IntaRNA::StackSeedDomain Class Reference

#include <StackSeedDomain.h>

Classes
struct	Occurrence

Public Member Functions
	StackSeedDomain (const SeedHandler &handler, size_t n, size_t m, size_t span1, size_t span2)
	StackSeedDomain (const std::vector< Occurrence > &occurrences, size_t n, size_t m, size_t span1, size_t span2)
size_t	seedLength (size_t i, size_t j) const
size_t	seedEndingLength (size_t i, size_t j) const
size_t	maxSeedLength () const
std::vector< Occurrence >	minimalOccurrences () const
void	forEachStart (const std::function< void(size_t, size_t)> &visit) const

Detailed Description

Admitted stack occurrences and the deduplicated union of eligible-start boxes. Coordinates are local, zero-based and increasing on both strands. Seed energies have already been filtered by the handler and are never reused as path weights.

Constructor & Destructor Documentation

StackSeedDomain() [1/2]

IntaRNA::StackSeedDomain::StackSeedDomain	(	const SeedHandler &	handler,
		size_t	n,
		size_t	m,
		size_t	span1,
		size_t	span2
	)

Compile a filled handler, requiring both endpoints inside the active range.

Parameters

handler	filled stack-only handler, including any index offset
n	first range length
m	second range length
span1	inclusive first-strand interaction span limit
span2	inclusive second-strand interaction span limit

StackSeedDomain() [2/2]

IntaRNA::StackSeedDomain::StackSeedDomain	(	const std::vector< Occurrence > &	occurrences,
		size_t	n,
		size_t	m,
		size_t	span1,
		size_t	span2
	)

Compile already admitted occurrences (also useful for independent weight models).

Parameters

occurrences	retained occurrences; out-of-range/overlong ones are excluded
n	first range length
m	second range length
span1	inclusive first span limit
span2	inclusive second span limit

Member Function Documentation

forEachStart()

void IntaRNA::StackSeedDomain::forEachStart

(

const std::function< void(size_t, size_t)> &

visit

)

const

Enumerate each eligible left boundary once, in row-major order. The caller intersects these boxes with accessible complementary vertices.

Parameters

visit

callback receiving local first/second coordinates

maxSeedLength()

size_t IntaRNA::StackSeedDomain::maxSeedLength ( ) const

inline

Returns

maximum retained occurrence length, zero for an empty family

minimalOccurrences()

std::vector< Occurrence > IntaRNA::StackSeedDomain::minimalOccurrences

(

)

const

Return the union-equivalent family without containing occurrences. A seed containing another admitted seed on its diagonal is redundant for exact union counting and cannot be the heuristic's first-completed owner: its inner seed completes earlier or wins the shortest co-ending tie. The original family remains available for annotations and native endpoint selection. Results are ordered by their starting pair.

Returns

admitted occurrences containing no other admitted occurrence

seedEndingLength()

size_t IntaRNA::StackSeedDomain::seedEndingLength ( size_t  i, size_t  j  ) const

inline

Returns

shortest admitted occurrence ending here, or zero

seedLength()

size_t IntaRNA::StackSeedDomain::seedLength ( size_t  i, size_t  j  ) const

inline

Returns

retained length at this start, or zero if no occurrence starts here

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

• src/IntaRNA/StackSeedDomain.h