| OpenMS 2.5.0

Classes | Public Member Functions | Static Public Attributes | Private Attributes | List of all members
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 ()
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 | ( | SHFeature * |  | ) |

## ◆ remove_feature() [2/2]

void remove_feature | ( | int | i | ) |

## ◆ remove_feature_by_ID() [1/2]

void remove_feature_by_ID | ( | SHFeature * |  | ) |

## ◆ remove_feature_by_ID() [2/2]

void remove_feature_by_ID | ( | int |  | ) |

## ◆ 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