SHFeature Class Reference

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

List of all members.

Public Member Functions
	~SHFeature ()
	SHFeature (const SHFeature &)
	SHFeature (const SHFeature *)
	SHFeature (double, double, int, int, int, int, float, float, float)
	SHFeature (float, int, int)
	SHFeature (MS2Feature *)
	SHFeature ()
SHFeature &	operator= (const SHFeature &)
void	show_info ()
void	showMS2consensSpectraInfo ()
bool	operator== (const SHFeature &)
void	add_MS2_info (MS2Info *)
void	add_MS2_info (std::map< double, std::vector< MS2Info > > *)
bool	get_MS2_info ()
bool	get_MS2_info (double)
bool	check_MS2_empty ()
void	removeAllMS2Information ()
int	get_MS2_SCANS_SIZE ()
std::map< double, std::vector < MS2Info > > *	get_MS2_SCAN_MAP ()
std::map< double, std::vector < MS2Info > >::iterator	get_MS2_SCANS_START ()
std::map< double, std::vector < MS2Info > >::iterator	get_MS2_SCANS_END ()
MS2Info *	get_best_MS2_SCAN ()
MS2Info *	get_best_MS2_SCAN (double)
void	setFeatureExtraInformation (std::string in)
std::string	getFeatureExtraInformation ()
void	add_matched_feature (SHFeature *)
std::map< int, SHFeature > *	get_match_list_REFERENCE ()
std::map< int, SHFeature >	get_match_list ()
std::map< int, SHFeature > ::iterator	get_match_list_start ()
std::map< int, SHFeature > ::iterator	get_match_list_end ()
std::map< int, SHFeature > ::iterator	find_match_by_id (int ID)
SHFeature *	get_feature (int)
double	get_MATCHED_peak_area ()
bool	check_match_by_id (int)
void	erase_match_list ()
std::map< int, double >	get_feature_profile ()
int	get_replicate_match_nb ()
int	get_matching_nb ()
double	get_replicate_intensity_sum ()
double	get_MZ ()
void	set_MZ (double in)
double	get_MZ_START ()
void	set_MZ_START (double IN)
double	get_MZ_END ()
void	set_MZ_END (double IN)
double	get_THEO_MZ ()
double	get_THEO_MZ (double T)
std::string	get_AC ()
std::string	get_AC (double T)
bool	check_AC (std::string IN)
bool	check_AC (std::string IN, double T)
std::string	get_SQ ()
std::string	get_SQ (double T)
std::string	get_TOTAL_SQ ()
std::string	get_TOTAL_SQ (double T)
std::string	get_MOD_SQ ()
std::string	get_MOD_SQ (double T)
double	get_pep_prob ()
double	get_pep_prob (double T)
std::string	get_MS2_TYPE_TAG ()
std::string	get_MS2_TYPE_TAG (double T)
int	get_MS2_scan ()
int	get_MS2_scan (double T)
std::map< double, std::vector < MS2Info > > *	get_MS2_SCAN_LIST ()
std::map< double, std::vector < MS2Info > >::iterator	get_MS2_SCAN_LIST_START ()
std::map< double, std::vector < MS2Info > >::iterator	get_MS2_SCAN_LIST_END ()
int	get_scan_number ()
void	set_scan_number (int IN)
int	get_scan_start ()
void	set_scan_start (int IN)
int	get_scan_end ()
void	set_scan_end (int IN)
int	get_charge_state ()
void	set_charge_state (int IN)
void	set_peak_area (float IN)
double	get_peak_area ()
double	get_peak_area (int)
double	get_apex_peak_intensity ()
void	set_apex_peak_intensity (double in)
void	normalize_peak_area_by_factor (double factor)
double	get_alignment_error_up ()
void	set_alignment_error_up (double IN)
double	get_alignment_error_down ()
void	set_alignment_error_down (double IN)
void	set_SCORE_HOLDER (double IN)
double	get_SCORE_HOLDER ()
double	get_retention_time ()
void	set_retention_time (double IN)
double	get_retention_time_START ()
void	set_retention_time_START (double IN)
double	get_retention_time_END ()
void	set_retention_time_END (double IN)
double	get_raw_retention_time_apex ()
void	set_raw_retention_time_apex (double IN)
double	get_raw_MZ ()
void	set_raw_MZ (double IN)
void	set_feature_ID (int IN)
int	get_feature_ID ()
void	set_spectrum_ID (int IN)
int	get_spectrum_ID ()
void	set_MASTER_ID (int IN)
int	get_MASTER_ID ()
int	get_nb_common_match ()
double	get_peak_score ()
void	set_peak_score (double in)
double	get_Molecular_Mass ()
double	get_FEATURE_PI ()
void	set_FEATURE_PI (double IN)
void	deriveChargeStates (SHFeature *)
void	setLCelutionProfile (FeatureLCProfile *IN)
FeatureLCProfile *	getLCelutionProfile ()
double	get_profile_retention_time ()
double	get_profile_Molecular_Mass ()
bool	get_feature_match_status ()
void	set_feature_match_status (bool IN)
void	addMS2Feature (MS2Feature *in)
void	removeMS2Feature ()
MS2Feature *	getMS2Feature ()
double	getSignalToNoise ()
void	setSignalToNoise (double in)
double	getBackgroundNoiseLevel ()
void	setBackgroundNoiseLevel (double in)
Static Public Member Functions
static double	get_MONO_H ()
static bool	compareFeatureMassValuesAtPPMLevel (double, double)
static double	getFeatureMassErrorAtPPMLevel (double)
Public Attributes
double	TR
double	MONO_MZ
double	TR_START
double	TR_END
int	charge_state
int	feature_ID
Private Attributes
std::map< double, std::vector < MS2Info > >	MS2_SCANS
int	scan_apex
int	scan_start
int	scan_end
double	total_peak_area
double	apex_peak_intensity
double	PEAK_SCORE
double	SignalToNoise
double	BackgroundNoise
double	alignment_error_up
double	alignment_error_down
double	SCORE_HOLDER
bool	feature_match_status
double	PI
int	spectrum_ID
int	MASTER_ID
std::string	featureExtraInformation
FeatureLCProfile *	LCprofile
std::map< int, SHFeature >	matched_feature_list
double	TR_APEX
double	MONO_MZ_START
double	MONO_MZ_END
double	MONO_MZ_ORIGINAL
MS2Feature *	MS2TraceFeature
Static Private Attributes
static double	_MONO_H
static double	_MONO_O

