35 #ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_TRANSITIONEXPERIMENT_H 36 #define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_TRANSITIONEXPERIMENT_H 41 #include <boost/shared_ptr.hpp> 43 #include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/OpenSwathAlgoConfig.h> 70 return transition_name;
80 return library_intensity;
85 library_intensity = l;
100 detecting_transition = d;
105 return detecting_transition;
110 quantifying_transition = q;
115 return quantifying_transition;
120 identifying_transition = i;
125 return identifying_transition;
130 site_identifying_transition = i;
135 return site_identifying_transition;
140 site_identifying_class = i;
145 return site_identifying_class;
207 if (peptide_reference_map_dirty_)
209 createPeptideReferenceMap_();
211 return *(peptide_reference_map_[ref]);
218 for (
size_t i = 0; i < getPeptides().size(); i++)
220 peptide_reference_map_[getPeptides()[i].id] = &getPeptides()[i];
222 peptide_reference_map_dirty_ =
false;
233 #endif // OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_TRANSITIONEXPERIMENT_H std::string getPeptideRef() const
Definition: TransitionExperiment.h:73
std::vector< LightProtein > & getProteins()
Definition: TransitionExperiment.h:200
double product_mz
Definition: TransitionExperiment.h:53
std::string id
Definition: TransitionExperiment.h:175
double library_intensity
Definition: TransitionExperiment.h:52
std::vector< int > site_identifying_transition
Definition: TransitionExperiment.h:60
std::vector< std::string > site_identifying_class
Definition: TransitionExperiment.h:61
std::vector< LightTransition > transitions
Definition: TransitionExperiment.h:187
int getChargeState() const
Definition: TransitionExperiment.h:165
std::string peptide_group_label
Definition: TransitionExperiment.h:162
std::vector< int > getSiteIdentifyingTransition() const
Definition: TransitionExperiment.h:133
bool isQuantifyingTransition() const
Definition: TransitionExperiment.h:113
bool detecting_transition
Definition: TransitionExperiment.h:57
std::vector< LightProtein > proteins
Definition: TransitionExperiment.h:189
int getProductChargeState() const
Definition: TransitionExperiment.h:63
bool isIdentifyingTransition() const
Definition: TransitionExperiment.h:123
std::string getNativeID() const
Definition: TransitionExperiment.h:68
int charge
Definition: TransitionExperiment.h:158
double precursor_mz
Definition: TransitionExperiment.h:54
std::map< std::string, LightPeptide * > peptide_reference_map_
Definition: TransitionExperiment.h:226
bool isDetectingTransition() const
Definition: TransitionExperiment.h:103
double getPrecursorMZ() const
Definition: TransitionExperiment.h:93
bool decoy
Definition: TransitionExperiment.h:56
std::vector< LightPeptide > peptides
Definition: TransitionExperiment.h:188
void setLibraryIntensity(double l)
Definition: TransitionExperiment.h:83
void createPeptideReferenceMap_()
Definition: TransitionExperiment.h:216
Definition: TransitionExperiment.h:155
bool peptide_reference_map_dirty_
Definition: TransitionExperiment.h:225
std::string sequence
Definition: TransitionExperiment.h:176
double getProductMZ() const
Definition: TransitionExperiment.h:88
int location
Definition: TransitionExperiment.h:151
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:190
LightTransition Transition
Definition: TransitionExperiment.h:183
std::string transition_name
Definition: TransitionExperiment.h:50
Definition: MRMScoring.h:51
std::vector< std::string > protein_refs
Definition: TransitionExperiment.h:160
LightPeptide Peptide
Definition: TransitionExperiment.h:184
void setQuantifyingTransition(bool q)
Definition: TransitionExperiment.h:108
void setIdentifyingTransition(bool i)
Definition: TransitionExperiment.h:118
std::string id
Definition: TransitionExperiment.h:163
std::string peptide_ref
Definition: TransitionExperiment.h:51
LightTargetedExperiment()
Definition: TransitionExperiment.h:181
std::string unimod_id
Definition: TransitionExperiment.h:152
void setSiteIdentifyingTransition(std::vector< int > i)
Definition: TransitionExperiment.h:128
Definition: TransitionExperiment.h:47
std::vector< LightPeptide > & getPeptides()
Definition: TransitionExperiment.h:195
bool identifying_transition
Definition: TransitionExperiment.h:59
int charge
Definition: TransitionExperiment.h:55
void setSiteIdentifyingClass(std::vector< std::string > i)
Definition: TransitionExperiment.h:138
void setDetectingTransition(bool d)
Definition: TransitionExperiment.h:98
double rt
Definition: TransitionExperiment.h:157
bool quantifying_transition
Definition: TransitionExperiment.h:58
std::vector< std::string > getSiteIdentifyingClass() const
Definition: TransitionExperiment.h:143
Definition: TransitionExperiment.h:173
double getLibraryIntensity() const
Definition: TransitionExperiment.h:78
Definition: TransitionExperiment.h:179
std::string sequence
Definition: TransitionExperiment.h:159
std::vector< LightModification > modifications
Definition: TransitionExperiment.h:170
const LightPeptide & getPeptideByRef(const std::string &ref)
Definition: TransitionExperiment.h:205
LightProtein Protein
Definition: TransitionExperiment.h:185
Definition: TransitionExperiment.h:149