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OpenPepXLAlgorithm.h
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1 // --------------------------------------------------------------------------
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: Eugen Netz $
32 // $Authors: Timo Sachsenberg, Eugen Netz $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/ProgressLogger.h>
38 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
39 #include <OpenMS/KERNEL/StandardTypes.h>
40 #include <OpenMS/KERNEL/ConsensusMap.h>
41 #include <OpenMS/FORMAT/FASTAFile.h>
42 #include <OpenMS/ANALYSIS/XLMS/OPXLDataStructs.h>
43
44 namespace OpenMS
45 {
46
47 //-------------------------------------------------------------
48 //Doxygen docu
49 //-------------------------------------------------------------
50
113 class OPENMS_DLLAPI OpenPepXLAlgorithm :
114 public DefaultParamHandler, public ProgressLogger
115 {
116 public:
117
119 enum ExitCodes
120 {
121 EXECUTION_OK,
122 ILLEGAL_PARAMETERS,
123 UNEXPECTED_RESULT,
124 INCOMPATIBLE_INPUT_DATA
125 };
126
128 OpenPepXLAlgorithm();
129
131 ~OpenPepXLAlgorithm() override;
132
145 ExitCodes run(PeakMap& unprocessed_spectra, ConsensusMap& cfeatures, std::vector<FASTAFile::FASTAEntry>& fasta_db, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids, OPXLDataStructs::PreprocessedPairSpectra& preprocessed_pair_spectra, std::vector< std::pair<Size, Size> >& spectrum_pairs, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms, PeakMap& spectra);
146
147 private:
148 void updateMembers_() override;
149
150 static OPXLDataStructs::PreprocessedPairSpectra preprocessPairs_(const PeakMap& spectra, const std::vector< std::pair<Size, Size> >& spectrum_pairs, const double cross_link_mass_iso_shift, double fragment_mass_tolerance, double fragment_mass_tolerance_xlinks, bool fragment_mass_tolerance_unit_ppm, bool deisotope);
151
152 String decoy_string_;
153 bool decoy_prefix_;
154
155 Int min_precursor_charge_;
156 Int max_precursor_charge_;
157 double precursor_mass_tolerance_;
158 bool precursor_mass_tolerance_unit_ppm_;
159 IntList precursor_correction_steps_;
160
161 double fragment_mass_tolerance_;
162 double fragment_mass_tolerance_xlinks_;
163 bool fragment_mass_tolerance_unit_ppm_;
164
165 StringList cross_link_residue1_;
166 StringList cross_link_residue2_;
167 double cross_link_mass_light_;
168 double cross_link_mass_iso_shift_;
169 DoubleList cross_link_mass_mono_link_;
170 String cross_link_name_;
171
172 StringList fixedModNames_;
173 StringList varModNames_;
174 Size max_variable_mods_per_peptide_;
175 Size peptide_min_size_;
176 Size missed_cleavages_;
177 String enzyme_name_;
178
179 Int number_top_hits_;
180 String deisotope_mode_;
181
182 String add_y_ions_;
183 String add_b_ions_;
184 String add_x_ions_;
185 String add_a_ions_;
186 String add_c_ions_;
187 String add_z_ions_;
188 String add_losses_;
189 };
190 }
OpenMS::OpenPepXLAlgorithm::add_a_ions_
String add_a_ions_
Definition: OpenPepXLAlgorithm.h:185
OpenMS::OpenPepXLAlgorithm::missed_cleavages_
Size missed_cleavages_
Definition: OpenPepXLAlgorithm.h:176
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::OpenPepXLAlgorithm::cross_link_name_
String cross_link_name_
Definition: OpenPepXLAlgorithm.h:170
OpenMS::OpenPepXLAlgorithm::ILLEGAL_PARAMETERS
Definition: OpenPepXLAlgorithm.h:122
OpenMS::OpenPepXLAlgorithm::fragment_mass_tolerance_xlinks_
double fragment_mass_tolerance_xlinks_
Definition: OpenPepXLAlgorithm.h:162
OpenMS::OpenPepXLAlgorithm::number_top_hits_
Int number_top_hits_
Definition: OpenPepXLAlgorithm.h:179
OpenMS::OpenPepXLAlgorithm::enzyme_name_
String enzyme_name_
Definition: OpenPepXLAlgorithm.h:177
OpenMS::OpenPepXLAlgorithm::add_y_ions_
String add_y_ions_
Definition: OpenPepXLAlgorithm.h:182
OpenMS::OpenPepXLAlgorithm::add_b_ions_
String add_b_ions_
Definition: OpenPepXLAlgorithm.h:183
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::OpenPepXLAlgorithm::deisotope_mode_
String deisotope_mode_
Definition: OpenPepXLAlgorithm.h:180
OpenMS::OpenPepXLAlgorithm::decoy_string_
String decoy_string_
Definition: OpenPepXLAlgorithm.h:152
OPXLDataStructs.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::OpenPepXLAlgorithm::EXECUTION_OK
Definition: OpenPepXLAlgorithm.h:121
OpenMS::OpenPepXLAlgorithm::add_c_ions_
String add_c_ions_
Definition: OpenPepXLAlgorithm.h:186
StandardTypes.h
OpenMS::OpenPepXLAlgorithm
Search for peptide pairs linked with a labeled cross-linker.
