Struct ScoringContext 

pub struct ScoringContext {

    pub substitution_matrix: Vec<Vec<i32>>,
    pub consweight_matrix: Vec<Vec<f64>>,
    pub polarity: [f64; 256],
    pub volume: [f64; 256],
    pub amino_map: [u8; 256],
    pub model: ScoringModel,
    pub seq_type: SeqType,
    pub gap: GapPenalties,
    pub nalphabets: usize,
    pub nscoredalphabets: usize,
    pub fft_matrix: Vec<Vec<i32>>,
    pub ln_matrix: Vec<Vec<f64>>,
    pub ribosumdis: Option<[[i32; 37]; 37]>,
}

The complete scoring context needed by alignment algorithms.

Owns the substitution matrix and all derived scoring data. This replaces the C globals amino_dis, n_dis, polarity[], etc.

Fields

substitution_matrix: Vec<Vec<i32>>

Substitution score matrix (indexed by internal residue codes). For proteins: 20x20 (or 26x26 with ambiguity codes). For DNA: 4x4 (or larger with ambiguity).

consweight_matrix: Vec<Vec<f64>>

Consistency-weighted version of the substitution matrix.

polarity: [f64; 256]

Polarity values for each residue (amino acid property).

volume: [f64; 256]

Volume values for each residue (amino acid property).

amino_map: [u8; 256]

Character-to-internal-index mapping.

model: ScoringModel

Scoring model in use.

seq_type: SeqType

Sequence type.

gap: GapPenalties

Gap penalties.

nalphabets: usize

Number of alphabets (26 for protein, 4-16 for DNA).

nscoredalphabets: usize

Number of scored alphabets (20 for protein standard AAs).

fft_matrix: Vec<Vec<i32>>

FFT-specific scoring matrix (n_dis + offset adjustment). Used by alignableReagion() for segment detection scoring.

ln_matrix: Vec<Vec<f64>>

Log-normal scoring matrix (n_dis + offset - offsetLN). Used in a specific refinement code path.

ribosumdis: Option<[[i32; 37]; 37]>

RNA ribosum composite matrix (37×37) for RNA secondary structure scoring. Only populated for DNA/RNA sequence types.

Implementations

impl ScoringContext

pub fn matrix_size(&self) -> usize

Trait Implementations

impl Clone for ScoringContext

fn clone(&self) -> ScoringContext

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for ScoringContext

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.