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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 
41 
42 namespace OpenMS
43 {
47  class OPENMS_DLLAPI OpenSwathHelper
48  {
49 
50 public:
51 
53  static void selectSwathTransitions(const OpenMS::TargetedExperiment& targeted_exp,
54  OpenMS::TargetedExperiment& transition_exp_used, double min_upper_edge_dist,
55  double lower, double upper);
56 
58  static void checkSwathMap(const OpenMS::MSExperiment<Peak1D>& swath_map,
59  double& lower, double& upper);
60 
62  static void selectSwathTransitions(const OpenSwath::LightTargetedExperiment& targeted_exp,
63  OpenSwath::LightTargetedExperiment& transition_exp_used, double min_upper_edge_dist,
64  double lower, double upper);
65 
66  template <class TargetedExperimentT>
68  const TargetedExperimentT& targeted_exp, TargetedExperimentT& transition_exp_used, double min_upper_edge_dist)
69  {
70  if (exp.size() == 0 || exp[0].getPrecursors().size() == 0)
71  {
72  std::cerr << "WARNING: File " << exp.getLoadedFilePath()
73  << " does not have any experiments or any precursors. Is it a SWATH map? "
74  << "I will move to the next map."
75  << std::endl;
76  return false;
77  }
78  double upper, lower;
79  OpenSwathHelper::checkSwathMap(exp, lower, upper);
80  OpenSwathHelper::selectSwathTransitions(targeted_exp, transition_exp_used, min_upper_edge_dist, lower, upper);
81  if (transition_exp_used.getTransitions().size() == 0)
82  {
83  std::cerr << "WARNING: For File " << exp.getLoadedFilePath()
84  << " no transition were within the precursor window of " << lower << " to " << upper
85  << "I will move to the next map."
86  << std::endl;
87  return false;
88  }
89  return true;
90 
91  }
92 
93  };
94 }
95 #endif
Size size() const
Definition: MSExperiment.h:117
A helper class that is used by several OpenSWATH tools.
Definition: OpenSwathHelper.h:47
const String & getLoadedFilePath() const
get the file_name_ which is the absolute path to the file loaded from
static bool checkSwathMapAndSelectTransitions(const OpenMS::MSExperiment< Peak1D > &exp, const TargetedExperimentT &targeted_exp, TargetedExperimentT &transition_exp_used, double min_upper_edge_dist)
Definition: OpenSwathHelper.h:67
This class stores an prediction of an SRM/MRM transition.
Definition: TargetedExperiment.h:53
Definition: TransitionExperiment.h:120
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 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:19 using doxygen 1.8.5