Definition: OpenPepXLAlgorithm.h:113
OpenMS::OpenPepXLAlgorithm::varModNames_
StringList varModNames_
Definition: OpenPepXLAlgorithm.h:173
OpenMS::OpenPepXLAlgorithm::max_variable_mods_per_peptide_
Size max_variable_mods_per_peptide_
Definition: OpenPepXLAlgorithm.h:174
ConsensusMap.h
OpenMS::OpenPepXLAlgorithm::ExitCodes
ExitCodes
Exit codes.
Definition: OpenPepXLAlgorithm.h:119
OpenMS::OpenPepXLAlgorithm::fragment_mass_tolerance_
double fragment_mass_tolerance_
Definition: OpenPepXLAlgorithm.h:161
OpenMS::OpenPepXLAlgorithm::add_x_ions_
String add_x_ions_
Definition: OpenPepXLAlgorithm.h:184
FASTAFile.h
ProgressLogger.h
OpenMS::DoubleList
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
OpenMS::OPXLDataStructs::PreprocessedPairSpectra
The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spe...
Definition: OPXLDataStructs.h:303
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::OpenPepXLAlgorithm::cross_link_mass_light_
double cross_link_mass_light_
Definition: OpenPepXLAlgorithm.h:167
OpenMS::OpenPepXLAlgorithm::precursor_mass_tolerance_
double precursor_mass_tolerance_
Definition: OpenPepXLAlgorithm.h:157
OpenMS::OpenPepXLAlgorithm::cross_link_residue2_
StringList cross_link_residue2_
Definition: OpenPepXLAlgorithm.h:166
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::OpenPepXLAlgorithm::max_precursor_charge_
Int max_precursor_charge_
Definition: OpenPepXLAlgorithm.h:156
OpenMS::OpenPepXLAlgorithm::add_z_ions_
String add_z_ions_
Definition: OpenPepXLAlgorithm.h:187
DefaultParamHandler.h
OpenMS::OpenPepXLAlgorithm::add_losses_
String add_losses_
Definition: OpenPepXLAlgorithm.h:188
OpenMS::OpenPepXLAlgorithm::fragment_mass_tolerance_unit_ppm_
bool fragment_mass_tolerance_unit_ppm_
Definition: OpenPepXLAlgorithm.h:163
OpenMS::OpenPepXLAlgorithm::precursor_correction_steps_
IntList precursor_correction_steps_
Definition: OpenPepXLAlgorithm.h:159
OpenMS::OpenPepXLAlgorithm::peptide_min_size_
Size peptide_min_size_
Definition: OpenPepXLAlgorithm.h:175
OpenMS::OpenPepXLAlgorithm::cross_link_residue1_
StringList cross_link_residue1_
Definition: OpenPepXLAlgorithm.h:165
OpenMS::OpenPepXLAlgorithm::min_precursor_charge_
Int min_precursor_charge_
Definition: OpenPepXLAlgorithm.h:155
OpenMS::OpenPepXLAlgorithm::decoy_prefix_
bool decoy_prefix_
Definition: OpenPepXLAlgorithm.h:153
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
int
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::OpenPepXLAlgorithm::cross_link_mass_mono_link_
DoubleList cross_link_mass_mono_link_
Definition: OpenPepXLAlgorithm.h:169
OpenMS::OpenPepXLAlgorithm::precursor_mass_tolerance_unit_ppm_
bool precursor_mass_tolerance_unit_ppm_
Definition: OpenPepXLAlgorithm.h:158
OpenMS::OpenPepXLAlgorithm::fixedModNames_
StringList fixedModNames_
Definition: OpenPepXLAlgorithm.h:172
OpenMS::OpenPepXLAlgorithm::cross_link_mass_iso_shift_
double cross_link_mass_iso_shift_
Definition: OpenPepXLAlgorithm.h:168
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::OpenPepXLAlgorithm::UNEXPECTED_RESULT
Definition: OpenPepXLAlgorithm.h:123