/// Create new aligner instance. The size hints help to
/// avoid unnecessary memory allocations.
///
/// # Arguments
///
/// * `m` - the expected size of x
/// * `n` - the expected size of y
/// * `gap_open` - the score for opening a gap (should be negative)
/// * `gap_extend` - the score for extending a gap (should be negative)
/// * `match_fn` - function that returns the score for substitutions
///    (see also [`bio::alignment::pairwise::Scoring`](struct.Scoring.html))
Create new aligner instance. The size hints help to
avoid unnecessary memory allocations.
Create new aligner instance . The size hints help to avoid unnecessary memory allocations .
pub fn with_capacity(m: usize, n: usize, gap_open: i32, gap_extend: i32, match_fn: F) -> Self {
        assert!(gap_open <= 0, "gap_open can't be positive");
        assert!(gap_extend <= 0, "gap_extend can't be positive");
        Aligner {
            I: [Vec::with_capacity(m + 1), Vec::with_capacity(m + 1)],
            D: [Vec::with_capacity(m + 1), Vec::with_capacity(m + 1)],
            S: [Vec::with_capacity(m + 1), Vec::with_capacity(m + 1)],
            Lx: Vec::with_capacity(n + 1),
            Ly: Vec::with_capacity(m + 1),
            Sn: Vec::with_capacity(m + 1),
            traceback: Traceback::with_capacity(m, n),
            scoring: Scoring::new(gap_open, gap_extend, match_fn),
        }
    }
pub fn with_capacity ( m : usize , n : usize , gap_open : i32 , gap_extend : i32 , match_fn : F ) -> Self { assert ! ( gap_open 0 " " ) ; assert ! ( gap_extend 0 " " ) ; Aligner { I : [ Vec :: with_capacity ( m + 1 ) , Vec :: with_capacity ( m + 1 ) ] , D : [ Vec :: with_capacity ( m + 1 ) , Vec :: with_capacity ( m + 1 ) ] , S : [ Vec :: with_capacity ( m + 1 ) , Vec :: with_capacity ( m + 1 ) ] , Lx : Vec :: with_capacity ( n + 1 ) , Ly : Vec :: with_capacity ( m + 1 ) , Sn : Vec :: with_capacity ( m + 1 ) , traceback : Traceback :: with_capacity ( m , n ) , scoring : Scoring :: new ( gap_open , gap_extend , match_fn ) , } }
Create new aligner instance.
Create new aligner instance .
m
usize
n
usize
gap_open
i32
gap_extend
i32
match_fn
F