40 #include <boost/shared_ptr.hpp> 42 #include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h> int getProductChargeState() const
Definition: TransitionExperiment.h:66
std::vector< std::string > protein_refs
Definition: TransitionExperiment.h:162
const std::vector< LightCompound > & getCompounds() const
Definition: TransitionExperiment.h:234
bool isProductChargeStateSet() const
Definition: TransitionExperiment.h:71
std::vector< LightModification > modifications
Definition: TransitionExperiment.h:198
std::string id
Definition: TransitionExperiment.h:203
LightTargetedExperiment()
Definition: TransitionExperiment.h:209
Definition: MRMScoring.h:49
LightTransition Transition
Definition: TransitionExperiment.h:211
std::string getNativeID() const
Definition: TransitionExperiment.h:76
std::string sequence
Definition: TransitionExperiment.h:161
double precursor_mz
Definition: TransitionExperiment.h:59
std::vector< LightProtein > proteins
Definition: TransitionExperiment.h:218
int charge
Definition: TransitionExperiment.h:160
void setQuantifyingTransition(bool q)
Definition: TransitionExperiment.h:121
bool decoy
Definition: TransitionExperiment.h:61
std::string id
Definition: TransitionExperiment.h:166
bool isQuantifyingTransition() const
Definition: TransitionExperiment.h:126
double getLibraryIntensity() const
Definition: TransitionExperiment.h:91
int getChargeState() const
Definition: TransitionExperiment.h:183
std::vector< LightCompound > compounds
Definition: TransitionExperiment.h:217
std::string compound_name
Definition: TransitionExperiment.h:170
Definition: TransitionExperiment.h:149
bool detecting_transition
Definition: TransitionExperiment.h:62
void setChargeState(int ch)
Definition: TransitionExperiment.h:178
LightCompound Compound
Definition: TransitionExperiment.h:213
void setLibraryIntensity(double l)
Definition: TransitionExperiment.h:96
double getPrecursorMZ() const
Definition: TransitionExperiment.h:106
const LightCompound & getPeptideByRef(const std::string &ref)
Definition: TransitionExperiment.h:250
std::string peptide_group_label
Definition: TransitionExperiment.h:164
LightProtein Protein
Definition: TransitionExperiment.h:214
std::string peptide_ref
Definition: TransitionExperiment.h:56
void setDetectingTransition(bool d)
Definition: TransitionExperiment.h:111
void setDriftTime(double d)
Definition: TransitionExperiment.h:188
bool identifying_transition
Definition: TransitionExperiment.h:64
bool quantifying_transition
Definition: TransitionExperiment.h:63
int location
Definition: TransitionExperiment.h:144
int unimod_id
Definition: TransitionExperiment.h:145
const std::vector< LightProtein > & getProteins() const
Definition: TransitionExperiment.h:244
bool isPeptide() const
Definition: TransitionExperiment.h:173
int fragment_charge
Definition: TransitionExperiment.h:60
std::string sum_formula
Definition: TransitionExperiment.h:169
std::string gene_name
Definition: TransitionExperiment.h:165
Definition: TransitionExperiment.h:142
Definition: TransitionExperiment.h:201
std::string getPeptideRef() const
Definition: TransitionExperiment.h:81
const std::vector< LightTransition > & getTransitions() const
Definition: TransitionExperiment.h:224
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:219
double library_intensity
Definition: TransitionExperiment.h:57
LightTransition()
Definition: TransitionExperiment.h:50
Definition: TransitionExperiment.h:207
void setIdentifyingTransition(bool i)
Definition: TransitionExperiment.h:131
double getProductMZ() const
Definition: TransitionExperiment.h:101
void createPeptideReferenceMap_()
Definition: TransitionExperiment.h:266
std::map< std::string, LightCompound * > compound_reference_map_
Definition: TransitionExperiment.h:277
double product_mz
Definition: TransitionExperiment.h:58
const LightCompound & getCompoundByRef(const std::string &ref)
Definition: TransitionExperiment.h:255
double getDriftTime() const
Definition: TransitionExperiment.h:193
Definition: TransitionExperiment.h:46
std::vector< LightTransition > transitions
Definition: TransitionExperiment.h:216
bool isDetectingTransition() const
Definition: TransitionExperiment.h:116
std::string getCompoundRef() const
Definition: TransitionExperiment.h:86
LightCompound()
Definition: TransitionExperiment.h:152
double rt
Definition: TransitionExperiment.h:159
std::string sequence
Definition: TransitionExperiment.h:204
std::vector< LightProtein > & getProteins()
Definition: TransitionExperiment.h:239
double drift_time
Definition: TransitionExperiment.h:158
bool isIdentifyingTransition() const
Definition: TransitionExperiment.h:136
LightCompound Peptide
Definition: TransitionExperiment.h:212
std::string transition_name
Definition: TransitionExperiment.h:55
std::vector< LightCompound > & getCompounds()
Definition: TransitionExperiment.h:229
bool compound_reference_map_dirty_
Definition: TransitionExperiment.h:276