	get_MASTER_ID ()
Static Public Attributes
static double	MINIMAL_PEP_PROPHET_THERSHOLD
Private Attributes
std::string	spec_name
std::vector< SHFeature >	feature_list
int	spectrum_id
int	MASTER_ID
std::map< int, std::string >	raw_spec_names
std::map< double, std::pair < double, double > >	ALIGNMENT_ERROR

---

Constructor & Destructor Documentation

~LCMS

(

)

LCMS

(

std::string

)

LCMS

(

)

LCMS

(

const LCMS *

)

LCMS

(

const LCMS &

)

---

Member Function Documentation

void add_alignment_error	(	double	TR,
		double	ERROR_UP,
		double	ERROR_DOWN
	)			[inline]

void add_feature

(

SHFeature *

IN

)

[inline]

References SHFeature::get_feature_ID(), and SHFeature::set_feature_ID().

void add_raw_spec_name	(	int	ID,
		std::string	name
	)			[inline]

void add_raw_spec_name_map

(

std::map< int, std::string >

IN

)

[inline]

References OpenMS::Constants::F.

bool check_feature_list_empty

(

)

[inline]

bool check_LCMS_name

(

std::string

)

bool check_raw_spec_name_empty

(

)

[inline]

void clear_feature_list

(

)

[inline]

float compare_feature_mass	(	const void *	,
		const void *
	)

SHFeature* find_feature_by_ID

(

int

)

bool find_LC_MS_by_ID

(

int

)

void get_alignment_error	(	double	,
		double *	,
		double *
	)

std::vector<SHFeature> get_feature_list

(

)

[inline]

std::vector<SHFeature>::iterator get_feature_list_begin

(

)

[inline]

std::vector<SHFeature>::iterator get_feature_list_end

(

)

[inline]

std::vector<SHFeature>* get_feature_list_reference

(

)

[inline]

int get_MASTER_ID

(

)

[inline]

int get_nb_common_peaks

(

int

)

unsigned int get_nb_features

(

)

[inline]

int get_nb_identified_features

(

)

[inline]

int get_nb_identified_features

(

double

PepProb_T

)

[inline]

int get_nb_raw_specs

(

)

[inline]

std::string get_raw_spec_name

(

int

ID

)

[inline]

std::map<int, std::string>::iterator get_raw_spec_name_end

(

)

[inline]

std::map<int, std::string> get_raw_spec_name_map

(

)

[inline]

std::map<int, std::string>::iterator get_raw_spec_name_start

(

)

[inline]

std::string get_spec_name

(

)

[inline]

int get_spectrum_ID

(

)

[inline]

LCMS& operator=

(

const LCMS &

)

void order_by_mass

(

)

void remove_feature

(

SHFeature *

)

void remove_feature

(

int

i

)

[inline]

void remove_feature_by_ID

(

int

)

void remove_feature_by_ID

(

SHFeature *

)

std::vector<SHFeature>::iterator remove_feature_from_list

(

std::vector< SHFeature >::iterator

IN

)

[inline]

void remove_raw_spec_name

(

int

ID

)

[inline]

void set_MASTER_ID

(

int

IN

)

[inline]

void set_spec_name

(

std::string

IN

)

[inline]

void set_spectrum_ID

(

int

IN

)

[inline]

void setFeatureLCMSID

(

)

void show_info

(

)

void tag_peaks_with_spectrum_ID

(

)

[inline]

---

Member Data Documentation

std::map<double, std::pair<double, double> > ALIGNMENT_ERROR [private]

std::vector<SHFeature> feature_list [private]

int MASTER_ID [private]

double MINIMAL_PEP_PROPHET_THERSHOLD [static]

std::map<int, std::string> raw_spec_names [private]

std::string spec_name [private]

int spectrum_id [private]