| OpenMS 2.5.0

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

## ◆ SHFeature() [1/6]

SHFeature | ( | const SHFeature & |  | ) |

## ◆ SHFeature() [2/6]

SHFeature | ( | const SHFeature * |  | ) |

## ◆ SHFeature() [3/6]

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

## ◆ SHFeature() [4/6]

SHFeature | ( | float | ,
|  | int | ,
|  | int |
| ) |  |

## ◆ SHFeature() [5/6]

SHFeature | ( | MS2Feature * |  | ) |

## ◆ SHFeature() [6/6]

SHFeature | ( |  | ) |

## Member Function Documentation

## ◆ add_matched_feature()

void add_matched_feature | ( | SHFeature * |  | ) |

## ◆ add_MS2_info() [1/2]

void add_MS2_info | ( | MS2Info * |  | ) |

## ◆ add_MS2_info() [2/2]

void add_MS2_info | ( | std::map< double, std::vector< MS2Info > > * |  | ) |

## ◆ addMS2Feature()

void addMS2Feature | ( | MS2Feature * | in | ) |

## ◆ check_AC() [1/2]

bool check_AC | ( | std::string | in | ) |

## ◆ check_AC() [2/2]

bool check_AC | ( | std::string | in,
|  | double | T
| ) |  |

## ◆ check_match_by_id()

bool check_match_by_id | ( | int |  | ) |

## ◆ check_MS2_empty()

bool check_MS2_empty | ( |  | ) |

## ◆ compareFeatureMassValuesAtPPMLevel()

static bool compareFeatureMassValuesAtPPMLevel | ( | double | ,
|  | double |
| ) |  |

static

## ◆ deriveChargeStates()

void deriveChargeStates | ( | SHFeature * |  | ) |

## ◆ erase_match_list()

void erase_match_list | ( |  | ) |

## ◆ find_match_by_id()

std::map<int, SHFeature>::iterator find_match_by_id | ( | int | ID | ) |

## ◆ get_AC() [1/2]

std::string get_AC | ( |  | ) |

## ◆ get_AC() [2/2]

std::string get_AC | ( | double | T | ) |

## ◆ get_alignment_error_down()

double get_alignment_error_down | ( |  | ) |

## ◆ get_alignment_error_up()

double get_alignment_error_up | ( |  | ) |

## ◆ get_apex_peak_intensity()

double get_apex_peak_intensity | ( |  | ) |

## ◆ get_best_MS2_SCAN() [1/2]

MS2Info* get_best_MS2_SCAN | ( |  | ) |

## ◆ get_best_MS2_SCAN() [2/2]

MS2Info* get_best_MS2_SCAN | ( | double |  | ) |

## ◆ get_charge_state()

int get_charge_state | ( |  | ) |

## ◆ get_feature()

SHFeature* get_feature | ( | int |  | ) |

## ◆ get_feature_ID()

int get_feature_ID | ( |  | ) |

## ◆ get_feature_match_status()

bool get_feature_match_status | ( |  | ) |

## ◆ get_FEATURE_PI()

double get_FEATURE_PI | ( |  | ) |

## ◆ get_feature_profile()

std::map<int, double> get_feature_profile | ( |  | ) |

## ◆ get_MASTER_ID()

int get_MASTER_ID | ( |  | ) |

## ◆ get_match_list()

std::map<int, SHFeature> get_match_list | ( |  | ) |

## ◆ get_match_list_end()

std::map<int, SHFeature>::iterator get_match_list_end | ( |  | ) |

## ◆ get_match_list_REFERENCE()

std::map<int, SHFeature>* get_match_list_REFERENCE | ( |  | ) |

## ◆ get_match_list_start()

std::map<int, SHFeature>::iterator get_match_list_start | ( |  | ) |

## ◆ get_MATCHED_peak_area()

double get_MATCHED_peak_area | ( |  | ) |

## ◆ get_matching_nb()

int get_matching_nb | ( |  | ) |

## ◆ get_MOD_SQ() [1/2]

std::string get_MOD_SQ | ( |  | ) |

## ◆ get_MOD_SQ() [2/2]

std::string get_MOD_SQ | ( | double | T | ) |

## ◆ get_Molecular_Mass()

double get_Molecular_Mass | ( |  | ) |

## ◆ get_MONO_H()

static double get_MONO_H | ( |  | ) |

static

## ◆ get_MS2_info() [1/2]

bool get_MS2_info | ( |  | ) |

## ◆ get_MS2_info() [2/2]

bool get_MS2_info | ( | double |  | ) |

## ◆ get_MS2_scan() [1/2]

int get_MS2_scan | ( |  | ) |

## ◆ get_MS2_scan() [2/2]

int get_MS2_scan | ( | double | T | ) |

## ◆ get_MS2_SCAN_LIST()

std::map<double, std::vector<MS2Info> >* get_MS2_SCAN_LIST | ( |  | ) |

## ◆ get_MS2_SCAN_LIST_END()

std::map<double, std::vector<MS2Info> >::iterator get_MS2_SCAN_LIST_END | ( |  | ) |

