LCMS Class Reference

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

Collaboration diagram for LCMS:

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

(

)

LCMS() [1/4]

LCMS

(

std::string

)

LCMS() [2/4]

LCMS

(

)

LCMS() [3/4]

LCMS

(

const LCMS *

)

LCMS() [4/4]

LCMS

(

const LCMS &

)

Member Function Documentation

add_alignment_error()

void add_alignment_error	(	double	TR,
		double	ERROR_UP,
		double	ERROR_DOWN
	)

add_feature()

void add_feature

(

SHFeature *

in

)

add_raw_spec_name()

void add_raw_spec_name	(	int	ID,
		std::string	name
	)

add_raw_spec_name_map()

void add_raw_spec_name_map

(

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

in

)

check_feature_list_empty()

bool check_feature_list_empty

(

)

check_LCMS_name()

bool check_LCMS_name

(

std::string

)

check_raw_spec_name_empty()

bool check_raw_spec_name_empty

(

)

clear_feature_list()

void clear_feature_list

(

)

compare_feature_mass()

float compare_feature_mass	(	const void *	,
		const void *
	)

find_feature_by_ID()

SHFeature* find_feature_by_ID

(

int

)

find_LC_MS_by_ID()

bool find_LC_MS_by_ID

(

int

)

get_alignment_error()

void get_alignment_error	(	double	,
		double *	,
		double *
	)

get_feature_list()

std::vector<SHFeature> get_feature_list

(

)

get_feature_list_begin()

std::vector<SHFeature>::iterator get_feature_list_begin

(

)

get_feature_list_end()

std::vector<SHFeature>::iterator get_feature_list_end

(

)

get_feature_list_reference()

std::vector<SHFeature>* get_feature_list_reference

(

)

get_MASTER_ID()

int get_MASTER_ID

(

)

get_nb_common_peaks()

int get_nb_common_peaks

(

int

)

get_nb_features()

unsigned int get_nb_features

(

)

get_nb_identified_features() [1/2]

int get_nb_identified_features

(

)

get_nb_identified_features() [2/2]

int get_nb_identified_features

(

double

PepProb_T

)

get_nb_raw_specs()

int get_nb_raw_specs

(

)

get_raw_spec_name()

std::string get_raw_spec_name

(

int

ID

)

get_raw_spec_name_end()

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

(

)

get_raw_spec_name_map()

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

(

)

get_raw_spec_name_start()

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

(

)

get_spec_name()

std::string get_spec_name

(

)

get_spectrum_ID()

int get_spectrum_ID

(

)

operator=()

LCMS& operator=

(

const LCMS &

)

order_by_mass()

void order_by_mass

(

)

remove_feature() [1/2]

void remove_feature

(

int

i

)

remove_feature() [2/2]

void remove_feature

(

SHFeature *

)

remove_feature_by_ID() [1/2]

void remove_feature_by_ID

(

int

)

remove_feature_by_ID() [2/2]

void remove_feature_by_ID

(

SHFeature *

)

remove_feature_from_list()

std::vector<SHFeature>::iterator remove_feature_from_list

(

std::vector< SHFeature >::iterator

in

)

remove_raw_spec_name()

void remove_raw_spec_name

(

int

ID

)

set_MASTER_ID()

void set_MASTER_ID

(

int

in

)

set_spec_name()

void set_spec_name

(

std::string

in

)

set_spectrum_ID()

void set_spectrum_ID

(

int

in

)

setFeatureLCMSID()

void setFeatureLCMSID

(

)

show_info()

void show_info

(

)

tag_peaks_with_spectrum_ID()

void tag_peaks_with_spectrum_ID

(

)

Member Data Documentation

ALIGNMENT_ERROR

std::map<double, std::pair<double, double> > ALIGNMENT_ERROR

private

feature_list

std::vector<SHFeature> feature_list

private

MASTER_ID

int MASTER_ID

private

MINIMAL_PEP_PROPHET_THERSHOLD

double MINIMAL_PEP_PROPHET_THERSHOLD

static

raw_spec_names

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

private

spec_name

std::string spec_name

private

spectrum_id

int spectrum_id

private