| OpenMS 2.5.0

AppliedProcessingStep.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/METADATA/ID/DataProcessingStep.h>
38 #include <OpenMS/METADATA/ID/ScoreType.h>
39
40 #include <boost/range/adaptor/reversed.hpp>
41 #include <boost/multi_index_container.hpp>
42 #include <boost/multi_index/member.hpp>
43 #include <boost/multi_index/ordered_index.hpp>
44 #include <boost/multi_index/sequenced_index.hpp>
45
46 namespace OpenMS
47 {
48 namespace IdentificationDataInternal
49 {
52 struct AppliedProcessingStep
53 {
54 // if there are only scores, the processing step may be missing:
55 boost::optional<ProcessingStepRef> processing_step_opt;
56 std::map<ScoreTypeRef, double> scores;
57
58 explicit AppliedProcessingStep(
59 const boost::optional<ProcessingStepRef>& processing_step_opt =
60 boost::none, const std::map<ScoreTypeRef, double>& scores =
61 std::map<ScoreTypeRef, double>()):
62 processing_step_opt(processing_step_opt), scores(scores)
63 {
64 }
65
66 bool operator==(const AppliedProcessingStep& other) const
67 {
68 return ((processing_step_opt == other.processing_step_opt) &&
69 (scores == other.scores));
70 }
71
77 std::vector<std::pair<ScoreTypeRef, double>> getScoresInOrder() const
78 {
79 std::vector<std::pair<ScoreTypeRef, double>> result;
80 std::set<ScoreTypeRef> scores_done;
81
82 if (processing_step_opt)
83 {
84 ProcessingSoftwareRef sw_ref = (*processing_step_opt)->software_ref;
85 for (ScoreTypeRef score_ref : sw_ref->assigned_scores)
86 {
87 auto pos = scores.find(score_ref);
88 if (pos != scores.end())
89 {
90 result.push_back(*pos);
91 scores_done.insert(score_ref);
92 }
93 }
94 }
95 for (const auto& pair: scores)
96 {
97 if (!scores_done.count(pair.first))
98 {
99 result.push_back(pair);
100 }
101 }
102 return result;
103 }
104 };
105
106 // we want to keep track of the processing steps in sequence (order of
107 // application), but also ensure there are no duplicate steps:
108 typedef boost::multi_index_container<
109 AppliedProcessingStep,
110 boost::multi_index::indexed_by<
111 boost::multi_index::sequenced<>,
112 boost::multi_index::ordered_unique<
113 boost::multi_index::member<
114 AppliedProcessingStep, boost::optional<ProcessingStepRef>,
115 &AppliedProcessingStep::processing_step_opt>>>
116 > AppliedProcessingSteps;
117
118 }
119 }
DataProcessingStep.h
OpenMS::IdentificationDataInternal::AppliedProcessingStep::AppliedProcessingStep
AppliedProcessingStep(const boost::optional< ProcessingStepRef > &processing_step_opt=boost::none, const std::map< ScoreTypeRef, double > &scores=std::map< ScoreTypeRef, double >())
Definition: AppliedProcessingStep.h:58
ScoreType.h
OpenMS::IdentificationDataInternal::IteratorWrapper< DataProcessingSoftwares::iterator >
OpenMS::IdentificationDataInternal::AppliedProcessingStep::scores
std::map< ScoreTypeRef, double > scores
Definition: AppliedProcessingStep.h:56
OpenMS::IdentificationDataInternal::AppliedProcessingSteps
boost::multi_index_container< AppliedProcessingStep, boost::multi_index::indexed_by< boost::multi_index::sequenced<>, boost::multi_index::ordered_unique< boost::multi_index::member< AppliedProcessingStep, boost::optional< ProcessingStepRef >, &AppliedProcessingStep::processing_step_opt > > > > AppliedProcessingSteps
Definition: AppliedProcessingStep.h:116
OpenMS::IdentificationDataInternal::AppliedProcessingStep::operator==
bool operator==(const AppliedProcessingStep &other) const
Definition: AppliedProcessingStep.h:66
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::IdentificationDataInternal::AppliedProcessingStep::processing_step_opt
boost::optional< ProcessingStepRef > processing_step_opt
Definition: AppliedProcessingStep.h:55
OpenMS::IdentificationDataInternal::AppliedProcessingStep::getScoresInOrder
std::vector< std::pair< ScoreTypeRef, double > > getScoresInOrder() const
Return scores in order of priority (primary first).
Definition: AppliedProcessingStep.h:77
OpenMS::IdentificationDataInternal::AppliedProcessingStep
A processing step that was applied to a data item, possibly with associated scores.
Definition: AppliedProcessingStep.h:52