OpenMS
OpenPepXLAlgorithm.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Eugen Netz $
6 // $Authors: Timo Sachsenberg, Eugen Netz $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
17 
18 namespace OpenMS
19 {
20 
21 //-------------------------------------------------------------
22 //Doxygen docu
23 //-------------------------------------------------------------
24 
87  class OPENMS_DLLAPI OpenPepXLAlgorithm :
88  public DefaultParamHandler, public ProgressLogger
89  {
90 public:
91 
93  enum ExitCodes
94  {
98  INCOMPATIBLE_INPUT_DATA
99  };
100 
103 
106 
120  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);
121 
122 private:
123  void updateMembers_() override;
124 
125  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);
126 
129 
135 
139 
146 
153 
156 
164  };
165 }
A container for consensus elements.
Definition: ConsensusMap.h:66
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:45
Search for peptide pairs linked with a labeled cross-linker.
Definition: OpenPepXLAlgorithm.h:89
Int number_top_hits_
Definition: OpenPepXLAlgorithm.h:154
String add_c_ions_
Definition: OpenPepXLAlgorithm.h:161
bool precursor_mass_tolerance_unit_ppm_
Definition: OpenPepXLAlgorithm.h:133
StringList fixedModNames_
Definition: OpenPepXLAlgorithm.h:147
bool fragment_mass_tolerance_unit_ppm_
Definition: OpenPepXLAlgorithm.h:138
StringList varModNames_
Definition: OpenPepXLAlgorithm.h:148
String add_x_ions_
Definition: OpenPepXLAlgorithm.h:159
double fragment_mass_tolerance_xlinks_
Definition: OpenPepXLAlgorithm.h:137
IntList precursor_correction_steps_
Definition: OpenPepXLAlgorithm.h:134
double cross_link_mass_light_
Definition: OpenPepXLAlgorithm.h:142
Size missed_cleavages_
Definition: OpenPepXLAlgorithm.h:151
OpenPepXLAlgorithm()
Default constructor.
Int max_precursor_charge_
Definition: OpenPepXLAlgorithm.h:131
String decoy_string_
Definition: OpenPepXLAlgorithm.h:127
Size peptide_min_size_
Definition: OpenPepXLAlgorithm.h:150
String add_y_ions_
Definition: OpenPepXLAlgorithm.h:157
double cross_link_mass_iso_shift_
Definition: OpenPepXLAlgorithm.h:143
bool decoy_prefix_
Definition: OpenPepXLAlgorithm.h:128
String add_losses_
Definition: OpenPepXLAlgorithm.h:163
double precursor_mass_tolerance_
Definition: OpenPepXLAlgorithm.h:132
Int min_precursor_charge_
Definition: OpenPepXLAlgorithm.h:130
String enzyme_name_
Definition: OpenPepXLAlgorithm.h:152
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)
Performs the main function of this class, the search for cross-linked peptides.
String cross_link_name_
Definition: OpenPepXLAlgorithm.h:145
StringList cross_link_residue1_
Definition: OpenPepXLAlgorithm.h:140
String deisotope_mode_
Definition: OpenPepXLAlgorithm.h:155
String add_b_ions_
Definition: OpenPepXLAlgorithm.h:158
DoubleList cross_link_mass_mono_link_
Definition: OpenPepXLAlgorithm.h:144
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
ExitCodes
Exit codes.
Definition: OpenPepXLAlgorithm.h:94
@ ILLEGAL_PARAMETERS
Definition: OpenPepXLAlgorithm.h:96
@ EXECUTION_OK
Definition: OpenPepXLAlgorithm.h:95
@ UNEXPECTED_RESULT
Definition: OpenPepXLAlgorithm.h:97
String add_a_ions_
Definition: OpenPepXLAlgorithm.h:160
String add_z_ions_
Definition: OpenPepXLAlgorithm.h:162
double fragment_mass_tolerance_
Definition: OpenPepXLAlgorithm.h:136
Size max_variable_mods_per_peptide_
Definition: OpenPepXLAlgorithm.h:149
StringList cross_link_residue2_
Definition: OpenPepXLAlgorithm.h:141
~OpenPepXLAlgorithm() override
Default destructor.
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)
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:27
A more convenient string class.
Definition: String.h:34
int Int
Signed integer type.
Definition: Types.h:72
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:29
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:44
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:36
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spe...
Definition: OPXLDataStructs.h:278