45 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCMS_H
46 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCMS_H
108 void order_by_mass();
111 float compare_feature_mass(
const void *,
const void *);
156 std::vector<SHFeature>::iterator p = feature_list.begin();
157 while (p != feature_list.end())
159 (*p).set_spectrum_ID(get_spectrum_ID());
165 int get_nb_common_peaks(
int);
174 {
return feature_list.clear(); }
176 {
return feature_list; }
178 {
return &feature_list; }
180 {
return feature_list.empty(); }
184 {
return feature_list.begin(); }
186 {
return feature_list.end(); }
196 feature_list.push_back(*IN);
202 void remove_feature_by_ID(
int);
207 if (i <
int(feature_list.size()))
209 feature_list.erase(feature_list.begin() + i);
215 {
return feature_list.erase(IN); }
219 {
return (
unsigned int) feature_list.size(); }
222 {
return spec_name; }
228 {
return spectrum_id; }
230 { spectrum_id = IN; }
233 void setFeatureLCMSID();
240 { raw_spec_names.erase(ID); }
242 { raw_spec_names.insert(make_pair(ID, name)); }
244 {
return raw_spec_names.empty(); }
246 {
return raw_spec_names.begin(); }
248 {
return raw_spec_names.end(); }
250 {
return raw_spec_names; }
252 {
return (
int) raw_spec_names.size(); }
255 std::map<int, std::string>::iterator p = raw_spec_names.find(ID);
256 if (p == raw_spec_names.end())
264 bool check_LCMS_name(std::string);
267 bool find_LC_MS_by_ID(
int);
272 std::map<int, std::string>::iterator p = IN.begin();
273 while (p != IN.end())
276 std::map<int, std::string>::iterator
F = raw_spec_names.find(ID);
277 if (F != raw_spec_names.end())
279 ID += (int) raw_spec_names.size();
281 raw_spec_names.insert(make_pair(ID, (*p).second));
290 std::vector<SHFeature>::iterator P = get_feature_list_begin();
291 while (P != get_feature_list_end())
293 if ((*P).get_MS2_info())
304 std::vector<SHFeature>::iterator P = get_feature_list_begin();
305 while (P != get_feature_list_end())
307 if ((*P).get_MS2_info(PepProb_T))
319 std::pair<double, double> tmp(ERROR_UP, ERROR_DOWN);
320 ALIGNMENT_ERROR.insert(std::pair<
double, std::pair<double, double> >(TR, tmp));
324 void get_alignment_error(
double,
double *,
double *);
330 {
return MASTER_ID; }
335 #endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCMS_H
int get_spectrum_ID()
Definition: LCMS.h:227
bool check_feature_list_empty()
Definition: LCMS.h:179
void remove_feature(int i)
Definition: LCMS.h:205
void set_spectrum_ID(int IN)
Definition: LCMS.h:229
void add_raw_spec_name(int ID, std::string name)
Definition: LCMS.h:241
int get_nb_identified_features(double PepProb_T)
Definition: LCMS.h:301
#define NULL
Definition: IsotopeWaveletParallelFor.h:41
int get_nb_raw_specs()
Definition: LCMS.h:251
void remove_raw_spec_name(int ID)
Definition: LCMS.h:239
void add_alignment_error(double TR, double ERROR_UP, double ERROR_DOWN)
Definition: LCMS.h:317
std::vector< SHFeature >::iterator get_feature_list_begin()
Definition: LCMS.h:183
void set_MASTER_ID(int IN)
Definition: LCMS.h:327
std::vector< SHFeature > feature_list
Definition: LCMS.h:67
int feature_ID
Definition: SHFeature.h:125
std::string get_spec_name()
Definition: LCMS.h:221
unsigned int get_nb_features()
Definition: LCMS.h:218
std::map< int, std::string > raw_spec_names
Definition: LCMS.h:76
int get_MASTER_ID()
Definition: LCMS.h:329
double MONO_MZ
Definition: SHFeature.h:121
std::map< int, std::string >::iterator get_raw_spec_name_end()
Definition: LCMS.h:247
bool check_raw_spec_name_empty()
Definition: LCMS.h:243
void set_feature_ID(int IN)
Definition: SHFeature.h:353
std::string spec_name
Definition: LCMS.h:64
void clear_feature_list()
Definition: LCMS.h:173
std::vector< SHFeature > get_feature_list()
Definition: LCMS.h:175
double TR
Definition: SHFeature.h:120
int spectrum_id
Definition: LCMS.h:70
void tag_peaks_with_spectrum_ID()
Definition: LCMS.h:154
std::vector< SHFeature >::iterator remove_feature_from_list(std::vector< SHFeature >::iterator IN)
Definition: LCMS.h:214
void set_spec_name(std::string IN)
Definition: LCMS.h:223
std::vector< SHFeature >::iterator get_feature_list_end()
Definition: LCMS.h:185
int get_feature_ID()
Definition: SHFeature.h:355
bool operator()(const SHFeature A, const SHFeature B) const
Definition: LCMS.h:138
std::map< int, std::string > get_raw_spec_name_map()
Definition: LCMS.h:249
void add_feature(SHFeature *IN)
Definition: LCMS.h:189
std::vector< SHFeature > * get_feature_list_reference()
Definition: LCMS.h:177
std::string get_raw_spec_name(int ID)
Definition: LCMS.h:253
int MASTER_ID
Definition: LCMS.h:73
Definition: SHFeature.h:51
int get_nb_identified_features()
Definition: LCMS.h:287
void add_raw_spec_name_map(std::map< int, std::string > IN)
Definition: LCMS.h:270
static double MINIMAL_PEP_PROPHET_THERSHOLD
Definition: LCMS.h:86
std::map< int, std::string >::iterator get_raw_spec_name_start()
Definition: LCMS.h:245
bool operator()(const SHFeature A, const SHFeature B) const
Definition: LCMS.h:118
std::map< double, std::pair< double, double > > ALIGNMENT_ERROR
Definition: LCMS.h:79