| OpenMS 2.5.0

IncludeExcludeTarget.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/METADATA/CVTermList.h>
39 #include <OpenMS/ANALYSIS/TARGETED/TargetedExperimentHelper.h>
40
41 #include <vector>
42
43 namespace OpenMS
44 {
52 class OPENMS_DLLAPI IncludeExcludeTarget :
53 public CVTermList
54 {
55
56 public:
57
58 typedef TargetedExperimentHelper::Configuration Configuration;
59 typedef TargetedExperimentHelper::RetentionTime RetentionTime;
60
64 IncludeExcludeTarget();
66
68 IncludeExcludeTarget(const IncludeExcludeTarget & rhs);
69
71 ~IncludeExcludeTarget() override;
73
75 IncludeExcludeTarget & operator=(const IncludeExcludeTarget & rhs);
76
80 void setName(const String & name);
81
82 const String & getName() const;
83
84 void setPeptideRef(const String & peptide_ref);
85
86 const String & getPeptideRef() const;
87
88 void setCompoundRef(const String & compound_ref);
89
90 const String & getCompoundRef() const;
91
93 void setPrecursorMZ(double mz);
94
95 double getPrecursorMZ() const;
96
97 void setPrecursorCVTermList(const CVTermList & list);
98
99 void addPrecursorCVTerm(const CVTerm & cv_term);
100
101 const CVTermList & getPrecursorCVTermList() const;
102
103 void setProductMZ(double mz);
104
105 double getProductMZ() const;
106
107 void setProductCVTermList(const CVTermList & list);
108
109 void addProductCVTerm(const CVTerm & cv_term);
110
111 const CVTermList & getProductCVTermList() const;
112
113 void setInterpretations(const std::vector<CVTermList> & interpretations);
114
115 const std::vector<CVTermList> & getInterpretations() const;
116
117 void addInterpretation(const CVTermList & interpretation);
118
119 void setConfigurations(const std::vector<Configuration> & configuration);
120
121 const std::vector<Configuration> & getConfigurations() const;
122
123 void addConfiguration(const Configuration & configuration);
124
125 void setPrediction(const CVTermList & prediction);
126
127 void addPredictionTerm(const CVTerm & prediction);
128
129 const CVTermList & getPrediction() const;
130
131 void setRetentionTime(RetentionTime rt);
132
133 const RetentionTime & getRetentionTime() const;
135
139 bool operator==(const IncludeExcludeTarget & rhs) const;
141
143 bool operator!=(const IncludeExcludeTarget & rhs) const;
145
146 protected:
147
148 void updateMembers_();
149
150 String name_;
151
152 double precursor_mz_;
153
154 CVTermList precursor_cv_terms_;
155
156 double product_mz_;
157
158 CVTermList product_cv_terms_;
159
160 std::vector<CVTermList> interpretation_list_;
161
162 String peptide_ref_;
163
164 String compound_ref_;
165
166 std::vector<Configuration> configurations_;
167
168 CVTermList prediction_;
169
170 RetentionTime rts_;
171
172 };
173 }
174
OpenMS::IncludeExcludeTarget::configurations_
std::vector< Configuration > configurations_
Definition: IncludeExcludeTarget.h:166
OpenMS::CVTermList
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::IncludeExcludeTarget::interpretation_list_
std::vector< CVTermList > interpretation_list_
Definition: IncludeExcludeTarget.h:160
OpenMS::IncludeExcludeTarget::RetentionTime
TargetedExperimentHelper::RetentionTime RetentionTime
Definition: IncludeExcludeTarget.h:59
OpenMS::IncludeExcludeTarget::rts_
RetentionTime rts_
Definition: IncludeExcludeTarget.h:170
OpenMS::IncludeExcludeTarget::Configuration
TargetedExperimentHelper::Configuration Configuration
Definition: IncludeExcludeTarget.h:58
OpenMS::IncludeExcludeTarget::peptide_ref_
String peptide_ref_
Definition: IncludeExcludeTarget.h:162
OpenMS::TargetedExperimentHelper::RetentionTime
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:127
OpenMS::IncludeExcludeTarget::product_mz_
double product_mz_
Definition: IncludeExcludeTarget.h:156
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
StandardTypes.h
OpenMS::TargetedExperimentHelper::Configuration
Definition: TargetedExperimentHelper.h:64
OpenMS::CVTerm
Representation of controlled vocabulary term.
Definition: CVTerm.h:52
OpenMS::IncludeExcludeTarget::compound_ref_
String compound_ref_
Definition: IncludeExcludeTarget.h:164
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::IncludeExcludeTarget::product_cv_terms_
CVTermList product_cv_terms_
Definition: IncludeExcludeTarget.h:158
CVTermList.h
OpenMS::IncludeExcludeTarget::precursor_mz_
double precursor_mz_
Definition: IncludeExcludeTarget.h:152
OpenMS::IncludeExcludeTarget
This class stores a SRM/MRM transition.
Definition: IncludeExcludeTarget.h:52
OpenMS::IncludeExcludeTarget::precursor_cv_terms_
CVTermList precursor_cv_terms_
Definition: IncludeExcludeTarget.h:154
OpenMS::IncludeExcludeTarget::prediction_
CVTermList prediction_
Definition: IncludeExcludeTarget.h:168
OpenMS::IncludeExcludeTarget::name_
String name_
Definition: IncludeExcludeTarget.h:150
TargetedExperimentHelper.h
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806