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OpenSwathHelper.h
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34 
35 #ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHHELPER_H
36 #define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHHELPER_H
37 
43 
44 namespace OpenMS
45 {
49  class OPENMS_DLLAPI OpenSwathHelper
50  {
51 
52 public:
53 
59  static void selectSwathTransitions(const OpenMS::TargetedExperiment& targeted_exp,
60  OpenMS::TargetedExperiment& transition_exp_used, double min_upper_edge_dist,
61  double lower, double upper);
62 
68  static void selectSwathTransitions(const OpenSwath::LightTargetedExperiment& targeted_exp,
69  OpenSwath::LightTargetedExperiment& transition_exp_used, double min_upper_edge_dist,
70  double lower, double upper);
71 
85  static void checkSwathMap(const OpenMS::PeakMap& swath_map,
86  double& lower, double& upper);
87 
91  template <class TargetedExperimentT>
93  const TargetedExperimentT& targeted_exp, TargetedExperimentT& transition_exp_used, double min_upper_edge_dist)
94  {
95  if (exp.size() == 0 || exp[0].getPrecursors().size() == 0)
96  {
97  std::cerr << "WARNING: File " << exp.getLoadedFilePath()
98  << " does not have any experiments or any precursors. Is it a SWATH map? "
99  << "I will move to the next map."
100  << std::endl;
101  return false;
102  }
103  double upper, lower;
104  OpenSwathHelper::checkSwathMap(exp, lower, upper);
105  OpenSwathHelper::selectSwathTransitions(targeted_exp, transition_exp_used, min_upper_edge_dist, lower, upper);
106  if (transition_exp_used.getTransitions().size() == 0)
107  {
108  std::cerr << "WARNING: For File " << exp.getLoadedFilePath()
109  << " no transition were within the precursor window of " << lower << " to " << upper
110  << "I will move to the next map."
111  << std::endl;
112  return false;
113  }
114  return true;
115 
116  }
117 
121  static std::pair<double,double> estimateRTRange(OpenSwath::LightTargetedExperiment & exp);
122 
133  static std::map<std::string, double> simpleFindBestFeature(
135  bool useQualCutoff = false, double qualCutoff = 0.0);
136  };
137 }
138 #endif // OPENMS_ANALYSIS_OPENSWATH_OPENSWATHHELPER_H
A helper class that is used by several OpenSWATH tools.
Definition: OpenSwathHelper.h:49
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:110
Size size() const
Definition: MSExperiment.h:132
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
const String & getLoadedFilePath() const
get the file_name_ which is the absolute path to the file loaded from
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
static void checkSwathMap(const OpenMS::PeakMap &swath_map, double &lower, double &upper)
Get the lower / upper offset for this SWATH map and do some sanity checks.
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:62
Definition: TransitionExperiment.h:195
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 bool checkSwathMapAndSelectTransitions(const OpenMS::PeakMap &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:92

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:02 using doxygen 1.8.13