IntaRNA 3.4.1
RNA-RNA interaction prediction | C++ API
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Classes | Public Types | Static Public Member Functions | List of all members
IntaRNA::SeededPartitionFunction Class Reference

#include <SeededPartitionFunction.h>

Classes

struct  Domain
 
struct  Result
 
struct  Weights
 

Public Types

using Pair = Interaction::BasePair
 Local zero-based pair, second strand in reversed coordinates.
 

Static Public Member Functions

static Result compute (const Domain &domain, const StackSeedDomain &seeds, const Weights &weights, bool pairs)
 

Detailed Description

Nonnegative seeded extension inside/outside computation. Paths belong to their left-most seed after removing containing occurrences. This is also the first completed seed, choosing the shortest co-ending seed: a containing seed cannot complete first, and remaining overlapping stacks have the same start and end order. Exact and heuristic prediction share seed-local tables joining seed-avoiding left extensions to unrestricted right extensions. A heuristic selector keeps one right endpoint for true two-sided extensions and retains every one-sided extension. Complete boundaries are accumulated in bounded batches; anchors crossing batches are recomputed. Batches without the seed's own start as a source need right tables only up to the chosen endpoint. Native energy ownership is supplied by the adapter: initiation once, one transition per successive pair, one boundary factor. All callbacks must be deterministic; zero denotes forbidden weight.

Member Typedef Documentation

◆ Pair

Local zero-based pair, second strand in reversed coordinates.

Member Function Documentation

◆ compute()

static Result IntaRNA::SeededPartitionFunction::compute ( const Domain &  domain,
const StackSeedDomain &  seeds,
const Weights &  weights,
bool  pairs 
)
static

Compute the union of seeded paths, optionally differentiating every pair.

Parameters
domainactive dimensions and structural constraints
seedsactive admitted seed occurrences
weightsweight/admission contract (no integer energy reconstruction)
pairsrequest the outside pass and raw local pair masses
Returns
successful raw result, including exact zero for an empty ensemble
Exceptions
std::range_erroron numerical failure; no partial result is returned

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