## ◆ get_MS2_SCAN_LIST_START()

std::map<double, std::vector<MS2Info> >::iterator get_MS2_SCAN_LIST_START | ( |  | ) |

## ◆ get_MS2_SCAN_MAP()

std::map<double, std::vector<MS2Info> >* get_MS2_SCAN_MAP | ( |  | ) |

## ◆ get_MS2_SCANS_END()

std::map<double, std::vector<MS2Info> >::iterator get_MS2_SCANS_END | ( |  | ) |

## ◆ get_MS2_SCANS_SIZE()

int get_MS2_SCANS_SIZE | ( |  | ) |

## ◆ get_MS2_SCANS_START()

std::map<double, std::vector<MS2Info> >::iterator get_MS2_SCANS_START | ( |  | ) |

## ◆ get_MS2_TYPE_TAG() [1/2]

std::string get_MS2_TYPE_TAG | ( |  | ) |

## ◆ get_MS2_TYPE_TAG() [2/2]

std::string get_MS2_TYPE_TAG | ( | double | T | ) |

## ◆ get_MZ()

double get_MZ | ( |  | ) |

## ◆ get_MZ_END()

double get_MZ_END | ( |  | ) |

## ◆ get_MZ_START()

double get_MZ_START | ( |  | ) |

## ◆ get_nb_common_match()

int get_nb_common_match | ( |  | ) |

## ◆ get_peak_area() [1/2]

double get_peak_area | ( |  | ) |

## ◆ get_peak_area() [2/2]

double get_peak_area | ( | int |  | ) |

## ◆ get_peak_score()

double get_peak_score | ( |  | ) |

## ◆ get_pep_prob() [1/2]

double get_pep_prob | ( |  | ) |

## ◆ get_pep_prob() [2/2]

double get_pep_prob | ( | double | T | ) |

## ◆ get_profile_Molecular_Mass()

double get_profile_Molecular_Mass | ( |  | ) |

## ◆ get_profile_retention_time()

double get_profile_retention_time | ( |  | ) |

## ◆ get_raw_MZ()

double get_raw_MZ | ( |  | ) |

## ◆ get_raw_retention_time_apex()

double get_raw_retention_time_apex | ( |  | ) |

## ◆ get_replicate_intensity_sum()

double get_replicate_intensity_sum | ( |  | ) |

## ◆ get_replicate_match_nb()

int get_replicate_match_nb | ( |  | ) |

## ◆ get_retention_time()

double get_retention_time | ( |  | ) |

## ◆ get_retention_time_END()

double get_retention_time_END | ( |  | ) |

## ◆ get_retention_time_START()

double get_retention_time_START | ( |  | ) |

## ◆ get_scan_end()

int get_scan_end | ( |  | ) |

## ◆ get_scan_number()

int get_scan_number | ( |  | ) |

## ◆ get_scan_start()

int get_scan_start | ( |  | ) |

## ◆ get_SCORE_HOLDER()

double get_SCORE_HOLDER | ( |  | ) |

## ◆ get_spectrum_ID()

int get_spectrum_ID | ( |  | ) |

## ◆ get_SQ() [1/2]

std::string get_SQ | ( |  | ) |

## ◆ get_SQ() [2/2]

std::string get_SQ | ( | double | T | ) |

## ◆ get_THEO_MZ() [1/2]

double get_THEO_MZ | ( |  | ) |

## ◆ get_THEO_MZ() [2/2]

double get_THEO_MZ | ( | double | T | ) |

## ◆ get_TOTAL_SQ() [1/2]

std::string get_TOTAL_SQ | ( |  | ) |

## ◆ get_TOTAL_SQ() [2/2]

std::string get_TOTAL_SQ | ( | double | T | ) |

## ◆ getBackgroundNoiseLevel()

double getBackgroundNoiseLevel | ( |  | ) |

## ◆ getFeatureExtraInformation()

std::string getFeatureExtraInformation | ( |  | ) |

## ◆ getFeatureMassErrorAtPPMLevel()

static double getFeatureMassErrorAtPPMLevel | ( | double |  | ) |

static

## ◆ getLCelutionProfile()

FeatureLCProfile* getLCelutionProfile | ( |  | ) |

## ◆ getMS2Feature()

MS2Feature* getMS2Feature | ( |  | ) |

## ◆ getSignalToNoise()

double getSignalToNoise | ( |  | ) |

## ◆ normalize_peak_area_by_factor()

void normalize_peak_area_by_factor | ( | double | factor | ) |

## ◆ operator=()

SHFeature& operator= | ( | const SHFeature & |  | ) |

## ◆ operator==()

bool operator== | ( | const SHFeature & |  | ) |

## ◆ removeAllMS2Information()

void removeAllMS2Information | ( |  | ) |

## ◆ removeMS2Feature()

void removeMS2Feature | ( |  | ) |

## ◆ set_alignment_error_down()

void set_alignment_error_down | ( | double | in | ) |

## ◆ set_alignment_error_up()

void set_alignment_error_up | ( | double | in | ) |

## ◆ set_apex_peak_intensity()

void set_apex_peak_intensity | ( | double | in | ) |

