40 #include <boost/shared_ptr.hpp> 42 #include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h> 73 return !(fragment_charge == 0);
98 library_intensity = l;
113 detecting_transition = d;
123 quantifying_transition = q;
133 identifying_transition = i;
175 return compound_name.empty();
252 return getCompoundByRef(ref);
257 if (compound_reference_map_dirty_)
259 createPeptideReferenceMap_();
261 return *(compound_reference_map_[ref]);
268 for (
size_t i = 0; i < getCompounds().size(); i++)
270 compound_reference_map_[getCompounds()[i].id] = &getCompounds()[i];
272 compound_reference_map_dirty_ =
false;
bool detecting_transition
Definition: TransitionExperiment.h:62
Definition: TransitionExperiment.h:46
std::string compound_name
Definition: TransitionExperiment.h:170
double rt
Definition: TransitionExperiment.h:159
void setLibraryIntensity(double l)
Definition: TransitionExperiment.h:96
double library_intensity
Definition: TransitionExperiment.h:57
LightTransition()
Definition: TransitionExperiment.h:50
const LightCompound & getPeptideByRef(const std::string &ref)
Definition: TransitionExperiment.h:250
std::string id
Definition: TransitionExperiment.h:166
std::string peptide_ref
Definition: TransitionExperiment.h:56
void setDetectingTransition(bool d)
Definition: TransitionExperiment.h:111
bool identifying_transition
Definition: TransitionExperiment.h:64
bool quantifying_transition
Definition: TransitionExperiment.h:63
int location
Definition: TransitionExperiment.h:144
double getDriftTime() const
Definition: TransitionExperiment.h:193
void setIdentifyingTransition(bool i)
Definition: TransitionExperiment.h:131
std::string peptide_group_label
Definition: TransitionExperiment.h:164
Definition: TransitionExperiment.h:149
void createPeptideReferenceMap_()
Definition: TransitionExperiment.h:266
Definition: TransitionExperiment.h:142
Definition: TransitionExperiment.h:201
int fragment_charge
Definition: TransitionExperiment.h:60
LightProtein Protein
Definition: TransitionExperiment.h:214
Definition: MRMScoring.h:49
bool compound_reference_map_dirty_
Definition: TransitionExperiment.h:276
std::vector< LightCompound > compounds
Definition: TransitionExperiment.h:217
std::string getPeptideRef() const
Definition: TransitionExperiment.h:81
std::vector< LightModification > modifications
Definition: TransitionExperiment.h:198
LightCompound()
Definition: TransitionExperiment.h:152
std::string sum_formula
Definition: TransitionExperiment.h:169
std::string getCompoundRef() const
Definition: TransitionExperiment.h:86
LightCompound Compound
Definition: TransitionExperiment.h:213
std::vector< LightProtein > proteins
Definition: TransitionExperiment.h:218
double getProductMZ() const
Definition: TransitionExperiment.h:101
void setDriftTime(double d)
Definition: TransitionExperiment.h:188
bool isPeptide() const
Definition: TransitionExperiment.h:173
double product_mz
Definition: TransitionExperiment.h:58
std::string sequence
Definition: TransitionExperiment.h:161
int getProductChargeState() const
Definition: TransitionExperiment.h:66
const std::vector< LightCompound > & getCompounds() const
Definition: TransitionExperiment.h:234
std::map< std::string, LightCompound * > compound_reference_map_
Definition: TransitionExperiment.h:277
bool isDetectingTransition() const
Definition: TransitionExperiment.h:116
bool isProductChargeStateSet() const
Definition: TransitionExperiment.h:71
const std::vector< LightTransition > & getTransitions() const
Definition: TransitionExperiment.h:224
bool isIdentifyingTransition() const
Definition: TransitionExperiment.h:136
std::string transition_name
Definition: TransitionExperiment.h:55
int getChargeState() const
Definition: TransitionExperiment.h:183
std::vector< LightTransition > transitions
Definition: TransitionExperiment.h:216
std::string getNativeID() const
Definition: TransitionExperiment.h:76
void setChargeState(int ch)
Definition: TransitionExperiment.h:178
std::string id
Definition: TransitionExperiment.h:203
Definition: TransitionExperiment.h:207
std::vector< LightCompound > & getCompounds()
Definition: TransitionExperiment.h:229
double precursor_mz
Definition: TransitionExperiment.h:59
std::vector< LightProtein > & getProteins()
Definition: TransitionExperiment.h:239
LightTargetedExperiment()
Definition: TransitionExperiment.h:209
void setQuantifyingTransition(bool q)
Definition: TransitionExperiment.h:121
const std::vector< LightProtein > & getProteins() const
Definition: TransitionExperiment.h:244
int unimod_id
Definition: TransitionExperiment.h:145
bool decoy
Definition: TransitionExperiment.h:61
const LightCompound & getCompoundByRef(const std::string &ref)
Definition: TransitionExperiment.h:255
bool isQuantifyingTransition() const
Definition: TransitionExperiment.h:126
std::string gene_name
Definition: TransitionExperiment.h:165
std::string sequence
Definition: TransitionExperiment.h:204
std::vector< std::string > protein_refs
Definition: TransitionExperiment.h:162
double getLibraryIntensity() const
Definition: TransitionExperiment.h:91
double getPrecursorMZ() const
Definition: TransitionExperiment.h:106
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:219
LightCompound Peptide
Definition: TransitionExperiment.h:212
int charge
Definition: TransitionExperiment.h:160
double drift_time
Definition: TransitionExperiment.h:158
LightTransition Transition
Definition: TransitionExperiment.h:211