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