Struct parasail_rs::Aligner

pub struct Aligner {
    pub matrix: Arc<Matrix>,
    pub gap_open: i32,
    pub gap_extend: i32,
    pub vec_strategy: String,
    /* private fields */
}

Aligner struct for sequence alignment

Fields

matrix: Arc<Matrix>

gap_open: i32

gap_extend: i32

vec_strategy: String

Implementations

impl Aligner

pub fn new() -> AlignerBuilder

Create a new default aligner builder.

pub fn align( &self, query: Option<&[u8]>, reference: &[u8] ) -> Result<AlignResult, AlignError>

Perform alignment between a query and reference sequence. If profile was set while building the aligner, pass None as the query sequence. Otherwise, wrap the query sequence in a Some variant (i.e. Some(query)).

pub fn banded_nw( &self, query: &[u8], reference: &[u8] ) -> Result<AlignResult, AlignError>

Peform banded global alignment between a query and reference sequence. Note that this function is not vectorized. However, it may be useful for aligning large sequences.

pub fn ssw( &self, query: Option<&[u8]>, reference: &[u8] ) -> Result<SSWResult, AlignError>

Perform Striped Smith-Waterman local alignment using SSE2 instructions.