## ◆ set_charge_state()

void set_charge_state | ( | int | in | ) |

## ◆ set_feature_ID()

void set_feature_ID | ( | int | in | ) |

## ◆ set_feature_match_status()

void set_feature_match_status | ( | bool | in | ) |

## ◆ set_FEATURE_PI()

void set_FEATURE_PI | ( | double | in | ) |

## ◆ set_MASTER_ID()

void set_MASTER_ID | ( | int | in | ) |

## ◆ set_MZ()

void set_MZ | ( | double | in | ) |

## ◆ set_MZ_END()

void set_MZ_END | ( | double | in | ) |

## ◆ set_MZ_START()

void set_MZ_START | ( | double | in | ) |

## ◆ set_peak_area()

void set_peak_area | ( | float | in | ) |

## ◆ set_peak_score()

void set_peak_score | ( | double | in | ) |

## ◆ set_raw_MZ()

void set_raw_MZ | ( | double | in | ) |

## ◆ set_raw_retention_time_apex()

void set_raw_retention_time_apex | ( | double | in | ) |

## ◆ set_retention_time()

void set_retention_time | ( | double | in | ) |

## ◆ set_retention_time_END()

void set_retention_time_END | ( | double | in | ) |

## ◆ set_retention_time_START()

void set_retention_time_START | ( | double | in | ) |

## ◆ set_scan_end()

void set_scan_end | ( | int | in | ) |

## ◆ set_scan_number()

void set_scan_number | ( | int | in | ) |

## ◆ set_scan_start()

void set_scan_start | ( | int | in | ) |

## ◆ set_SCORE_HOLDER()

void set_SCORE_HOLDER | ( | double | in | ) |

## ◆ set_spectrum_ID()

void set_spectrum_ID | ( | int | in | ) |

## ◆ setBackgroundNoiseLevel()

void setBackgroundNoiseLevel | ( | double | in | ) |

## ◆ setFeatureExtraInformation()

void setFeatureExtraInformation | ( | std::string | in | ) |

## ◆ setLCelutionProfile()

void setLCelutionProfile | ( | FeatureLCProfile * | in | ) |

## ◆ setSignalToNoise()

void setSignalToNoise | ( | double | in | ) |

## ◆ show_info()

void show_info | ( |  | ) |

## ◆ showMS2consensSpectraInfo()

void showMS2consensSpectraInfo | ( |  | ) |

## Member Data Documentation

## ◆ _MONO_H

double _MONO_H

static private

## ◆ _MONO_O

double _MONO_O

static private

## ◆ alignment_error_down

double alignment_error_down

private

## ◆ alignment_error_up

double alignment_error_up

private

## ◆ apex_peak_intensity

double apex_peak_intensity

private

## ◆ BackgroundNoise

double BackgroundNoise

private

## ◆ charge_state

int charge_state

## ◆ feature_ID

int feature_ID

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

## ◆ feature_match_status

bool feature_match_status

private

## ◆ featureExtraInformation

std::string featureExtraInformation

private

## ◆ LCprofile

FeatureLCProfile* LCprofile

private

## ◆ MASTER_ID

int MASTER_ID

private

## ◆ matched_feature_list

std::map<int, SHFeature> matched_feature_list

private

## ◆ MONO_MZ

double MONO_MZ

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

## ◆ MONO_MZ_END

double MONO_MZ_END

private

## ◆ MONO_MZ_ORIGINAL

double MONO_MZ_ORIGINAL

private

## ◆ MONO_MZ_START

double MONO_MZ_START

private

## ◆ MS2_SCANS

std::map<double, std::vector<MS2Info> > MS2_SCANS

private

## ◆ MS2TraceFeature

MS2Feature* MS2TraceFeature

private

## ◆ PEAK_SCORE

double PEAK_SCORE

private

## ◆ PI

double PI

private

## ◆ scan_apex

int scan_apex

private

## ◆ scan_end

int scan_end

private

## ◆ scan_start

int scan_start

private

## ◆ SCORE_HOLDER

double SCORE_HOLDER

private

## ◆ SignalToNoise

double SignalToNoise

private

## ◆ spectrum_ID

int spectrum_ID

private

## ◆ total_peak_area

double total_peak_area

private

## ◆ TR

double TR

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

## ◆ TR_APEX

double TR_APEX

private

## ◆ TR_END

double TR_END

## ◆ TR_START

double TR_START