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