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OpenMS
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40 #include <boost/shared_ptr.hpp>
42 #include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>
std::string id
Definition: TransitionExperiment.h:165
int location
Definition: TransitionExperiment.h:144
const std::vector< LightTransition > & getTransitions() const
Definition: TransitionExperiment.h:223
bool isQuantifyingTransition() const
Definition: TransitionExperiment.h:126
std::vector< std::string > protein_refs
Definition: TransitionExperiment.h:162
int unimod_id
Definition: TransitionExperiment.h:145
double product_mz
Definition: TransitionExperiment.h:58
bool compound_reference_map_dirty_
Definition: TransitionExperiment.h:275
Definition: MRMScoring.h:50
double library_intensity
Definition: TransitionExperiment.h:57
bool detecting_transition
Definition: TransitionExperiment.h:62
void setDriftTime(double d)
Definition: TransitionExperiment.h:187
std::string getPeptideRef() const
Definition: TransitionExperiment.h:81
bool decoy
Definition: TransitionExperiment.h:61
double precursor_mz
Definition: TransitionExperiment.h:59
int fragment_charge
Definition: TransitionExperiment.h:60
const std::vector< LightCompound > & getCompounds() const
Definition: TransitionExperiment.h:233
double getLibraryIntensity() const
Definition: TransitionExperiment.h:91
LightTargetedExperiment()
Definition: TransitionExperiment.h:208
std::string getCompoundRef() const
Definition: TransitionExperiment.h:86
std::string transition_name
Definition: TransitionExperiment.h:55
bool isPeptide() const
Definition: TransitionExperiment.h:172
Definition: TransitionExperiment.h:206
void setLibraryIntensity(double l)
Definition: TransitionExperiment.h:96
bool isIdentifyingTransition() const
Definition: TransitionExperiment.h:136
Definition: TransitionExperiment.h:200
std::vector< LightProtein > & getProteins()
Definition: TransitionExperiment.h:238
double drift_time
Definition: TransitionExperiment.h:158
Definition: TransitionExperiment.h:149
std::vector< LightCompound > & getCompounds()
Definition: TransitionExperiment.h:228
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:218
LightTransition Transition
Definition: TransitionExperiment.h:210
std::map< std::string, LightCompound * > compound_reference_map_
Definition: TransitionExperiment.h:276
std::vector< LightCompound > compounds
Definition: TransitionExperiment.h:216
double getDriftTime() const
Definition: TransitionExperiment.h:192
LightCompound()
Definition: TransitionExperiment.h:152
std::string sum_formula
Definition: TransitionExperiment.h:168
std::string peptide_group_label
Definition: TransitionExperiment.h:164
bool identifying_transition
Definition: TransitionExperiment.h:64
LightTransition()
Definition: TransitionExperiment.h:50
void setIdentifyingTransition(bool i)
Definition: TransitionExperiment.h:131
const std::vector< LightProtein > & getProteins() const
Definition: TransitionExperiment.h:243
double rt
Definition: TransitionExperiment.h:159
std::vector< LightTransition > transitions
Definition: TransitionExperiment.h:215
const LightCompound & getCompoundByRef(const std::string &ref)
Definition: TransitionExperiment.h:254
Definition: TransitionExperiment.h:142
double getPrecursorMZ() const
Definition: TransitionExperiment.h:106
std::string peptide_ref
Definition: TransitionExperiment.h:56
int getChargeState() const
Definition: TransitionExperiment.h:182
std::vector< LightModification > modifications
Definition: TransitionExperiment.h:197
std::string sequence
Definition: TransitionExperiment.h:203
void setQuantifyingTransition(bool q)
Definition: TransitionExperiment.h:121
std::string getNativeID() const
Definition: TransitionExperiment.h:76
LightProtein Protein
Definition: TransitionExperiment.h:213
double getProductMZ() const
Definition: TransitionExperiment.h:101
bool isDetectingTransition() const
Definition: TransitionExperiment.h:116
std::vector< LightProtein > proteins
Definition: TransitionExperiment.h:217
std::string sequence
Definition: TransitionExperiment.h:161
std::string id
Definition: TransitionExperiment.h:202
int charge
Definition: TransitionExperiment.h:160
LightCompound Compound
Definition: TransitionExperiment.h:212
std::string compound_name
Definition: TransitionExperiment.h:169
int getProductChargeState() const
Definition: TransitionExperiment.h:66
const LightCompound & getPeptideByRef(const std::string &ref)
Definition: TransitionExperiment.h:249
Definition: TransitionExperiment.h:46
bool quantifying_transition
Definition: TransitionExperiment.h:63
bool isProductChargeStateSet() const
Definition: TransitionExperiment.h:71
LightCompound Peptide
Definition: TransitionExperiment.h:211
void createPeptideReferenceMap_()
Definition: TransitionExperiment.h:265
void setChargeState(int ch)
Definition: TransitionExperiment.h:177
void setDetectingTransition(bool d)
Definition: TransitionExperiment.h:111