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> 74 return !(fragment_charge == 0);
99 library_intensity = l;
114 detecting_transition = d;
124 quantifying_transition = q;
134 identifying_transition = i;
173 return compound_name.empty();
240 return getCompoundByRef(ref);
245 if (compound_reference_map_dirty_)
247 createPeptideReferenceMap_();
249 return *(compound_reference_map_[ref]);
256 for (
size_t i = 0; i < getCompounds().size(); i++)
258 compound_reference_map_[getCompounds()[i].id] = &getCompounds()[i];
260 compound_reference_map_dirty_ =
false;
272 #endif // OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_TRANSITIONEXPERIMENT_H std::vector< LightProtein > & getProteins()
Definition: TransitionExperiment.h:227
double product_mz
Definition: TransitionExperiment.h:59
const std::vector< LightCompound > & getCompounds() const
Definition: TransitionExperiment.h:222
std::string id
Definition: TransitionExperiment.h:191
double library_intensity
Definition: TransitionExperiment.h:58
LightCompound()
Definition: TransitionExperiment.h:153
const std::vector< LightProtein > & getProteins() const
Definition: TransitionExperiment.h:232
std::vector< LightTransition > transitions
Definition: TransitionExperiment.h:204
bool isQuantifyingTransition() const
Definition: TransitionExperiment.h:127
const std::vector< LightTransition > & getTransitions() const
Definition: TransitionExperiment.h:212
std::vector< LightModification > modifications
Definition: TransitionExperiment.h:186
bool detecting_transition
Definition: TransitionExperiment.h:63
std::vector< LightProtein > proteins
Definition: TransitionExperiment.h:206
double rt
Definition: TransitionExperiment.h:158
int fragment_charge
Definition: TransitionExperiment.h:61
double getLibraryIntensity() const
Definition: TransitionExperiment.h:92
std::vector< LightCompound > compounds
Definition: TransitionExperiment.h:205
std::string getPeptideRef() const
Definition: TransitionExperiment.h:82
double precursor_mz
Definition: TransitionExperiment.h:60
bool compound_reference_map_dirty_
Definition: TransitionExperiment.h:264
const LightCompound & getCompoundByRef(const std::string &ref)
Definition: TransitionExperiment.h:243
const LightCompound & getPeptideByRef(const std::string &ref)
Definition: TransitionExperiment.h:238
bool decoy
Definition: TransitionExperiment.h:62
int getChargeState() const
Definition: TransitionExperiment.h:181
std::string getCompoundRef() const
Definition: TransitionExperiment.h:87
void setLibraryIntensity(double l)
Definition: TransitionExperiment.h:97
void createPeptideReferenceMap_()
Definition: TransitionExperiment.h:254
bool isIdentifyingTransition() const
Definition: TransitionExperiment.h:137
std::string peptide_group_label
Definition: TransitionExperiment.h:163
std::string sequence
Definition: TransitionExperiment.h:192
int location
Definition: TransitionExperiment.h:145
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:207
LightTransition Transition
Definition: TransitionExperiment.h:199
std::string transition_name
Definition: TransitionExperiment.h:56
Definition: MRMScoring.h:51
LightCompound Peptide
Definition: TransitionExperiment.h:200
int unimod_id
Definition: TransitionExperiment.h:146
std::string getNativeID() const
Definition: TransitionExperiment.h:77
std::string sum_formula
Definition: TransitionExperiment.h:167
double getPrecursorMZ() const
Definition: TransitionExperiment.h:107
void setQuantifyingTransition(bool q)
Definition: TransitionExperiment.h:122
void setIdentifyingTransition(bool i)
Definition: TransitionExperiment.h:132
std::string peptide_ref
Definition: TransitionExperiment.h:57
LightCompound Compound
Definition: TransitionExperiment.h:201
Definition: TransitionExperiment.h:150
std::string sequence
Definition: TransitionExperiment.h:160
LightTargetedExperiment()
Definition: TransitionExperiment.h:197
std::vector< std::string > protein_refs
Definition: TransitionExperiment.h:161
Definition: TransitionExperiment.h:47
bool identifying_transition
Definition: TransitionExperiment.h:65
void setChargeState(int ch)
Definition: TransitionExperiment.h:176
bool isDetectingTransition() const
Definition: TransitionExperiment.h:117
double getProductMZ() const
Definition: TransitionExperiment.h:102
int getProductChargeState() const
Definition: TransitionExperiment.h:67
LightTransition()
Definition: TransitionExperiment.h:51
std::vector< LightCompound > & getCompounds()
Definition: TransitionExperiment.h:217
void setDetectingTransition(bool d)
Definition: TransitionExperiment.h:112
bool isPeptide() const
Definition: TransitionExperiment.h:171
std::string compound_name
Definition: TransitionExperiment.h:168
std::string id
Definition: TransitionExperiment.h:164
std::map< std::string, LightCompound * > compound_reference_map_
Definition: TransitionExperiment.h:265
bool quantifying_transition
Definition: TransitionExperiment.h:64
int charge
Definition: TransitionExperiment.h:159
Definition: TransitionExperiment.h:189
Definition: TransitionExperiment.h:195
bool isProductChargeStateSet() const
Definition: TransitionExperiment.h:72
LightProtein Protein
Definition: TransitionExperiment.h:202
Definition: TransitionExperiment.h:143