| OpenMS 2.5.0

MRMFeatureQC.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Douglas McCloskey $
32 // $Authors: Douglas McCloskey $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/MRMFeature.h>
38 #include <OpenMS/KERNEL/Feature.h>
39 #include <OpenMS/KERNEL/FeatureMap.h>
40 #include <OpenMS/FORMAT/QcMLFile.h>
41
42 #include <OpenMS/DATASTRUCTURES/String.h>
43 #include <OpenMS/CONCEPT/LogStream.h>
44
45 namespace OpenMS
46 {
47
60 class OPENMS_DLLAPI MRMFeatureQC
61 {
62
63 public:
64
66 MRMFeatureQC();
68
70 ~MRMFeatureQC();
72
73 // Members
74 //
81 struct ComponentQCs
82 {
84 String component_name;
85
86 // Feature members
88 double retention_time_l { 0.0 };
90 double retention_time_u { 1e12 };
92 double intensity_l { 0.0 };
94 double intensity_u { 1e12 };
96 double overall_quality_l { 0.0 };
98 double overall_quality_u { 1e12 };
99
101 std::map<String,std::pair<double,double>> meta_value_qc;
102
103 };
104
111 struct ComponentGroupQCs
112 {
114 String component_group_name;
115
117 double retention_time_l { 0.0 };
119 double retention_time_u { 1e12 };
121 double intensity_l { 0.0 };
123 double intensity_u { 1e12 };
125 double overall_quality_l { 0.0 };
127 double overall_quality_u { 1e12 };
128
129 // number of transitions and labels
131 Int n_heavy_l { 0 };
133 Int n_heavy_u { 100 };
134 Int n_light_l { 0 };
135 Int n_light_u { 100 };
136 Int n_detecting_l { 0 };
137 Int n_detecting_u { 100 };
138 Int n_quantifying_l { 0 };
139 Int n_quantifying_u { 100 };
140 Int n_identifying_l { 0 };
141 Int n_identifying_u { 100 };
142 Int n_transitions_l { 0 };
143 Int n_transitions_u { 100 };
144
145 // Ion Ratio QCs
146 String ion_ratio_pair_name_1;
147 String ion_ratio_pair_name_2;
148 double ion_ratio_l { 0.0 };
149 double ion_ratio_u { 1e12 };
150 String ion_ratio_feature_name;
151 std::map<String,std::pair<double,double>> meta_value_qc;
152
153 };
154
162 struct ComponentGroupPairQCs
163 {
164
166 String component_group_name;
168 String resolution_pair_name;
170 double resolution_l;
172 double resolution_u;
174 double rt_diff_l;
176 double rt_diff_u;
177 };
178
179 //members
181 std::vector<ComponentQCs> component_qcs;
183 std::vector<ComponentGroupQCs> component_group_qcs;
185 std::vector<ComponentGroupPairQCs> component_group_pair_qcs;
186 };
187 }
188
189
QcMLFile.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
Feature.h
OpenMS::MRMFeatureQC::ComponentQCs::component_name
String component_name
name of the component
Definition: MRMFeatureQC.h:84
OpenMS::MRMFeatureQC::ComponentGroupPairQCs::resolution_u
double resolution_u
resolution upper bound
Definition: MRMFeatureQC.h:172
OpenMS::MRMFeatureQC::ComponentQCs
Quality Controls (QCs) for individual components.
Definition: MRMFeatureQC.h:81
OpenMS::MRMFeatureQC::component_group_qcs
std::vector< ComponentGroupQCs > component_group_qcs
list of all component group QCs
Definition: MRMFeatureQC.h:183
FeatureMap.h
OpenMS::MRMFeatureQC::ComponentGroupQCs
Quality Controls (QCs) within a component group.
Definition: MRMFeatureQC.h:111
OpenMS::MRMFeatureQC::ComponentGroupPairQCs
Quality Controls (QCs) for multiple components (between or within component_groups) ...
Definition: MRMFeatureQC.h:162
String.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
LogStream.h
OpenMS::MRMFeatureQC::ComponentGroupQCs::component_group_name
String component_group_name
name of the component group
Definition: MRMFeatureQC.h:114
OpenMS::MRMFeatureQC::ComponentGroupPairQCs::rt_diff_l
double rt_diff_l
retention time lower bound
Definition: MRMFeatureQC.h:174
MRMFeature.h
OpenMS::MRMFeatureQC::component_group_pair_qcs
std::vector< ComponentGroupPairQCs > component_group_pair_qcs
list of all component group pair QCs
Definition: MRMFeatureQC.h:185
OpenMS::MRMFeatureQC::component_qcs
std::vector< ComponentQCs > component_qcs
list of all component QCs
Definition: MRMFeatureQC.h:181
int
OpenMS::MRMFeatureQC::ComponentQCs::meta_value_qc
std::map< String, std::pair< double, double > > meta_value_qc
Feature MetaValues.
Definition: MRMFeatureQC.h:101
OpenMS::MRMFeatureQC::ComponentGroupPairQCs::rt_diff_u
double rt_diff_u
retention time upper bound
Definition: MRMFeatureQC.h:176
OpenMS::MRMFeatureQC::ComponentGroupQCs::ion_ratio_pair_name_2
String ion_ratio_pair_name_2
Definition: MRMFeatureQC.h:147
OpenMS::MRMFeatureQC::ComponentGroupQCs::ion_ratio_feature_name
String ion_ratio_feature_name
Definition: MRMFeatureQC.h:150
OpenMS::MRMFeatureQC
The MRMFeatureQC is a class to handle the parameters and options for MRMFeatureFilter.
Definition: MRMFeatureQC.h:60
OpenMS::MRMFeatureQC::ComponentGroupPairQCs::resolution_l
double resolution_l
resolution lower bound
Definition: MRMFeatureQC.h:170
OpenMS::MRMFeatureQC::ComponentGroupPairQCs::resolution_pair_name
String resolution_pair_name
name of the component to calculate the resolution or retention time
Definition: MRMFeatureQC.h:168
OpenMS::MRMFeatureQC::ComponentGroupQCs::ion_ratio_pair_name_1
String ion_ratio_pair_name_1
Definition: MRMFeatureQC.h:146