---

Constructor & Destructor Documentation

~SHFeature

(

)

SHFeature

(

const SHFeature &

)

SHFeature

(

const SHFeature *

)

SHFeature	(	double	,
		double	,
		int	,
		int	,
		int	,
		int	,
		float	,
		float	,
		float
	)

SHFeature	(	float	,
		int	,
		int
	)

SHFeature

(

MS2Feature *

)

SHFeature

(

)

---

Member Function Documentation

void add_matched_feature

(

SHFeature *

)

void add_MS2_info

(

MS2Info *

)

void add_MS2_info

(

std::map< double, std::vector< MS2Info > > *

)

void addMS2Feature

(

MS2Feature *

in

)

[inline]

bool check_AC

(

std::string

IN

)

[inline]

bool check_AC	(	std::string	IN,
		double	T
	)			[inline]

bool check_match_by_id

(

int

)

bool check_MS2_empty

(

)

[inline]

static bool compareFeatureMassValuesAtPPMLevel	(	double	,
		double
	)			[static]

void deriveChargeStates

(

SHFeature *

)

void erase_match_list

(

)

[inline]

std::map<int, SHFeature>::iterator find_match_by_id

(

int

ID

)

[inline]

std::string get_AC

(

)

[inline]

std::string get_AC

(

double

T

)

[inline]

double get_alignment_error_down

(

)

[inline]

double get_alignment_error_up

(

)

[inline]

double get_apex_peak_intensity

(

)

[inline]

MS2Info* get_best_MS2_SCAN

(

double

)

MS2Info* get_best_MS2_SCAN

(

)

int get_charge_state

(

)

[inline]

SHFeature* get_feature

(

int

)

int get_feature_ID

(

)

[inline]

Referenced by LCMS::add_feature().

bool get_feature_match_status

(

)

[inline]

double get_FEATURE_PI

(

)

[inline]

References OpenMS::Constants::PI.

std::map<int, double> get_feature_profile

(

)

int get_MASTER_ID

(

)

[inline]

std::map<int, SHFeature> get_match_list

(

)

[inline]

std::map<int, SHFeature>::iterator get_match_list_end

(

)

[inline]

std::map<int, SHFeature>* get_match_list_REFERENCE

(

)

[inline]

std::map<int, SHFeature>::iterator get_match_list_start

(

)

[inline]

double get_MATCHED_peak_area

(

)

int get_matching_nb

(

)

[inline]

std::string get_MOD_SQ

(

)

[inline]

std::string get_MOD_SQ

(

double

T

)

[inline]

double get_Molecular_Mass

(

)

static double get_MONO_H

(

)

[inline, static]

bool get_MS2_info

(

double

)

bool get_MS2_info

(

)

int get_MS2_scan

(

)

[inline]

int get_MS2_scan

(

double

T

)

[inline]

std::map<double, std::vector<MS2Info> >* get_MS2_SCAN_LIST

(

)

[inline]

std::map<double, std::vector<MS2Info> >::iterator get_MS2_SCAN_LIST_END

(

)

[inline]

std::map<double, std::vector<MS2Info> >::iterator get_MS2_SCAN_LIST_START

(

)

[inline]

std::map<double, std::vector<MS2Info> >* get_MS2_SCAN_MAP

(

)

[inline]

std::map<double, std::vector<MS2Info> >::iterator get_MS2_SCANS_END

(

)

[inline]

int get_MS2_SCANS_SIZE

(

)

[inline]

std::map<double, std::vector<MS2Info> >::iterator get_MS2_SCANS_START

(

)

[inline]

std::string get_MS2_TYPE_TAG

(

double

T

)

[inline]

std::string get_MS2_TYPE_TAG

(

)

[inline]

double get_MZ

(

)

[inline]

double get_MZ_END

(

)

