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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 
42 
43 namespace OpenMS
44 {
48  class OPENMS_DLLAPI OpenSwathHelper
49  {
50 
51 public:
52 
58  static void selectSwathTransitions(const OpenMS::TargetedExperiment& targeted_exp,
59  OpenMS::TargetedExperiment& transition_exp_used, double min_upper_edge_dist,
60  double lower, double upper);
61 
67  static void selectSwathTransitions(const OpenSwath::LightTargetedExperiment& targeted_exp,
68  OpenSwath::LightTargetedExperiment& transition_exp_used, double min_upper_edge_dist,
69  double lower, double upper);
70 
84  static void checkSwathMap(const OpenMS::MSExperiment<Peak1D>& swath_map,
85  double& lower, double& upper);
86 
90  template <class TargetedExperimentT>
92  const TargetedExperimentT& targeted_exp, TargetedExperimentT& transition_exp_used, double min_upper_edge_dist)
93  {
94  if (exp.size() == 0 || exp[0].getPrecursors().size() == 0)
95  {
96  std::cerr << "WARNING: File " << exp.getLoadedFilePath()
97  << " does not have any experiments or any precursors. Is it a SWATH map? "
98  << "I will move to the next map."
99  << std::endl;
100  return false;
101  }
102  double upper, lower;
103  OpenSwathHelper::checkSwathMap(exp, lower, upper);
104  OpenSwathHelper::selectSwathTransitions(targeted_exp, transition_exp_used, min_upper_edge_dist, lower, upper);
105  if (transition_exp_used.getTransitions().size() == 0)
106  {
107  std::cerr << "WARNING: For File " << exp.getLoadedFilePath()
108  << " no transition were within the precursor window of " << lower << " to " << upper
109  << "I will move to the next map."
110  << std::endl;
111  return false;
112  }
113  return true;
114 
115  }
116 
120  static std::pair<double,double> estimateRTRange(OpenSwath::LightTargetedExperiment & exp);
121 
132  static std::map<std::string, double> simpleFindBestFeature(
134  bool useQualCutoff = false, double qualCutoff = 0.0);
135 
136  };
137 }
138 #endif
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
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
This class stores an prediction of an SRM/MRM transition.
Definition: TargetedExperiment.h:53
Definition: TransitionExperiment.h:179
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.

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:53:51 using doxygen 1.8.9.1