OpenMS
MetaboTargetedTargetDecoy.h
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1 // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Oliver Alka $
6 // $Authors: Oliver Alka $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
13 
14 
15 namespace OpenMS
16 {
17 
23  class OPENMS_DLLAPI MetaboTargetedTargetDecoy
24  {
25  public:
31  {
32  public:
33 
37  std::vector<double> target_product_masses;
38  std::vector<double> decoy_product_masses;
39  };
40 
47  static std::vector<MetaboTargetDecoyMassMapping> constructTargetDecoyMassMapping(const TargetedExperiment& t_exp);
48 
58  static void resolveOverlappingTargetDecoyMassesByDecoyMassShift(TargetedExperiment& t_exp, std::vector<MetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping>& mappings, const double& mass_to_add, const double& mz_tol, const String& mz_tol_unit);
59 
68  static void generateMissingDecoysByMassShift(TargetedExperiment& t_exp, std::vector<MetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping>& mappings, const double& mass_to_add);
69 
70  protected:
76  static std::map<String, std::vector<OpenMS::ReactionMonitoringTransition> > constructTransitionsMap_(const TargetedExperiment& t_exp);
77  };
78 
79 } // namespace OpenMS
Resolve overlapping fragments and missing decoys for experimental specific decoy generation in target...
Definition: MetaboTargetedTargetDecoy.h:24
String target_compound_ref
unique identifier (e.g. m_id)
Definition: MetaboTargetedTargetDecoy.h:35
std::vector< double > target_product_masses
identifier which allows to reference back to the decoy (e.g. decoy_transitions_id)
Definition: MetaboTargetedTargetDecoy.h:37
static std::map< String, std::vector< OpenMS::ReactionMonitoringTransition > > constructTransitionsMap_(const TargetedExperiment &t_exp)
Generate a TransitionMap based on Compound_Ref and ReactionMonitoringTransitions.
String decoy_compound_ref
identifier which allows to reference back to the target (e.g. target_transitions_id)
Definition: MetaboTargetedTargetDecoy.h:36
static void resolveOverlappingTargetDecoyMassesByDecoyMassShift(TargetedExperiment &t_exp, std::vector< MetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping > &mappings, const double &mass_to_add, const double &mz_tol, const String &mz_tol_unit)
Resolves overlapping target and decoy transition masses by adding a specifiable mass (e....
static void generateMissingDecoysByMassShift(TargetedExperiment &t_exp, std::vector< MetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping > &mappings, const double &mass_to_add)
Generate a decoy for targets where fragmentation tree re-rooting was not possible,...
std::vector< double > decoy_product_masses
masses of target transitions
Definition: MetaboTargetedTargetDecoy.h:38
String identifier
Definition: MetaboTargetedTargetDecoy.h:34
static std::vector< MetaboTargetDecoyMassMapping > constructTargetDecoyMassMapping(const TargetedExperiment &t_exp)
Constructs a mass mapping of targets and decoys using the unique m_id identifier.
MetaboTargetDecoyMassMapping introduces a mapping of target and decoy masses and their respective com...
Definition: MetaboTargetedTargetDecoy.h:31
A more convenient string class.
Definition: String.h:34
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:39
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19