ProteinGroupArrowExport_impl.h File Reference

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/FORMAT/ArrowIOHelpers.h>
#include <OpenMS/METADATA/ExperimentalDesign.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <algorithm>
#include <map>
#include <set>
#include <string>
#include <tuple>
#include <unordered_map>
#include <vector>

Go to the source code of this file.

Classes
struct	QuantChannel
	One label of a quantification unit and the sample it resolves to in the design. More...
struct	QuantUnit
	One QPX quantification unit: exactly one OpenMS experimental-design fraction group. More...
class	QuantificationUnits
struct	FractionGroupAbundanceData
	Parsed parallel arrays carrying protein quantities at (fraction_group, label) grain. More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.
namespace	OpenMS::Internal
	Namespace used to hide implementation details from users.

Functions
const ProteinIdentification::ProteinGroup::FloatDataArray *	sampleAbundances (const ProteinIdentification::ProteinGroup &group)
FractionGroupAbundanceData	fractionGroupAbundances (const ProteinIdentification::ProteinGroup &group)
	Read PeptideAndProteinQuant's named unit-level arrays and validate their parallel-key contract.
std::string	validateQuantificationAnnotations (const ProteinIdentification::ProteinGroup::FloatDataArray *sample_abundances, const FractionGroupAbundanceData &quantities, Size design_samples, const QuantificationUnits &units, const std::set< std::pair< UInt, UInt > > &expected_quantity_keys)
	Validate one protein group's complete QPX 1.1 quantification annotation contract.

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Class Documentation

OpenMS::Internal::QuantChannel

struct OpenMS::Internal::QuantChannel

One label of a quantification unit and the sample it resolves to in the design.

Class Members
unsigned	label = 1	design label / channel number, 1-based
string	qpx_label	QPX intensity label ("LFQ", "TMT126", ...)
Size	sample = 0	design sample, retained to validate consistent run/sample resolution

OpenMS::Internal::QuantUnit

struct OpenMS::Internal::QuantUnit

One QPX quantification unit: exactly one OpenMS experimental-design fraction group.

Class Members
vector< QuantChannel >	channels	one per label the unit's runs carry
UInt	fraction_group = 0	OpenMS fraction_group defining this unit.
vector< string >	runs	QPX run names, in fraction order.

OpenMS::Internal::FractionGroupAbundanceData

struct OpenMS::Internal::FractionGroupAbundanceData

Parsed parallel arrays carrying protein quantities at (fraction_group, label) grain.

Class Members
string	error
bool	present = false
bool	valid = true
map< pair< UInt, UInt >, float >	values