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SHFeature Class Reference

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

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 ()
 
SHFeatureoperator= (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 ()
 
MS2Infoget_best_MS2_SCAN ()
 
MS2Infoget_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, SHFeatureget_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)
 
SHFeatureget_feature (int)
 
double get_MATCHED_peak_area ()
 
bool check_match_by_id (int)
 
void erase_match_list ()
 
std::map< int, doubleget_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)
 
FeatureLCProfilegetLCelutionProfile ()
 
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 ()
 
MS2FeaturegetMS2Feature ()
 
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
 
FeatureLCProfileLCprofile
 
std::map< int, SHFeaturematched_feature_list
 
double TR_APEX
 
double MONO_MZ_START
 
double MONO_MZ_END
 
double MONO_MZ_ORIGINAL
 
MS2FeatureMS2TraceFeature
 

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 ( )

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)
bool check_AC ( std::string  in)
bool check_AC ( std::string  in,
double  T 
)
bool check_match_by_id ( int  )
bool check_MS2_empty ( )
static bool compareFeatureMassValuesAtPPMLevel ( double  ,
double   
)
static
void deriveChargeStates ( SHFeature )
void erase_match_list ( )
std::map<int, SHFeature>::iterator find_match_by_id ( int  ID)
std::string get_AC ( )
std::string get_AC ( double  T)
double get_alignment_error_down ( )
double get_alignment_error_up ( )
double get_apex_peak_intensity ( )
MS2Info* get_best_MS2_SCAN ( )
MS2Info* get_best_MS2_SCAN ( double  )
int get_charge_state ( )
SHFeature* get_feature ( int  )
int get_feature_ID ( )
bool get_feature_match_status ( )
double get_FEATURE_PI ( )
std::map<int, double> get_feature_profile ( )
int get_MASTER_ID ( )
std::map<int, SHFeature> get_match_list ( )
std::map<int, SHFeature>::iterator get_match_list_end ( )
std::map<int, SHFeature>* get_match_list_REFERENCE ( )
std::map<int, SHFeature>::iterator get_match_list_start ( )
double get_MATCHED_peak_area ( )
int get_matching_nb ( )
std::string get_MOD_SQ ( )
std::string get_MOD_SQ ( double  T)
double get_Molecular_Mass ( )
static double get_MONO_H ( )
static
bool get_MS2_info ( )
bool get_MS2_info ( double  )
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_END ( )
std::map<double, std::vector<MS2Info> >::iterator get_MS2_SCAN_LIST_START ( )
std::map<double, std::vector<MS2Info> >* get_MS2_SCAN_MAP ( )
std::map<double, std::vector<MS2Info> >::iterator get_MS2_SCANS_END ( )
int get_MS2_SCANS_SIZE ( )
std::map<double, std::vector<MS2Info> >::iterator get_MS2_SCANS_START ( )
std::string get_MS2_TYPE_TAG ( )
std::string get_MS2_TYPE_TAG ( double  T)
double get_MZ ( )
double get_MZ_END ( )
double get_MZ_START ( )
int get_nb_common_match ( )
double get_peak_area ( )
double get_peak_area ( int  )
double get_peak_score ( )
double get_pep_prob ( )
double get_pep_prob ( double  T)
double get_profile_Molecular_Mass ( )
double get_profile_retention_time ( )
double get_raw_MZ ( )
double get_raw_retention_time_apex ( )
double get_replicate_intensity_sum ( )
int get_replicate_match_nb ( )
double get_retention_time ( )
double get_retention_time_END ( )
double get_retention_time_START ( )
int get_scan_end ( )
int get_scan_number ( )
int get_scan_start ( )
double get_SCORE_HOLDER ( )
int get_spectrum_ID ( )
std::string get_SQ ( )
std::string get_SQ ( double  T)
double get_THEO_MZ ( )
double get_THEO_MZ ( double  T)
std::string get_TOTAL_SQ ( )
std::string get_TOTAL_SQ ( double  T)
double getBackgroundNoiseLevel ( )
std::string getFeatureExtraInformation ( )
static double getFeatureMassErrorAtPPMLevel ( double  )
static
FeatureLCProfile* getLCelutionProfile ( )
MS2Feature* getMS2Feature ( )
double getSignalToNoise ( )
void normalize_peak_area_by_factor ( double  factor)
SHFeature& operator= ( const SHFeature )
bool operator== ( const SHFeature )
void removeAllMS2Information ( )
void removeMS2Feature ( )
void set_alignment_error_down ( double  in)
void set_alignment_error_up ( double  in)
void set_apex_peak_intensity ( double  in)
void set_charge_state ( int  in)
void set_feature_ID ( int  in)
void set_feature_match_status ( bool  in)
void set_FEATURE_PI ( double  in)
void set_MASTER_ID ( int  in)
void set_MZ ( double  in)
void set_MZ_END ( double  in)
void set_MZ_START ( double  in)
void set_peak_area ( float  in)
void set_peak_score ( double  in)
void set_raw_MZ ( double  in)
void set_raw_retention_time_apex ( double  in)
void set_retention_time ( double  in)
void set_retention_time_END ( double  in)
void set_retention_time_START ( double  in)
void set_scan_end ( int  in)
void set_scan_number ( int  in)
void set_scan_start ( int  in)
void set_SCORE_HOLDER ( double  in)
void set_spectrum_ID ( int  in)
void setBackgroundNoiseLevel ( double  in)
void setFeatureExtraInformation ( std::string  in)
void setLCelutionProfile ( FeatureLCProfile in)
void setSignalToNoise ( double  in)
void show_info ( )
void showMS2consensSpectraInfo ( )

Member Data Documentation

double _MONO_H
staticprivate
double _MONO_O
staticprivate
double alignment_error_down
private
double alignment_error_up
private
double apex_peak_intensity
private
double BackgroundNoise
private
int charge_state
int feature_ID
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
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
double TR_APEX
private
double TR_END
double TR_START

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:54:06 using doxygen 1.8.9.1