[inline]

double get_MZ_START

(

)

[inline]

int get_nb_common_match

(

)

double get_peak_area

(

)

[inline]

double get_peak_area

(

int

)

double get_peak_score

(

)

[inline]

double get_pep_prob

(

)

[inline]

double get_pep_prob

(

double

T

)

[inline]

double get_profile_Molecular_Mass

(

)

double get_profile_retention_time

(

)

double get_raw_MZ

(

)

[inline]

double get_raw_retention_time_apex

(

)

[inline]

double get_replicate_intensity_sum

(

)

int get_replicate_match_nb

(

)

[inline]

double get_retention_time

(

)

[inline]

double get_retention_time_END

(

)

[inline]

double get_retention_time_START

(

)

[inline]

int get_scan_end

(

)

[inline]

int get_scan_number

(

)

[inline]

int get_scan_start

(

)

[inline]

double get_SCORE_HOLDER

(

)

[inline]

int get_spectrum_ID

(

)

[inline]

std::string get_SQ

(

)

[inline]

std::string get_SQ

(

double

T

)

[inline]

double get_THEO_MZ

(

)

[inline]

double get_THEO_MZ

(

double

T

)

[inline]

std::string get_TOTAL_SQ

(

)

[inline]

std::string get_TOTAL_SQ

(

double

T

)

[inline]

double getBackgroundNoiseLevel

(

)

[inline]

std::string getFeatureExtraInformation

(

)

[inline]

static double getFeatureMassErrorAtPPMLevel

(

double

)

[static]

FeatureLCProfile* getLCelutionProfile

(

)

[inline]

MS2Feature* getMS2Feature

(

)

[inline]

double getSignalToNoise

(

)

[inline]

void normalize_peak_area_by_factor

(

double

factor

)

[inline]

SHFeature& operator=

(

const SHFeature &

)

bool operator==

(

const SHFeature &

)

void removeAllMS2Information

(

)

[inline]

void removeMS2Feature

(

)

[inline]

void set_alignment_error_down

(

double

IN

)

[inline]

void set_alignment_error_up

(

double

IN

)

[inline]

void set_apex_peak_intensity

(

double

in

)

[inline]

void set_charge_state

(

int

IN

)

[inline]

void set_feature_ID

(

int

IN

)

[inline]

Referenced by LCMS::add_feature().

void set_feature_match_status

(

bool

IN

)

[inline]

void set_FEATURE_PI

(

double

IN

)

[inline]

References OpenMS::Constants::PI.

void set_MASTER_ID

(

int

IN

)

[inline]

void set_MZ

(

double

in

)

[inline]

void set_MZ_END

(

double

IN

)

[inline]

void set_MZ_START

(

double

IN

)

[inline]

void set_peak_area

(

float

IN

)

[inline]

void set_peak_score

(

double

in

)

[inline]

void set_raw_MZ

(

double

IN

)

[inline]

void set_raw_retention_time_apex

(

double

IN

)

[inline]

void set_retention_time

(

double

IN

)

[inline]

void set_retention_time_END

(

double

IN

)

[inline]

void set_retention_time_START

(

double

IN

)

[inline]

void set_scan_end

(

int

IN

)

[inline]

void set_scan_number

(

int

IN

)

[inline]

void set_scan_start

(

int

IN

)

[inline]

void set_SCORE_HOLDER

(

double

IN

)

[inline]

void set_spectrum_ID

(

int

IN

)

[inline]

void setBackgroundNoiseLevel

(

double

in

)

[inline]

void setFeatureExtraInformation

(

std::string

in

)

[inline]

void setLCelutionProfile

(

FeatureLCProfile *

IN

)

[inline]

void setSignalToNoise

(

double

in

)

[inline]

void show_info

(

)

void showMS2consensSpectraInfo

(

)

---

Member Data Documentation

double _MONO_H [static, private]

double _MONO_O [static, private]

double alignment_error_down [private]

double alignment_error_up [private]

double apex_peak_intensity [private]

double BackgroundNoise [private]

int charge_state

int feature_ID

Referenced by LCMS::OPERATOR_FeatureCompare::operator()().

bool feature_match_status [private]

std::string featureExtraInformation [private]

FeatureLCProfile* LCprofile [private]

int MASTER_ID [private]

std::map<int, SHFeature> matched_feature_list [private]

double MONO_MZ

Referenced by LCMS::OPERATOR_MZ::operator()().

double MONO_MZ_END [private]

double MONO_MZ_ORIGINAL [private]

double MONO_MZ_START [private]

std::map<double, std::vector<MS2Info> > MS2_SCANS [private]

MS2Feature* MS2TraceFeature [private]

double PEAK_SCORE [private]

double PI [private]

int scan_apex [private]

int scan_end [private]

int scan_start [private]

double SCORE_HOLDER [private]

double SignalToNoise [private]

int spectrum_ID [private]

double total_peak_area [private]

double TR

Referenced by MS1FeatureMerger::OPERATOR_FEATURE_TR::operator()(), and LCMS::OPERATOR_MZ::operator()().

double TR_APEX [private]

double TR_END

double TR_START