IntaRNA::BasePairProbabilities Class Reference

#include <BasePairProbabilities.h>

Public Types
enum class	Status { pending , nonempty , empty , failed }

Public Member Functions
	BasePairProbabilities (size_t targetLength, size_t queryLength, bool collectSeedPairs=false)
void	addRegion (const IndexRange &target, const IndexRange &query, Z_type denominator, const Matrix< Z_type > &masses, const Matrix< unsigned char > *seedPairs=nullptr)
void	finalize ()
void	fail () noexcept
Status	status () const
Z_type	getZ () const
const Matrix< Z_type > &	rawMasses () const
bool	collectsSeedPairs () const
void	markApproximate ()
bool	isApproximate () const
const Matrix< unsigned char > &	seedPairs () const
Matrix< Z_type >	probabilities () const

Detailed Description

Success-only accumulator for one target/query pair. Raw numerators and Z are merged over disjoint searched rectangles, then normalized explicitly. All stored coordinates follow the original sequences' 5'-to-3' order. This is conditional on an allowed interaction, without an unbound-state contribution. A destructor never publishes data. Not thread safe: use one owner per pair.

Member Enumeration Documentation

Status

enum class IntaRNA::BasePairProbabilities::Status

strong

Pending accumulation, successful nonempty/empty completion, or failure.

Enumerator
pending
nonempty
empty
failed

Constructor & Destructor Documentation

BasePairProbabilities()

IntaRNA::BasePairProbabilities::BasePairProbabilities	(	size_t	targetLength,
		size_t	queryLength,
		bool	collectSeedPairs = false
	)

Allocate raw masses for the full original target/query sequences.

Parameters

targetLength	number of target positions
queryLength	number of query positions
collectSeedPairs	retain admitted seed-cell annotations for SVG output

Member Function Documentation

addRegion()

void IntaRNA::BasePairProbabilities::addRegion	(	const IndexRange &	target,
		const IndexRange &	query,
		Z_type	denominator,
		const Matrix< Z_type > &	masses,
		const Matrix< unsigned char > *	seedPairs = nullptr
	)

Commit one completed region, after validating ALL sums and disjointness.

Parameters

target	inclusive original target region
query	inclusive original query region
denominator	raw region Z
masses	raw region numerators in original orientation (local indices)
seedPairs	optional regional seed mask in the same orientation as masses; required when collecting annotations (nonzero denotes an admitted seed pair)

Exceptions

on	invalid/overlapping regions or numerical failure, marking failed

collectsSeedPairs()

bool IntaRNA::BasePairProbabilities::collectsSeedPairs ( ) const

inline

Returns

whether this sink requests admitted seed-cell annotations

fail()

void IntaRNA::BasePairProbabilities::fail ( )

inlinenoexcept

Mark this pair failed after any error or cancellation.

finalize()

void IntaRNA::BasePairProbabilities::finalize

(

)

Finalize only after all requested regions succeeded; validate normalized masses, row/column exclusivity and numerical range before publication.

Exceptions

on	failed computation or inconsistent masses

getZ()

Z_type IntaRNA::BasePairProbabilities::getZ ( ) const

inline

Returns

the raw merged denominator (not usable as a result after failure)

isApproximate()

bool IntaRNA::BasePairProbabilities::isApproximate ( ) const

inline

Returns

whether the represented interaction ensemble is heuristic

markApproximate()

void IntaRNA::BasePairProbabilities::markApproximate

(

)

Mark an ensemble restricted by heuristic continuation choices. Must be called while pending, before publication.

probabilities()

Matrix< Z_type > IntaRNA::BasePairProbabilities::probabilities

(

)

const

Returns

validated matrix; only available for finalized nonempty results. Successful empty output is represented by status()==empty, not zeroes.

rawMasses()

const Matrix< Z_type > & IntaRNA::BasePairProbabilities::rawMasses ( ) const

inline

Returns

raw merged pair numerators (original coordinates)

seedPairs()

const Matrix< unsigned char > & IntaRNA::BasePairProbabilities::seedPairs ( ) const

inline

Returns

seed-cell mask in original coordinates, empty when not requested

status()

BasePairProbabilities::Status IntaRNA::BasePairProbabilities::status ( ) const

inline

Returns

explicit lifecycle status

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The documentation for this class was generated from the following file:

• src/IntaRNA/BasePairProbabilities.h