OpenMS  2.8.0
OpenPepXLLFAlgorithm.h
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35 
36 #pragma once
37 
43 
44 namespace OpenMS
45 {
46 
47  //-------------------------------------------------------------
48  //Doxygen docu
49  //-------------------------------------------------------------
50 
103  class OPENMS_DLLAPI OpenPepXLLFAlgorithm :
104  public DefaultParamHandler, public ProgressLogger
105  {
106 public:
107 
110  {
114  INCOMPATIBLE_INPUT_DATA
115  };
116 
119 
122 
135  ExitCodes run(PeakMap& unprocessed_spectra, std::vector<FASTAFile::FASTAEntry>& fasta_db, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms, PeakMap& spectra);
136 
137 private:
138  void updateMembers_() override;
139 
142 
148 
152 
158 
165 
170 
178  };
179 }
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:93
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
Search for cross-linked peptide pairs in tandem MS spectra.
Definition: OpenPepXLLFAlgorithm.h:105
ExitCodes run(PeakMap &unprocessed_spectra, std::vector< FASTAFile::FASTAEntry > &fasta_db, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, PeakMap &spectra)
Performs the main function of this class, the search for cross-linked peptides.
Int number_top_hits_
Definition: OpenPepXLLFAlgorithm.h:166
String add_c_ions_
Definition: OpenPepXLLFAlgorithm.h:175
bool precursor_mass_tolerance_unit_ppm_
Definition: OpenPepXLLFAlgorithm.h:146
StringList fixedModNames_
Definition: OpenPepXLLFAlgorithm.h:159
bool fragment_mass_tolerance_unit_ppm_
Definition: OpenPepXLLFAlgorithm.h:151
Size sequence_tag_min_length_
Definition: OpenPepXLLFAlgorithm.h:169
StringList varModNames_
Definition: OpenPepXLLFAlgorithm.h:160
String add_x_ions_
Definition: OpenPepXLLFAlgorithm.h:173
double fragment_mass_tolerance_xlinks_
Definition: OpenPepXLLFAlgorithm.h:150
IntList precursor_correction_steps_
Definition: OpenPepXLLFAlgorithm.h:147
Size missed_cleavages_
Definition: OpenPepXLLFAlgorithm.h:163
Int max_precursor_charge_
Definition: OpenPepXLLFAlgorithm.h:144
double cross_link_mass_
Definition: OpenPepXLLFAlgorithm.h:155
String decoy_string_
Definition: OpenPepXLLFAlgorithm.h:140
Size peptide_min_size_
Definition: OpenPepXLLFAlgorithm.h:162
bool use_sequence_tags_
Definition: OpenPepXLLFAlgorithm.h:168
String add_y_ions_
Definition: OpenPepXLLFAlgorithm.h:171
bool decoy_prefix_
Definition: OpenPepXLLFAlgorithm.h:141
String add_losses_
Definition: OpenPepXLLFAlgorithm.h:177
double precursor_mass_tolerance_
Definition: OpenPepXLLFAlgorithm.h:145
Int min_precursor_charge_
Definition: OpenPepXLLFAlgorithm.h:143
String enzyme_name_
Definition: OpenPepXLLFAlgorithm.h:164
String cross_link_name_
Definition: OpenPepXLLFAlgorithm.h:157
StringList cross_link_residue1_
Definition: OpenPepXLLFAlgorithm.h:153
String deisotope_mode_
Definition: OpenPepXLLFAlgorithm.h:167
String add_b_ions_
Definition: OpenPepXLLFAlgorithm.h:172
DoubleList cross_link_mass_mono_link_
Definition: OpenPepXLLFAlgorithm.h:156
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
OpenPepXLLFAlgorithm()
Default constructor.
ExitCodes
Exit codes.
Definition: OpenPepXLLFAlgorithm.h:110
@ ILLEGAL_PARAMETERS
Definition: OpenPepXLLFAlgorithm.h:112
@ EXECUTION_OK
Definition: OpenPepXLLFAlgorithm.h:111
@ UNEXPECTED_RESULT
Definition: OpenPepXLLFAlgorithm.h:113
String add_a_ions_
Definition: OpenPepXLLFAlgorithm.h:174
String add_z_ions_
Definition: OpenPepXLLFAlgorithm.h:176
double fragment_mass_tolerance_
Definition: OpenPepXLLFAlgorithm.h:149
Size max_variable_mods_per_peptide_
Definition: OpenPepXLLFAlgorithm.h:161
StringList cross_link_residue2_
Definition: OpenPepXLLFAlgorithm.h:154
~OpenPepXLLFAlgorithm() override
Default destructor.
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:47