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OpenMS
2.5.0
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116 INCOMPATIBLE_INPUT_DATA
137 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);
140 void updateMembers_()
override;
String add_y_ions_
Definition: OpenPepXLLFAlgorithm.h:173
DoubleList cross_link_mass_mono_link_
Definition: OpenPepXLLFAlgorithm.h:158
double fragment_mass_tolerance_
Definition: OpenPepXLLFAlgorithm.h:151
void registerOptionsAndFlags_() override
Sets the valid command line options (with argument) and flags (without argument).
Definition: OpenPepXLLF.cpp:135
Base class for TOPP applications.
Definition: TOPPBase.h:144
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a MzIdentML file.
bool use_sequence_tags_
Definition: OpenPepXLLFAlgorithm.h:170
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
String deisotope_mode_
Definition: OpenPepXLLFAlgorithm.h:169
double fragment_mass_tolerance_xlinks_
Definition: OpenPepXLLFAlgorithm.h:152
String add_z_ions_
Definition: OpenPepXLLFAlgorithm.h:178
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
IntList precursor_correction_steps_
Definition: OpenPepXLLFAlgorithm.h:149
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
Definition: OpenPepXLLFAlgorithm.h:105
File adapter for MzML files.
Definition: MzMLFile.h:55
String add_x_ions_
Definition: OpenPepXLLFAlgorithm.h:175
A more convenient string class.
Definition: String.h:58
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
void addMSLevel(int level)
adds a desired MS level for peaks to load
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Size sequence_tag_min_length_
Definition: OpenPepXLLFAlgorithm.h:171
StringList cross_link_residue1_
Definition: OpenPepXLLFAlgorithm.h:155
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
TOPPOpenPepXLLF()
Definition: OpenPepXLLF.cpp:129
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
Int number_top_hits_
Definition: OpenPepXLLFAlgorithm.h:168
bool precursor_mass_tolerance_unit_ppm_
Definition: OpenPepXLLFAlgorithm.h:148
String add_b_ions_
Definition: OpenPepXLLFAlgorithm.h:174
int main(int argc, const char **argv)
Definition: OpenPepXLLF.cpp:291
void endProgress() const
Ends the progress display.
String add_losses_
Definition: OpenPepXLLFAlgorithm.h:179
String decoy_string_
Definition: OpenPepXLLFAlgorithm.h:142
String cross_link_name_
Definition: OpenPepXLLFAlgorithm.h:159
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
String enzyme_name_
Definition: OpenPepXLLFAlgorithm.h:166
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.
bool decoy_prefix_
Definition: OpenPepXLLFAlgorithm.h:143
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Used to load and store xQuest result files.
Definition: XQuestResultXMLFile.h:55
Definition: OpenPepXLLFAlgorithm.h:114
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
StringList fixedModNames_
Definition: OpenPepXLLFAlgorithm.h:161
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
String db
The used database.
Definition: ProteinIdentification.h:224
double cross_link_mass_
Definition: OpenPepXLLFAlgorithm.h:157
String add_a_ions_
Definition: OpenPepXLLFAlgorithm.h:176
StringList cross_link_residue2_
Definition: OpenPepXLLFAlgorithm.h:156
String add_c_ions_
Definition: OpenPepXLLFAlgorithm.h:177
void setParameters(const Param ¶m)
Sets the parameters.
Int min_precursor_charge_
Definition: OpenPepXLLFAlgorithm.h:145
Definition: OpenPepXLLFAlgorithm.h:113
const Param & getParameters() const
Non-mutable access to the parameters.
A container for consensus elements.
Definition: ConsensusMap.h:79
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
ExitCodes main_(int, const char **) override
The actual "main" method. main_() is invoked by main().
Definition: OpenPepXLLF.cpp:163
bool update(const Param &p_outdated, const bool add_unknown=false)
Rescue parameter values from p_outdated to current param.
Size peptide_min_size_
Definition: OpenPepXLLFAlgorithm.h:164
Logger::LogStream OpenMS_Log_debug
Global static instance of a LogStream to capture messages classified as debug output....
Size max_variable_mods_per_peptide_
Definition: OpenPepXLLFAlgorithm.h:163
static void load(const String &filename, std::vector< FASTAEntry > &data)
loads a FASTA file given by 'filename' and stores the information in 'data'
Definition: OpenPepXLLF.cpp:125
double precursor_mass_tolerance_
Definition: OpenPepXLLFAlgorithm.h:147
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
ExitCodes
Exit codes.
Definition: TOPPBase.h:149
void clearMSLevels()
clears the MS levels
Management and storage of parameters / INI files.
Definition: Param.h:73
bool fragment_mass_tolerance_unit_ppm_
Definition: OpenPepXLLFAlgorithm.h:153
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a xQuest XML file.
Search parameters of the DB search.
Definition: ProteinIdentification.h:221
ExitCodes main(int argc, const char **argv)
Main routine of all TOPP applications.
Int max_precursor_charge_
Definition: OpenPepXLLFAlgorithm.h:146
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
Size missed_cleavages_
Definition: OpenPepXLLFAlgorithm.h:165
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
Used to load and store idXML files.
Definition: IdXMLFile.h:63
Definition: OpenPepXLLFAlgorithm.h:115
ExitCodes
Exit codes.
Definition: OpenPepXLLFAlgorithm.h:111
StringList varModNames_
Definition: OpenPepXLLFAlgorithm.h:162