| OpenMS 2.5.0

OpenSwathHelper.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/KERNEL/MSExperiment.h>
39 #include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
40 #include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
41 #include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
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
123 static void selectSwathTransitions(const OpenSwath::LightTargetedExperiment& targeted_exp,
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>
160 static bool checkSwathMapAndSelectTransitions(const OpenMS::PeakMap& exp,
161 const TargetedExperimentT& targeted_exp,
162 TargetedExperimentT& selected_transitions,
163 double min_upper_edge_dist)
164 {
165 if (exp.size() == 0 || exp[0].getPrecursors().size() == 0)
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
OpenMS::DocumentIdentifier::getLoadedFilePath
const String & getLoadedFilePath() const
get the file_name_ which is the absolute path to the file loaded from
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::OpenSwathHelper
A helper class that is used by several OpenSWATH tools.
Definition: OpenSwathHelper.h:48
OpenMS::Constants::k
const double k
TargetedExperiment.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
StandardTypes.h
MRMFeatureFinderScoring.h
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::OpenSwathHelper::computeTransitionGroupId
static String computeTransitionGroupId(const String &precursor_id)
Compute transition group id.
Definition: OpenSwathHelper.h:81
OpenMS::OpenSwathHelper::computePrecursorId
static String computePrecursorId(const String &transition_group_id, int isotope)
Compute unique precursor identifier.
Definition: OpenSwathHelper.h:65
MSExperiment.h
OpenSwath::LightTargetedExperiment
Definition: TransitionExperiment.h:207
OpenMS::String::prefix
String prefix(SizeType length) const
returns the prefix of length length
OpenMS::OpenSwathHelper::checkSwathMapAndSelectTransitions
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
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:127
OpenMS::String::split
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:109
TransitionExperiment.h
OpenMS::OpenSwathHelper::checkSwathMap
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.
OpenMS::OpenSwathHelper::selectSwathTransitions
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.
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127