OpenMS
OpenPepXLAlgorithm.h
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31 // $Maintainer: Eugen Netz $
32 // $Authors: Timo Sachsenberg, Eugen Netz $
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34 
35 #pragma once
36 
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 
120  {
124  INCOMPATIBLE_INPUT_DATA
125  };
126 
129 
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 
154 
160 
164 
171 
178 
181 
189  };
190 }
A container for consensus elements.
Definition: ConsensusMap.h:92
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
Search for peptide pairs linked with a labeled cross-linker.
Definition: OpenPepXLAlgorithm.h:115
Int number_top_hits_
Definition: OpenPepXLAlgorithm.h:179
String add_c_ions_
Definition: OpenPepXLAlgorithm.h:186
bool precursor_mass_tolerance_unit_ppm_
Definition: OpenPepXLAlgorithm.h:158
StringList fixedModNames_
Definition: OpenPepXLAlgorithm.h:172
bool fragment_mass_tolerance_unit_ppm_
Definition: OpenPepXLAlgorithm.h:163
StringList varModNames_
Definition: OpenPepXLAlgorithm.h:173
String add_x_ions_
Definition: OpenPepXLAlgorithm.h:184
double fragment_mass_tolerance_xlinks_
Definition: OpenPepXLAlgorithm.h:162
IntList precursor_correction_steps_
Definition: OpenPepXLAlgorithm.h:159
double cross_link_mass_light_
Definition: OpenPepXLAlgorithm.h:167
Size missed_cleavages_
Definition: OpenPepXLAlgorithm.h:176
OpenPepXLAlgorithm()
Default constructor.
Int max_precursor_charge_
Definition: OpenPepXLAlgorithm.h:156
String decoy_string_
Definition: OpenPepXLAlgorithm.h:152
Size peptide_min_size_
Definition: OpenPepXLAlgorithm.h:175
String add_y_ions_
Definition: OpenPepXLAlgorithm.h:182
double cross_link_mass_iso_shift_
Definition: OpenPepXLAlgorithm.h:168
bool decoy_prefix_
Definition: OpenPepXLAlgorithm.h:153
String add_losses_
Definition: OpenPepXLAlgorithm.h:188
double precursor_mass_tolerance_
Definition: OpenPepXLAlgorithm.h:157
Int min_precursor_charge_
Definition: OpenPepXLAlgorithm.h:155
String enzyme_name_
Definition: OpenPepXLAlgorithm.h:177
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:170
StringList cross_link_residue1_
Definition: OpenPepXLAlgorithm.h:165
String deisotope_mode_
Definition: OpenPepXLAlgorithm.h:180
String add_b_ions_
Definition: OpenPepXLAlgorithm.h:183
DoubleList cross_link_mass_mono_link_
Definition: OpenPepXLAlgorithm.h:169
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:120
@ ILLEGAL_PARAMETERS
Definition: OpenPepXLAlgorithm.h:122
@ EXECUTION_OK
Definition: OpenPepXLAlgorithm.h:121
@ UNEXPECTED_RESULT
Definition: OpenPepXLAlgorithm.h:123
String add_a_ions_
Definition: OpenPepXLAlgorithm.h:185
String add_z_ions_
Definition: OpenPepXLAlgorithm.h:187
double fragment_mass_tolerance_
Definition: OpenPepXLAlgorithm.h:161
Size max_variable_mods_per_peptide_
Definition: OpenPepXLAlgorithm.h:174
StringList cross_link_residue2_
Definition: OpenPepXLAlgorithm.h:166
~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:53
A more convenient string class.
Definition: String.h:60
int Int
Signed integer type.
Definition: Types.h:102
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spe...
Definition: OPXLDataStructs.h:304