45 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_SHFEATURE_H 
   46 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_SHFEATURE_H 
  136     SHFeature(
double, 
double, 
int, 
int, 
int, 
int, 
float, 
float, 
float);
 
  147     void showMS2consensSpectraInfo();
 
  155     void add_MS2_info(std::map<
double, std::vector<MS2Info> > *);
 
  157     bool get_MS2_info(
double);
 
  161       return MS2_SCANS.empty();
 
  166       return MS2_SCANS.clear();
 
  171       return (
int) MS2_SCANS.size();
 
  180     {   
return MS2_SCANS.begin(); }
 
  182     {   
return MS2_SCANS.end(); }
 
  185     MS2Info * get_best_MS2_SCAN(
double);
 
  188     {   featureExtraInformation = in; }
 
  190     {   
return featureExtraInformation; }
 
  195     {   
return &matched_feature_list; }
 
  197     {   
return matched_feature_list; }
 
  199     {   
return matched_feature_list.begin(); }
 
  201     {   
return matched_feature_list.end(); }
 
  203     {   
return matched_feature_list.find(ID); }
 
  209     double get_MATCHED_peak_area();
 
  210     bool check_match_by_id(
int);
 
  212     {   matched_feature_list.clear(); }
 
  214     std::map<int, double> get_feature_profile();
 
  218     {   
return (
int) (matched_feature_list.size() + 1); }
 
  220     {   
return get_replicate_match_nb(); }
 
  222     double get_replicate_intensity_sum();
 
  235     {   
return MONO_MZ_START; }
 
  237     {   MONO_MZ_START = IN; }
 
  239     {   
return MONO_MZ_END; }
 
  241     {   MONO_MZ_END = IN; }
 
  244     {   
return get_best_MS2_SCAN()->get_MONO_MZ(); }
 
  246     {   
return get_best_MS2_SCAN(T)->get_MONO_MZ(); }
 
  248     {   
return get_best_MS2_SCAN()->get_AC(); }
 
  250     {   
return get_best_MS2_SCAN(T)->get_AC(); }
 
  252     {   
return get_best_MS2_SCAN()->compare_AC(IN); }
 
  254     {   
return get_best_MS2_SCAN(T)->compare_AC(IN); }
 
  256     {   
return get_best_MS2_SCAN()->get_SQ(); }
 
  258     {   
return get_best_MS2_SCAN(T)->get_SQ(); }
 
  260     {   
return get_best_MS2_SCAN()->get_TOTAL_SQ(); }
 
  262     {   
return get_best_MS2_SCAN(T)->get_TOTAL_SQ(); }
 
  264     {   
return get_best_MS2_SCAN()->get_MOD_SQ(); }
 
  266     {   
return get_best_MS2_SCAN(T)->get_MOD_SQ(); }
 
  268     {   
return get_best_MS2_SCAN()->get_PEP_PROB(); }
 
  270     {   
return get_best_MS2_SCAN(T)->get_PEP_PROB(); }
 
  272     {   
return get_best_MS2_SCAN()->get_MS2_TYPE_TAG(); }
 
  274     {   
return get_best_MS2_SCAN(T)->get_MS2_TYPE_TAG(); }
 
  276     {   
return get_best_MS2_SCAN()->get_SCAN_START(); }
 
  278     {   
return get_best_MS2_SCAN(T)->get_SCAN_START(); }
 
  280     {   
return &(MS2_SCANS); }
 
  282     {   
return MS2_SCANS.begin(); }
 
  284     {   
return MS2_SCANS.end(); }
 
  287     {   
return scan_apex; }
 
  291     {   
return scan_start; }
 
  299     {   
return charge_state; }
 
  301     {   charge_state = IN; }
 
  303     {   total_peak_area = IN; }
 
  305     {   
return total_peak_area; }
 
  307     double get_peak_area(
int);
 
  309     {   
return apex_peak_intensity; }
 
  311     {   apex_peak_intensity = in; }
 
  313     {   total_peak_area *= factor; }
 
  316     {   
return alignment_error_up; }
 
  318     {   alignment_error_up = IN; }
 
  320     {   
return alignment_error_down; }
 
  322     {   alignment_error_down = IN; }
 
  325     {   SCORE_HOLDER = IN; }
 
  327     {   
return SCORE_HOLDER; }
 
  348     {   
return MONO_MZ_ORIGINAL; }
 
  350     {   MONO_MZ_ORIGINAL = IN; }
 
  356     {   
return feature_ID; }
 
  369     {   
return spectrum_ID; }
 
  374     {   
return MASTER_ID; }
 
  377     int get_nb_common_match();
 
  381     {   
return PEAK_SCORE; }
 
  386     double get_Molecular_Mass();
 
  404     {   
return LCprofile; }
 
  408     double get_profile_retention_time();
 
  409     double get_profile_Molecular_Mass();
 
