35 #ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHHELPER_H
36 #define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHHELPER_H
60 double lower,
double upper);
69 double lower,
double upper);
85 double& lower,
double& upper);
90 template <
class TargetedExperimentT>
92 const TargetedExperimentT& targeted_exp, TargetedExperimentT& transition_exp_used,
double min_upper_edge_dist)
94 if (exp.
size() == 0 || exp[0].getPrecursors().
size() == 0)
97 <<
" does not have any experiments or any precursors. Is it a SWATH map? "
98 <<
"I will move to the next map."
105 if (transition_exp_used.getTransitions().size() == 0)
108 <<
" no transition were within the precursor window of " << lower <<
" to " << upper
109 <<
"I will move to the next map."
129 static std::map<std::string, double> simpleFindBestFeature(
131 bool useQualCutoff =
false,
double qualCutoff = 0.0);
Size size() const
Definition: MSExperiment.h:117
A helper class that is used by several OpenSWATH tools.
Definition: OpenSwathHelper.h:48
const String & getLoadedFilePath() const
get the file_name_ which is the absolute path to the file loaded from
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:110
static bool checkSwathMapAndSelectTransitions(const OpenMS::MSExperiment< Peak1D > &exp, const TargetedExperimentT &targeted_exp, TargetedExperimentT &transition_exp_used, double min_upper_edge_dist)
Check the map and select transition in one function.
Definition: OpenSwathHelper.h:91
This class stores an prediction of an SRM/MRM transition.
Definition: TargetedExperiment.h:53
Definition: TransitionExperiment.h:125
static void selectSwathTransitions(const OpenMS::TargetedExperiment &targeted_exp, OpenMS::TargetedExperiment &transition_exp_used, double min_upper_edge_dist, double lower, double upper)
Select transitions between lower and upper and write them into the new TargetedExperiment.
static void checkSwathMap(const OpenMS::MSExperiment< Peak1D > &swath_map, double &lower, double &upper)
Get the lower / upper offset for this SWATH map and do some sanity checks.