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OpenMS
2.5.0
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126 INCOMPATIBLE_INPUT_DATA
147 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);
150 void updateMembers_()
override;
152 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);
Definition: OpenPepXLAlgorithm.h:123
double fragment_mass_tolerance_
Definition: OpenPepXLAlgorithm.h:163
Definition: OpenMSInfo.cpp:68
int main(int argc, const char **argv)
Definition: OpenPepXL.cpp:297
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.
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.
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
void registerOptionsAndFlags_() override
Sets the valid command line options (with argument) and flags (without argument).
Definition: OpenPepXL.cpp:141
String getOSAsString() const
Definition: OpenMSInfo.cpp:80
String enzyme_name_
Definition: OpenPepXLAlgorithm.h:179
double cross_link_mass_iso_shift_
Definition: OpenPepXLAlgorithm.h:170
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.
String add_y_ions_
Definition: OpenPepXLAlgorithm.h:184
String add_b_ions_
Definition: OpenPepXLAlgorithm.h:185
StringList varModNames_
Definition: OpenPepXLAlgorithm.h:175
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
static String getTime()
Return the build time of OpenMS.
String deisotope_mode_
Definition: OpenPepXLAlgorithm.h:182
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:58
StringList cross_link_residue2_
Definition: OpenPepXLAlgorithm.h:168
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
Definition: OpenMSInfo.cpp:58
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
Definition: OpenPepXLAlgorithm.h:125
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
bool precursor_mass_tolerance_unit_ppm_
Definition: OpenPepXLAlgorithm.h:160
String add_losses_
Definition: OpenPepXLAlgorithm.h:190
double fragment_mass_tolerance_xlinks_
Definition: OpenPepXLAlgorithm.h:164
Definition: OpenPepXLAlgorithm.h:124
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
Size peptide_min_size_
Definition: OpenPepXLAlgorithm.h:177
Definition: OpenMSInfo.cpp:60
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
Definition: OpenMSInfo.cpp:58
String add_c_ions_
Definition: OpenPepXLAlgorithm.h:188
std::string OpenMS_OSNames[]
Definition: OpenMSInfo.cpp:59
StringList fixedModNames_
Definition: OpenPepXLAlgorithm.h:174
StringList cross_link_residue1_
Definition: OpenPepXLAlgorithm.h:167
void endProgress() const
Ends the progress display.
static OpenMSOSInfo getOSInfo()
Definition: OpenMSInfo.cpp:92
double cross_link_mass_light_
Definition: OpenPepXLAlgorithm.h:169
bool decoy_prefix_
Definition: OpenPepXLAlgorithm.h:155
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
TOPPOpenPepXL()
Definition: OpenPepXL.cpp:135
Size max_variable_mods_per_peptide_
Definition: OpenPepXLAlgorithm.h:176
The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spe...
Definition: OPXLDataStructs.h:303
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
DoubleList cross_link_mass_mono_link_
Definition: OpenPepXLAlgorithm.h:171
Used to load and store xQuest result files.
Definition: XQuestResultXMLFile.h:55
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
Definition: OpenMSInfo.cpp:60
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
Definition: OpenMSInfo.cpp:58
Definition: OpenMSInfo.cpp:60
String cross_link_name_
Definition: OpenPepXLAlgorithm.h:172
String add_z_ions_
Definition: OpenPepXLAlgorithm.h:189
void setParameters(const Param ¶m)
Sets the parameters.
Definition: OpenMSInfo.cpp:58
OpenMS_Architecture arch
Definition: OpenMSInfo.cpp:78
std::string OpenMS_ArchNames[]
Definition: OpenMSInfo.cpp:61
static String getVersion()
Return the version number of OpenMS.
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
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
String add_a_ions_
Definition: OpenPepXLAlgorithm.h:187
static String getRevision()
Return the revision number from revision control system, e.g. git.
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
static String getUserDirectory()
Definition: OpenPepXLAlgorithm.h:115
bool update(const Param &p_outdated, const bool add_unknown=false)
Rescue parameter values from p_outdated to current param.
Definition: OpenPepXL.cpp:131
Logger::LogStream OpenMS_Log_debug
Global static instance of a LogStream to capture messages classified as debug output....
static void load(const String &filename, std::vector< FASTAEntry > &data)
loads a FASTA file given by 'filename' and stores the information in 'data'
Int min_precursor_charge_
Definition: OpenPepXLAlgorithm.h:157
static String getOpenMSDataPath()
Returns the OpenMS data path (environment variable overwrites the default installation path)
String os_version
Definition: OpenMSInfo.cpp:77
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
ExitCodes
Exit codes.
Definition: TOPPBase.h:149
Size missed_cleavages_
Definition: OpenPepXLAlgorithm.h:178
void clearMSLevels()
clears the MS levels
Management and storage of parameters / INI files.
Definition: Param.h:73
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
ExitCodes
Exit codes.
Definition: OpenPepXLAlgorithm.h:121
static String getBranch()
Return the branch name from revision control system, e.g. git.
String add_x_ions_
Definition: OpenPepXLAlgorithm.h:186
OpenMS_Architecture
Definition: OpenMSInfo.cpp:60
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS_OS
Definition: OpenMSInfo.cpp:58
OpenMSOSInfo()
Definition: OpenMSInfo.cpp:70
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a xQuest XML file.
IntList precursor_correction_steps_
Definition: OpenPepXLAlgorithm.h:161
ExitCodes main_(int, const char **) override
The actual "main" method. main_() is invoked by main().
Definition: OpenPepXL.cpp:172
Search parameters of the DB search.
Definition: ProteinIdentification.h:221
String getArchAsString() const
Definition: OpenMSInfo.cpp:85
ExitCodes main(int argc, const char **argv)
Main routine of all TOPP applications.
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!
double precursor_mass_tolerance_
Definition: OpenPepXLAlgorithm.h:159
OpenMS_OS os
Definition: OpenMSInfo.cpp:76
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
OpenMS_Architecture getBinaryArchitecture()
Definition: OpenMSInfo.cpp:191
Int max_precursor_charge_
Definition: OpenPepXLAlgorithm.h:158
String decoy_string_
Definition: OpenPepXLAlgorithm.h:154
bool fragment_mass_tolerance_unit_ppm_
Definition: OpenPepXLAlgorithm.h:165
Int number_top_hits_
Definition: OpenPepXLAlgorithm.h:181