| OpenMS 2.5.0

PercolatorFeatureSetHelper.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Mathias Walzer $
32 // $Authors: Mathias Walzer, Matthew The $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <vector>
38 #include <iostream>
39 #include <cmath>
40 #include <string>
41 #include <map>
42 #include <algorithm>
43 #include <limits>
44
45 #include <OpenMS/CONCEPT/Types.h>
46 #include <OpenMS/KERNEL/StandardTypes.h>
47 #include <OpenMS/FORMAT/FileHandler.h>
48 #include <OpenMS/DATASTRUCTURES/DataValue.h>
49 #include <OpenMS/METADATA/PeptideIdentification.h>
50 #include <OpenMS/METADATA/ProteinIdentification.h>
51 #include <OpenMS/CONCEPT/LogStream.h>
52
53 #include <boost/lexical_cast.hpp>
54
55 namespace OpenMS
56 {
67 class OPENMS_DLLAPI PercolatorFeatureSetHelper
68 {
69
70 public:
79 static void concatMULTISEPeptideIds(std::vector<PeptideIdentification>& all_peptide_ids, std::vector<PeptideIdentification>& new_peptide_ids, String search_engine);
80
89 static void mergeMULTISEPeptideIds(std::vector<PeptideIdentification>& all_peptide_ids, std::vector<PeptideIdentification>& new_peptide_ids, String search_engine);
90
98 static void mergeMULTISEProteinIds(std::vector<ProteinIdentification>& all_protein_ids, std::vector<ProteinIdentification>& new_protein_ids);
99
100
108 static void addMSGFFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& feature_set);
109
117 static void addXTANDEMFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& feature_set);
118
126 static void addCOMETFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& feature_set);
127
135 static void addMASCOTFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& feature_set);
136
147 static void addMULTISEFeatures(std::vector<PeptideIdentification>& peptide_ids, StringList& search_engines_used, StringList& feature_set, bool complete_only = true, bool limits_imputation = false);
148
157 static void addCONCATSEFeatures(std::vector<PeptideIdentification>& peptide_id_list, StringList& search_engines_used, StringList& feature_set);
158
166 static void checkExtraFeatures(const std::vector<PeptideHit> &psms, StringList& extra_features);
167
168
169 protected:
171 static double rescaleFragmentFeature_(double featureValue, int NumMatchedMainIons);
172
174 static void assignDeltaScore_(std::vector<PeptideHit>& hits, String score_ref, String output_ref);
175
177 static String getScanMergeKey_(std::vector<PeptideIdentification>::iterator it, std::vector<PeptideIdentification>::iterator start);
178
180 struct lq_ProteinHit
181 {
182 inline bool operator() (const ProteinHit& h1, const ProteinHit& h2)
183 {
184 return (h1.getAccession() < h2.getAccession());
185 }
186 };
187
189 struct lq_PeptideEvidence
190 {
191 inline bool operator() (const PeptideEvidence& h1, const PeptideEvidence& h2)
192 {
193 return (h1.getProteinAccession() < h2.getProteinAccession());
194 }
195 };
196
197 };
198
199 } //namespace OpenMS
200
201
ProteinIdentification.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ProteinHit::getAccession
const String & getAccession() const
returns the accession of the protein
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:57
StandardTypes.h
OpenMS::PeptideEvidence
Representation of a peptide evidence.
Definition: PeptideEvidence.h:50
Types.h
OpenMS::PercolatorFeatureSetHelper
Percolator feature set and integration helper.
Definition: PercolatorFeatureSetHelper.h:67
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::PercolatorFeatureSetHelper::lq_PeptideEvidence
For accession dependent sorting of PeptideEvidences.
Definition: PercolatorFeatureSetHelper.h:189
LogStream.h
FileHandler.h
OpenMS::PercolatorFeatureSetHelper::lq_ProteinHit
For accession dependent sorting of ProteinHits.
Definition: PercolatorFeatureSetHelper.h:180
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
DataValue.h
OpenMS::PeptideEvidence::getProteinAccession
const String & getProteinAccession() const
get the protein accession the peptide matches to. If not available the empty string is returned...