#include <OpenMS/FORMAT/ProteinGroupArrowExport_impl.h>

Public Member Functions
	QuantificationUnits ()=default

	QuantificationUnits (const ExperimentalDesign &design, const std::set< std::pair< std::string, unsigned > > &known_cells)

bool	empty () const

bool	inconsistent () const
	A design assigning one (run, label) to several samples; the rows would be wrong.

const std::string &	ambiguousLabel () const
	Non-empty when one label of a unit means several samples; the row cannot be written.

const std::string &	raggedUnit () const
	Non-empty when a unit's runs do not all carry every label it publishes.

const std::set< std::string > &	droppedRuns () const
	Design files the ConsensusMap has no column header for, left out of every unit.

const std::string &	missingCell () const
	Non-empty when a run that IS in the map lacks a header for a label the design declares.

const std::string &	invalidSample () const
	Non-empty when a design row refers outside its sample section.

const std::string &	runInSeveralGroups () const
	Non-empty when one run is assigned to multiple fraction groups.

const std::vector< QuantUnit > &	units () const

size_t	indexOf (const std::string &run) const
	Index of the unit containing `run`, or units().size() when the design does not list it.

template<typename LabelFor >
bool	resolveLabels (LabelFor label_for, const std::string &context)

Private Attributes
std::vector< QuantUnit >	units_

std::unordered_map< std::string, size_t >	unit_of_run_

std::set< std::string >	dropped_runs_

std::string	missing_cell_

std::string	ambiguous_label_

std::string	ragged_unit_

std::string	invalid_sample_

std::string	run_in_several_groups_

bool	inconsistent_ = false

Detailed Description

The quantification units of an experimental design, indexed by run name.

Active QPX 1.1 defines OpenMS fraction_group as grouped_runs: all files in one fraction group form one quantity, and label is the orthogonal channel dimension. A sample may occur in several fraction groups (technical replicates or a shared reference) without joining them. PeptideAndProteinQuant preserves quantities at exactly this grain before protein aggregation.

Constructor & Destructor Documentation

◆ QuantificationUnits() [1/2]

QuantificationUnits ( )

default

◆ QuantificationUnits() [2/2]

QuantificationUnits	(	const ExperimentalDesign &	design,
		const std::set< std::pair< std::string, unsigned > > &	known_cells
	)

inline

Parameters

design	the design that drove quantification
known_cells	the (QPX run name, label) cells the ConsensusMap has a column header for. A design row for a file that is not in the map contributed nothing, so naming it in grouped_runs would claim an aggregation that did not happen – and would put a run in the pg view that the psm and feature views cannot join to.

The set holds CELLS, not runs, because the two absences mean different things:

a run with NO cell at all is simply not part of this map – a design listing files beyond the current input, which ProteomicsLFQ produces routinely by filtering the design by basename. Dropped, with a diagnostic.
a run that IS present but whose declared label has no header means the design and the data disagree about the channel layout – a TMT10-shaped design against a 6-plex map, say. Reading that cell would invent an intensity label ("LFQ" for channel 1, otherwise the bare channel number) that joins to nothing, so it is recorded and refused instead.

< this run's label -> sample