#include <OpenMS/config.h>
#include <OpenMS/FORMAT/ArrowIOHelpers.h>
#include <OpenMS/METADATA/PeptideHit.h>
#include <map>
#include <set>
#include <memory>
#include <optional>
#include <string>
#include <utility>
#include <vector>

Classes
class	QPXDatasetExport
	The parts of a QPX dataset that a search engine adds to the views of QPXFile. More...

struct	QPXDatasetExport::PeakFilter
	The peak filter of the mz view: the `top` most intense peaks per `window` Th (`top` 0: all peaks), and the annotated ones (keptPeaks()) More...

struct	QPXDatasetExport::MzView

struct	QPXDatasetExport::RunSample
	A sample of a run (the run view's `samples`) More...

struct	QPXDatasetExport::Run
	A run of the dataset (a row of the run view, runView()) More...

struct	QPXDatasetExport::Sample
	A sample of the dataset (a row of the sample view, sampleView()) More...

struct	QPXDatasetExport::ProvenanceStep
	A step of the processing (a row of the provenance view, provenanceView()) More...

struct	QPXDatasetExport::View
	A view of the dataset for writeDataset() More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

Class Documentation

◆ OpenMS::QPXDatasetExport::PeakFilter

struct OpenMS::QPXDatasetExport::PeakFilter

The peak filter of the mz view: the top most intense peaks per window Th (top 0: all peaks), and the annotated ones (keptPeaks())

Class Members
bool	cap_at_precursor = true	The deisotoper capped the fragment charge at the precursor's charge.
bool	deisotoped = false	The fragment annotation is of deisotoped spectra (e.g. ProSE's 'Search:fragment:deisotope' with a high-resolution fragment tolerance): the deisotoper moved each fragment of charge z (up to `max_charge`, or the precursor's charge with `cap_at_precursor`) to its 1+ m/z, which is no peak of the spectrum as the file has it.
int	max_charge = 3	The highest fragment charge of the deisotoper.
Size	top = 100	The most intense peaks kept per window; 0: all peaks.
double	window = 100.0	The width of a window (Th)

◆ OpenMS::QPXDatasetExport::MzView

struct OpenMS::QPXDatasetExport::MzView

The QPX mz view of the spectra of the PSMs of one run (mzView()). It is of that run only: its key id, the native ID, is unique within the run, not across runs (writeDataset() refuses an mz view with an id twice)

Class Members
vector< bool >	has_spectrum	Per element of the peptide identifications whether the view has the row of its spectrum (false for an element without hits, and for all if `table` is null)
Size	peaks_kept = 0	The peaks of the rows (kept by the peak filter)
Size	peaks_read = 0	The peaks of the spectra of the rows.
shared_ptr< Table >	table	The mz view (null if it could not be built; the error is logged)
Size	unresolved = 0	The PSMs whose native ID has the row of a spectrum that is not theirs: several spectra share the native ID (at different RTs), and the row is of another one than the PSM's, or none of them is at the PSM's RT
Size	without_spectrum = 0	The PSMs without a spectrum of their native ID (and RT), whose native ID has no row either.

◆ OpenMS::QPXDatasetExport::RunSample

struct OpenMS::QPXDatasetExport::RunSample

A sample of a run (the run view's samples)

Class Members
string	accession	The sample's `sample_accession` (of the sample view)
optional< Int32 >	biological_replicate	The biological replicate (none: null)
string	label = "LFQ"	The label of the sample in the run ("LFQ" for label-free)
optional< Int32 >	technical_replicate	The technical replicate (none: null)

◆ OpenMS::QPXDatasetExport::Run

struct OpenMS::QPXDatasetExport::Run

A run of the dataset (a row of the run view, runView())

Class Members
string	accession	The `run_accession`.
optional< string >	acquisition_method	The `acquisition_method` (none or "": null)
optional< string >	dissociation_method	The `dissociation_method` (none or "": null)
vector< string >	enzymes	The `enzymes` (empty: null)
string	file_name	The `file_name` (e.g. the base name of the input file; "": null)
vector< string >	fixed_modifications	The fixed modifications of the search, by their OpenMS names (e.g. "Carbamidomethyl (C)")
optional< string >	fraction	The `fraction` (none or "": null)
optional< string >	instrument	The `instrument` (none or "": null)
string	run_file_name	The `run_file_name` (as in the psm and mz views)
vector< RunSample >	samples	The samples of the run.
vector< string >	variable_modifications	The variable modifications of the search, by their OpenMS names (e.g. "Oxidation (M)")

◆ OpenMS::QPXDatasetExport::Sample

struct OpenMS::QPXDatasetExport::Sample

A sample of the dataset (a row of the sample view, sampleView())

Class Members
string	accession	The `sample_accession`.
string	organism = "not available"	The `organism` ("not available", as SDRF has it, if unknown)
string	organism_part = "not available"	The `organism_part` ("not available", as SDRF has it, if unknown)

◆ OpenMS::QPXDatasetExport::ProvenanceStep

struct OpenMS::QPXDatasetExport::ProvenanceStep

A step of the processing (a row of the provenance view, provenanceView())

Class Members
string	category	The `step_category` (e.g. "database_search")
string	config	The `config` (e.g. paramToJSON() of the tool's parameters; "": null)
string	name	The `step_name` (e.g. "peptide_search")
vector< string >	output_views	The `output_views` (e.g. "psm"; empty: null)
vector< pair< string, string > >	parameters	The `parameters`, as key and value, in this order.
string	tool	The `tool_name` (e.g. "ProSE")

◆ OpenMS::QPXDatasetExport::View

struct OpenMS::QPXDatasetExport::View

A view of the dataset for writeDataset()

Class Members
ParquetWriteConfig	config	The writer configuration.
map< string, string >	metadata	Extra keys of the file's footer (ArrowIOHelpers::qpxFileMetadata())
vector< shared_ptr< Table > >	tables	The tables of the view, concatenated (same schema); empty: the view is not written; a null table: the view fails

Classes

Namespaces