  414     {   
return feature_match_status; }
 
  416     {   feature_match_status = IN; }
 
  423     {   
delete MS2TraceFeature; MS2TraceFeature = 
NULL; }
 
  425     {   
return MS2TraceFeature; }
 
  428     {   
return SignalToNoise; }
 
  430     {   SignalToNoise = in; }
 
  433     {   
return BackgroundNoise; }
 
  435     {   BackgroundNoise = in; }
 
  445     static bool compareFeatureMassValuesAtPPMLevel(
double, 
double);
 
  448     static double getFeatureMassErrorAtPPMLevel(
double);
 
  454 #endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_SHFEATURE_H 
double TR_START
Definition: SHFeature.h:122
std::map< double, std::vector< MS2Info > >::iterator get_MS2_SCAN_LIST_END()
Definition: SHFeature.h:283
double get_retention_time_START()
Definition: SHFeature.h:333
double get_retention_time_END()
Definition: SHFeature.h:337
double PI
Definition: SHFeature.h:82
double MONO_MZ_ORIGINAL
Definition: SHFeature.h:109
void set_apex_peak_intensity(double in)
Definition: SHFeature.h:310
void setBackgroundNoiseLevel(double in)
Definition: SHFeature.h:434
void set_peak_score(double in)
Definition: SHFeature.h:382
int scan_end
Definition: SHFeature.h:69
std::map< int, SHFeature > get_match_list()
Definition: SHFeature.h:196
std::string get_SQ()
Definition: SHFeature.h:255
double get_peak_score()
Definition: SHFeature.h:380
int get_MS2_scan()
Definition: SHFeature.h:275
static double _MONO_H
Definition: SHFeature.h:98
double get_FEATURE_PI()
Definition: SHFeature.h:389
double alignment_error_down
Definition: SHFeature.h:79
double BackgroundNoise
Definition: SHFeature.h:74
void set_retention_time_START(double IN)
Definition: SHFeature.h:335
std::string get_SQ(double T)
Definition: SHFeature.h:257
bool check_MS2_empty()
Definition: SHFeature.h:159
std::string get_AC(double T)
Definition: SHFeature.h:249
std::map< int, SHFeature > * get_match_list_REFERENCE()
Definition: SHFeature.h:194
double get_SCORE_HOLDER()
Definition: SHFeature.h:326
void normalize_peak_area_by_factor(double factor)
Definition: SHFeature.h:312
int get_scan_number()
Definition: SHFeature.h:286
void set_MZ_END(double IN)
Definition: SHFeature.h:240
#define NULL
Definition: IsotopeWaveletParallelFor.h:41
std::string get_MOD_SQ(double T)
Definition: SHFeature.h:265
bool check_AC(std::string IN, double T)
Definition: SHFeature.h:253
std::map< double, std::vector< MS2Info > > MS2_SCANS
Definition: SHFeature.h:62
std::string get_MOD_SQ()
Definition: SHFeature.h:263
void setLCelutionProfile(FeatureLCProfile *IN)
Definition: SHFeature.h:401
double TR_END
Definition: SHFeature.h:123
std::string getFeatureExtraInformation()
Definition: SHFeature.h:189
int get_MS2_SCANS_SIZE()
Definition: SHFeature.h:169
void set_raw_MZ(double IN)
Definition: SHFeature.h:349
double get_THEO_MZ()
Definition: SHFeature.h:243
int scan_apex
Definition: SHFeature.h:67
double get_retention_time()
Definition: SHFeature.h:329
double get_MZ_START()
Definition: SHFeature.h:234
void set_SCORE_HOLDER(double IN)
Definition: SHFeature.h:324
double get_THEO_MZ(double T)
Definition: SHFeature.h:245
void set_MASTER_ID(int IN)
Definition: SHFeature.h:371
void set_MZ(double in)
Definition: SHFeature.h:232
void setFeatureExtraInformation(std::string in)
Definition: SHFeature.h:187
void set_scan_start(int IN)
Definition: SHFeature.h:292
void set_scan_end(int IN)
Definition: SHFeature.h:296
double MONO_MZ_START
Definition: SHFeature.h:107
FeatureLCProfile * getLCelutionProfile()
Definition: SHFeature.h:403
void removeAllMS2Information()
Definition: SHFeature.h:164
bool check_AC(std::string IN)
Definition: SHFeature.h:251
int get_matching_nb()
Definition: SHFeature.h:219
std::string get_TOTAL_SQ()
Definition: SHFeature.h:259
int feature_ID
Definition: SHFeature.h:125
int get_scan_start()
Definition: SHFeature.h:290
double apex_peak_intensity
Definition: SHFeature.h:71
void setSignalToNoise(double in)
Definition: SHFeature.h:429
int spectrum_ID
Definition: SHFeature.h:86
Definition: MS2Feature.h:54
double PEAK_SCORE
Definition: SHFeature.h:72
void erase_match_list()
