 |
OpenMS
|
Writer for the consensus-spectrum MGF file consumed by GNPS Feature-Based / Ion-Identity Molecular Networking. More...
#include <OpenMS/FORMAT/GNPSMGFFile.h>
Public Member Functions | |
| GNPSMGFFile () | |
| Default constructor; installs the export parameters (see class docs) | |
| void | store (const std::string &consensus_file_path, const StringList &mzml_file_paths, const std::string &out) const |
| Write the consensus-spectrum MGF for GNPS molecular networking. | |
 Public Member Functions inherited from DefaultParamHandler | |
| DefaultParamHandler (const std::string &name) | |
| Constructor with name that is displayed in error messages. | |
| DefaultParamHandler (const DefaultParamHandler &rhs) | |
| Copy constructor. | |
| virtual | ~DefaultParamHandler () |
| Destructor. | |
| DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| Assignment operator. | |
| virtual bool | operator== (const DefaultParamHandler &rhs) const |
| Equality operator. | |
| void | setParameters (const Param ¶m) |
| Sets the parameters. | |
| const Param & | getParameters () const |
| Non-mutable access to the parameters. | |
| const Param & | getDefaults () const |
| Non-mutable access to the default parameters. | |
| const std::string & | getName () const |
| Non-mutable access to the name. | |
| void | setName (const std::string &name) |
| Mutable access to the name. | |
| const std::vector< std::string > & | getSubsections () const |
| Non-mutable access to the registered subsections. | |
| Public Member Functions inherited from ProgressLogger | |
| ProgressLogger () | |
| Constructor. | |
| virtual | ~ProgressLogger () |
| Destructor. | |
| ProgressLogger (const ProgressLogger &other) | |
| Copy constructor. | |
| ProgressLogger & | operator= (const ProgressLogger &other) |
| Assignment Operator. | |
| void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! | |
| LogType | getLogType () const |
| Returns the type of progress log being used. | |
| void | setLogger (ProgressLoggerImpl *logger) |
| Sets the logger to be used for progress logging. | |
| void | startProgress (SignedSize begin, SignedSize end, const std::string &label) const |
| Initializes the progress display. | |
| void | setProgress (SignedSize value) const |
| Sets the current progress. | |
| void | endProgress (UInt64 bytes_processed=0) const |
| void | nextProgress () const |
| increment progress by 1 (according to range begin-end) | |
Static Private Attributes | |
| static constexpr double | DEF_COSINE_SIMILARITY = 0.9 |
| Default cosine-similarity threshold used when merging multiple MS2 scans into one representative spectrum. | |
| static constexpr double | DEF_MERGE_BIN_SIZE = static_cast<double>(BinnedSpectrum::DEFAULT_BIN_WIDTH_HIRES) |
| Default m/z bin width for the binned-spectrum representation used during merging (high-res default) | |
| static constexpr int | DEF_PEPT_CUTOFF = 5 |
Default value of the peptide_cutoff parameter — how many top-intensity peptides per consensus element to consider when output_type is merged_spectra (-1 = all) | |
| static constexpr int | DEF_MSMAP_CACHE = 50 |
| Declared default but currently not wired to any parameter — kept for source compatibility with earlier versions of the writer. | |
Additional Inherited Members | |
| Public Types inherited from ProgressLogger | |
| enum | LogType { CMD , GUI , NONE } |
| Possible log types. More... | |
| Static Public Member Functions inherited from DefaultParamHandler | |
| static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="") |
| Writes all parameters to meta values. | |
| Protected Member Functions inherited from DefaultParamHandler | |
| virtual void | updateMembers_ () |
| This method is used to update extra member variables at the end of the setParameters() method. | |
| void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. | |
| Protected Attributes inherited from DefaultParamHandler | |
| Param | param_ |
| Container for current parameters. | |
| Param | defaults_ |
| Container for default parameters. This member should be filled in the constructor of derived classes! | |
| std::vector< std::string > | subsections_ |
| Container for registered subsections. This member should be filled in the constructor of derived classes! | |
| std::string | error_name_ |
| Name that is displayed in error messages during the parameter checking. | |
| bool | check_defaults_ |
| If this member is set to false no checking if parameters in done;. | |
| bool | warn_empty_defaults_ |
| If this member is set to false no warning is emitted when defaults are empty;. | |
| Protected Attributes inherited from ProgressLogger | |
| LogType | type_ |
| time_t | last_invoke_ |
| ProgressLoggerImpl * | current_logger_ |
| Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ |
Writer for the consensus-spectrum MGF file consumed by GNPS Feature-Based / Ion-Identity Molecular Networking.
For each consensus feature in a ConsensusMap, the GNPS workflow expects one representative MS2 spectrum. This class reads the spectrum references stored on each consensus element, resolves them to the original mzML files, optionally merges multiple MS2 scans per feature into a single binned consensus spectrum, and writes the result as an MGF file ready to be uploaded to GNPS.
Configurable behaviour is exposed through DefaultParamHandler — see the defaults installed by the constructor for the supported keys (output_type — "most_intense" or "merged_spectra"; peptide_cutoff — how many top-intensity peptides to consider per consensus element; ms2_bin_size — bin width when merging fragment ions; merged_spectra:cos_similarity — cosine threshold for merging).
Used by the GNPSExport tool. See its page for the recommended OpenMS metabolomics workflow producing the consensusXML input.
| GNPSMGFFile | ( | ) |
Default constructor; installs the export parameters (see class docs)
| void store | ( | const std::string & | consensus_file_path, |
| const StringList & | mzml_file_paths, | ||
| const std::string & | out | ||
| ) | const |
Write the consensus-spectrum MGF for GNPS molecular networking.
The consensusXML at consensus_file_path must reference MS2 spectra in mzml_file_paths (typically the same mzMLs that fed the feature finder). Per consensus feature, the referenced MS2 scans are optionally merged into a single representative spectrum (per the cosine-similarity / bin-width / peak-cutoff parameters) and appended to the output MGF.
| [in] | consensus_file_path | Path to a consensusXML file with spectrum references on each consensus element. |
| [in] | mzml_file_paths | Paths to the mzML files referenced by the consensusXML. |
| [in] | out | Output MGF path; one spectrum block per consensus feature. |
Referenced by TOPPGNPSExport::main_().
|
staticconstexprprivate |
Default cosine-similarity threshold used when merging multiple MS2 scans into one representative spectrum.
|
staticconstexprprivate |
Default m/z bin width for the binned-spectrum representation used during merging (high-res default)
|
staticconstexprprivate |
Declared default but currently not wired to any parameter — kept for source compatibility with earlier versions of the writer.
|
staticconstexprprivate |
Default value of the peptide_cutoff parameter — how many top-intensity peptides per consensus element to consider when output_type is merged_spectra (-1 = all)
1.9.8 