QPXPgSchema Struct Reference

Schema for QPX protein group export (quantms Parquet eXchange format, pg table) More...

#include <OpenMS/FORMAT/ArrowSchemaRegistry.h>

Static Public Member Functions
static std::shared_ptr< arrow::DataType >	groupedRunsType ()
	Arrow type for grouped_runs: list<utf8> — the raw files of one quantification unit.
static std::shared_ptr< arrow::DataType >	additionalIntensitiesType ()
	Arrow type for additional intensities: list<struct{label, intensities: list<struct{...}>}>
static std::shared_ptr< arrow::DataType >	peptidesType ()
	Arrow type for peptides: list<struct{protein_name, peptide_count}>
static std::shared_ptr< arrow::DataType >	peptideCountsType ()
	Arrow type for peptide_counts: struct{unique_sequences, total_sequences}.
static std::shared_ptr< arrow::DataType >	featureCountsType ()
	Arrow type for feature_counts: struct{unique_features, total_features}.
static std::shared_ptr< arrow::DataType >	additionalScoresType ()
	Arrow type for additional scores (delegates to QPXPSMSchema::additionalScoresType)
static std::shared_ptr< arrow::DataType >	cvParamsType ()
	Arrow type for CV params (delegates to QPXPSMSchema::cvParamsType)
static std::shared_ptr< arrow::Schema >	schema ()
	Complete Arrow schema for QPX pg table (22 fields)

Static Public Attributes
static constexpr const char *	PG_ID = "pg_id"
	Mandatory opaque identity and primary key; see QPXIdentity.
static constexpr const char *	PG_ACCESSIONS = "pg_accessions"
static constexpr const char *	PG_NAMES = "pg_names"
static constexpr const char *	GG_ACCESSIONS = "gg_accessions"
static constexpr const char *	GG_NAMES = "gg_names"
static constexpr const char *	GG_QVALUE = "gg_qvalue"
static constexpr const char *	ANCHOR_PROTEIN = "anchor_protein"
static constexpr const char *	GROUPED_RUNS = "grouped_runs"
static constexpr const char *	GLOBAL_QVALUE = "global_qvalue"
static constexpr const char *	PG_QVALUE = "pg_qvalue"
static constexpr const char *	LABEL = "label"
static constexpr const char *	INTENSITY = "intensity"
static constexpr const char *	ADDITIONAL_INTENSITIES = "additional_intensities"
static constexpr const char *	IS_DECOY = "is_decoy"
static constexpr const char *	CONTAMINANT = "contaminant"
static constexpr const char *	PEPTIDES = "peptides"
static constexpr const char *	PEPTIDE_COUNTS = "peptide_counts"
static constexpr const char *	FEATURE_COUNTS = "feature_counts"
static constexpr const char *	SEQUENCE_COVERAGE = "sequence_coverage"
static constexpr const char *	MOLECULAR_WEIGHT = "molecular_weight"
static constexpr const char *	ADDITIONAL_SCORES = "additional_scores"
static constexpr const char *	CV_PARAMS = "cv_params"

Detailed Description

Schema for QPX protein group export (quantms Parquet eXchange format, pg table)

Defines column names, nested Arrow types, and the complete schema for protein group data in the QPX format. Supports both quantified (ConsensusMap) and identification-only (search engine) output — quantification columns are nullable.

Note

QPX 1.1 keys this view on anchor_protein, grouped_runs, and label. One protein-group quantity applies to one experimental-design fraction group and one label. The psm and feature views keep their scalar run_file_name and nested intensity representation.

Member Function Documentation

additionalIntensitiesType()

static std::shared_ptr< arrow::DataType > additionalIntensitiesType ( )

static

Arrow type for additional intensities: list<struct{label, intensities: list<struct{...}>}>

additionalScoresType()

static std::shared_ptr< arrow::DataType > additionalScoresType ( )

static

Arrow type for additional scores (delegates to QPXPSMSchema::additionalScoresType)

cvParamsType()

static std::shared_ptr< arrow::DataType > cvParamsType ( )

static

Arrow type for CV params (delegates to QPXPSMSchema::cvParamsType)

featureCountsType()

static std::shared_ptr< arrow::DataType > featureCountsType ( )

static

Arrow type for feature_counts: struct{unique_features, total_features}.

groupedRunsType()

static std::shared_ptr< arrow::DataType > groupedRunsType ( )

static

Arrow type for grouped_runs: list<utf8> — the raw files of one quantification unit.

peptideCountsType()

static std::shared_ptr< arrow::DataType > peptideCountsType ( )

static

Arrow type for peptide_counts: struct{unique_sequences, total_sequences}.

peptidesType()

static std::shared_ptr< arrow::DataType > peptidesType ( )

static

Arrow type for peptides: list<struct{protein_name, peptide_count}>

schema()

static std::shared_ptr< arrow::Schema > schema ( )

static

Complete Arrow schema for QPX pg table (22 fields)

Member Data Documentation

ADDITIONAL_INTENSITIES

constexpr const char* ADDITIONAL_INTENSITIES = "additional_intensities"

staticconstexpr

ADDITIONAL_SCORES

constexpr const char* ADDITIONAL_SCORES = "additional_scores"

staticconstexpr

ANCHOR_PROTEIN

constexpr const char* ANCHOR_PROTEIN = "anchor_protein"

staticconstexpr

CONTAMINANT

constexpr const char* CONTAMINANT = "contaminant"

staticconstexpr

CV_PARAMS

constexpr const char* CV_PARAMS = "cv_params"

staticconstexpr

FEATURE_COUNTS

constexpr const char* FEATURE_COUNTS = "feature_counts"

staticconstexpr

GG_ACCESSIONS

constexpr const char* GG_ACCESSIONS = "gg_accessions"

staticconstexpr

GG_NAMES

constexpr const char* GG_NAMES = "gg_names"

staticconstexpr

GG_QVALUE

constexpr const char* GG_QVALUE = "gg_qvalue"

staticconstexpr

GLOBAL_QVALUE

constexpr const char* GLOBAL_QVALUE = "global_qvalue"

staticconstexpr

GROUPED_RUNS

constexpr const char* GROUPED_RUNS = "grouped_runs"

staticconstexpr

INTENSITY

constexpr const char* INTENSITY = "intensity"

staticconstexpr

IS_DECOY

constexpr const char* IS_DECOY = "is_decoy"

staticconstexpr

LABEL

constexpr const char* LABEL = "label"

staticconstexpr

MOLECULAR_WEIGHT

constexpr const char* MOLECULAR_WEIGHT = "molecular_weight"

staticconstexpr

PEPTIDE_COUNTS

constexpr const char* PEPTIDE_COUNTS = "peptide_counts"

staticconstexpr

PEPTIDES

constexpr const char* PEPTIDES = "peptides"

staticconstexpr

PG_ACCESSIONS

constexpr const char* PG_ACCESSIONS = "pg_accessions"

staticconstexpr

PG_ID

constexpr const char* PG_ID = "pg_id"

staticconstexpr

Mandatory opaque identity and primary key; see QPXIdentity.

PG_NAMES

constexpr const char* PG_NAMES = "pg_names"

staticconstexpr

PG_QVALUE

constexpr const char* PG_QVALUE = "pg_qvalue"

staticconstexpr

SEQUENCE_COVERAGE

constexpr const char* SEQUENCE_COVERAGE = "sequence_coverage"

staticconstexpr