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LCMS Class Reference

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

Classes

struct  OPERATOR_FeatureCompare
 
struct  OPERATOR_MZ
 

Public Member Functions

 ~LCMS ()
 
 LCMS (std::string)
 
 LCMS ()
 
 LCMS (const LCMS *)
 
 LCMS (const LCMS &)
 
void show_info ()
 
LCMSoperator= (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< SHFeatureget_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 ()
 
SHFeaturefind_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< SHFeaturefeature_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 
)
void add_feature ( SHFeature in)
void add_raw_spec_name ( int  ID,
std::string  name 
)
void add_raw_spec_name_map ( std::map< int, std::string >  in)
bool check_feature_list_empty ( )
bool check_LCMS_name ( std::string  )
bool check_raw_spec_name_empty ( )
void clear_feature_list ( )
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 ( )
std::vector<SHFeature>::iterator get_feature_list_begin ( )
std::vector<SHFeature>::iterator get_feature_list_end ( )
std::vector<SHFeature>* get_feature_list_reference ( )
int get_MASTER_ID ( )
int get_nb_common_peaks ( int  )
unsigned int get_nb_features ( )
int get_nb_identified_features ( )
int get_nb_identified_features ( double  PepProb_T)
int get_nb_raw_specs ( )
std::string get_raw_spec_name ( int  ID)
std::map<int, std::string>::iterator get_raw_spec_name_end ( )
std::map<int, std::string> get_raw_spec_name_map ( )
std::map<int, std::string>::iterator get_raw_spec_name_start ( )
std::string get_spec_name ( )
int get_spectrum_ID ( )
LCMS& operator= ( const LCMS )
void order_by_mass ( )
void remove_feature ( SHFeature )
void remove_feature ( int  i)
void remove_feature_by_ID ( SHFeature )
void remove_feature_by_ID ( int  )
std::vector<SHFeature>::iterator remove_feature_from_list ( std::vector< SHFeature >::iterator  in)
void remove_raw_spec_name ( int  ID)
void set_MASTER_ID ( int  in)
void set_spec_name ( std::string  in)
void set_spectrum_ID ( int  in)
void setFeatureLCMSID ( )
void show_info ( )
void tag_peaks_with_spectrum_ID ( )

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

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:13:54 using doxygen 1.8.9.1