OpenMS  2.8.0
OpenSwathHelper.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
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34 
35 #pragma once
36 
42 
43 namespace OpenMS
44 {
48  class OPENMS_DLLAPI OpenSwathHelper
49  {
50 
51 public:
52 
65  static String computePrecursorId(const String& transition_group_id, int isotope)
66  {
67  return transition_group_id + "_Precursor_i" + String(isotope);
68  }
69 
81  static String computeTransitionGroupId(const String& precursor_id)
82  {
83  std::vector<String> substrings;
84  precursor_id.split("_", substrings);
85 
86  if (substrings.size() == 3) return substrings[0];
87  else if (substrings.size() > 3)
88  {
89  String r;
90  for (Size k = 0; k < substrings.size() - 2; k++) r += substrings[k] + "_";
91  return r.prefix(r.size() - 1);
92  }
93  return "";
94  }
95 
107  static void selectSwathTransitions(const OpenMS::TargetedExperiment& targeted_exp,
108  OpenMS::TargetedExperiment& selected_transitions,
109  double min_upper_edge_dist,
110  double lower, double upper);
111 
124  OpenSwath::LightTargetedExperiment& selected_transitions,
125  double min_upper_edge_dist,
126  double lower, double upper);
127 
145  static void checkSwathMap(const OpenMS::PeakMap& swath_map,
146  double& lower, double& upper, double& center);
147 
159  template <class TargetedExperimentT>
161  const TargetedExperimentT& targeted_exp,
162  TargetedExperimentT& selected_transitions,
163  double min_upper_edge_dist)
164  {
165  if (exp.empty() || exp[0].getPrecursors().empty())
166  {
167  std::cerr << "WARNING: File " << exp.getLoadedFilePath()
168  << " does not have any experiments or any precursors. Is it a SWATH map? "
169  << "I will move to the next map."
170  << std::endl;
171  return false;
172  }
173  double upper, lower, center;
174  OpenSwathHelper::checkSwathMap(exp, lower, upper, center);
175  OpenSwathHelper::selectSwathTransitions(targeted_exp, selected_transitions, min_upper_edge_dist, lower, upper);
176  if (selected_transitions.getTransitions().size() == 0)
177  {
178  std::cerr << "WARNING: For File " << exp.getLoadedFilePath()
179  << " no transition were within the precursor window of " << lower << " to " << upper
180  << std::endl;
181  return false;
182  }
183  return true;
184 
185  }
186 
196  static std::pair<double,double> estimateRTRange(const OpenSwath::LightTargetedExperiment & exp);
197 
212  static std::map<std::string, double> simpleFindBestFeature(const OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType & transition_group_map,
213  bool useQualCutoff = false,
214  double qualCutoff = 0.0);
215  };
216 
217 } // namespace OpenMS
218 
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:105
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
bool empty() const
Definition: MSExperiment.h:130
A helper class that is used by several OpenSWATH tools.
Definition: OpenSwathHelper.h:49
static bool checkSwathMapAndSelectTransitions(const OpenMS::PeakMap &exp, const TargetedExperimentT &targeted_exp, TargetedExperimentT &selected_transitions, double min_upper_edge_dist)
Check the map and select transition in one function.
Definition: OpenSwathHelper.h:160
static String computePrecursorId(const String &transition_group_id, int isotope)
Compute unique precursor identifier.
Definition: OpenSwathHelper.h:65
static String computeTransitionGroupId(const String &precursor_id)
Compute transition group id.
Definition: OpenSwathHelper.h:81
static void selectSwathTransitions(const OpenMS::TargetedExperiment &targeted_exp, OpenMS::TargetedExperiment &selected_transitions, double min_upper_edge_dist, double lower, double upper)
Select transitions between lower and upper and write them into the new TargetedExperiment.
static std::map< std::string, double > simpleFindBestFeature(const OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType &transition_group_map, bool useQualCutoff=false, double qualCutoff=0.0)
Returns the feature with the highest score for each transition group.
static void selectSwathTransitions(const OpenSwath::LightTargetedExperiment &targeted_exp, OpenSwath::LightTargetedExperiment &selected_transitions, double min_upper_edge_dist, double lower, double upper)
Select transitions between lower and upper and write them into the new TargetedExperiment.
static std::pair< double, double > estimateRTRange(const OpenSwath::LightTargetedExperiment &exp)
Computes the min and max retention time value.
static void checkSwathMap(const OpenMS::PeakMap &swath_map, double &lower, double &upper, double &center)
Get the lower / upper offset for this SWATH map and do some sanity checks.
A more convenient string class.
Definition: String.h:60
String prefix(SizeType length) const
returns the prefix of length length
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:65
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
const double k
Definition: Constants.h:153
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Definition: TransitionExperiment.h:207