Definition: SHFeature.h:211
void set_FEATURE_PI(double IN)
Definition: SHFeature.h:391
double MONO_MZ
Definition: SHFeature.h:121
std::map< double, std::vector< MS2Info > > * get_MS2_SCAN_MAP()
Definition: SHFeature.h:174
double SignalToNoise
Definition: SHFeature.h:73
double TR_APEX
Definition: SHFeature.h:106
void set_retention_time_END(double IN)
Definition: SHFeature.h:339
std::map< int, SHFeature >::iterator get_match_list_end()
Definition: SHFeature.h:200
std::string get_TOTAL_SQ(double T)
Definition: SHFeature.h:261
std::map< int, SHFeature > matched_feature_list
Definition: SHFeature.h:103
void set_feature_ID(int IN)
Definition: SHFeature.h:353
std::string featureExtraInformation
Definition: SHFeature.h:91
Definition: FeatureLCProfile.h:66
int get_MS2_scan(double T)
Definition: SHFeature.h:277
int scan_start
Definition: SHFeature.h:68
void set_feature_match_status(bool IN)
Definition: SHFeature.h:415
std::map< int, SHFeature >::iterator find_match_by_id(int ID)
Definition: SHFeature.h:202
double get_MZ()
Definition: SHFeature.h:230
void set_MZ_START(double IN)
Definition: SHFeature.h:236
void set_raw_retention_time_apex(double IN)
Definition: SHFeature.h:345
std::map< double, std::vector< MS2Info > >::iterator get_MS2_SCANS_START()
Definition: SHFeature.h:179
double get_alignment_error_up()
Definition: SHFeature.h:315
void set_alignment_error_down(double IN)
Definition: SHFeature.h:321
double TR
Definition: SHFeature.h:120
FeatureLCProfile * LCprofile
Definition: SHFeature.h:95
std::map< double, std::vector< MS2Info > > * get_MS2_SCAN_LIST()
Definition: SHFeature.h:279
void set_spectrum_ID(int IN)
Definition: SHFeature.h:358
void set_retention_time(double IN)
Definition: SHFeature.h:331
int MASTER_ID
Definition: SHFeature.h:87
void removeMS2Feature()
Definition: SHFeature.h:422
int get_charge_state()
Definition: SHFeature.h:298
double get_MZ_END()
Definition: SHFeature.h:238
std::map< double, std::vector< MS2Info > >::iterator get_MS2_SCANS_END()
Definition: SHFeature.h:181
int get_feature_ID()
Definition: SHFeature.h:355
int get_MASTER_ID()
Definition: SHFeature.h:373
double get_raw_retention_time_apex()
Definition: SHFeature.h:343
std::string get_MS2_TYPE_TAG(double T)
Definition: SHFeature.h:273
MS2Feature * MS2TraceFeature
Definition: SHFeature.h:113
void set_alignment_error_up(double IN)
Definition: SHFeature.h:317
static double _MONO_O
Definition: SHFeature.h:99
bool get_feature_match_status()
Definition: SHFeature.h:413
std::map< double, std::vector< MS2Info > >::iterator get_MS2_SCAN_LIST_START()
Definition: SHFeature.h:281
double MONO_MZ_END
Definition: SHFeature.h:108
double get_apex_peak_intensity()
Definition: SHFeature.h:308
double get_raw_MZ()
Definition: SHFeature.h:347
void set_scan_number(int IN)
Definition: SHFeature.h:288
double get_pep_prob(double T)
Definition: SHFeature.h:269
void set_charge_state(int IN)
Definition: SHFeature.h:300
static double get_MONO_H()
Definition: SHFeature.h:440
void set_peak_area(float IN)
Definition: SHFeature.h:302
double getBackgroundNoiseLevel()
Definition: SHFeature.h:432
int get_replicate_match_nb()
Definition: SHFeature.h:217
MS2Feature * getMS2Feature()
Definition: SHFeature.h:424
double total_peak_area
Definition: SHFeature.h:70
int get_spectrum_ID()
Definition: SHFeature.h:368
int charge_state
Definition: SHFeature.h:124
std::string get_AC()
Definition: SHFeature.h:247
Definition: SHFeature.h:51
void addMS2Feature(MS2Feature *in)
Definition: SHFeature.h:420
double alignment_error_up
Definition: SHFeature.h:78
bool feature_match_status
Definition: SHFeature.h:81
std::string get_MS2_TYPE_TAG()
Definition: SHFeature.h:271
double getSignalToNoise()
Definition: SHFeature.h:427
double get_alignment_error_down()
Definition: SHFeature.h:319
std::map< int, SHFeature >::iterator get_match_list_start()
Definition: SHFeature.h:198
int get_scan_end()
Definition: SHFeature.h:294
double get_peak_area()
Definition: SHFeature.h:304
double SCORE_HOLDER
Definition: SHFeature.h:80
double get_pep_prob()
Definition: SHFeature.h:267