This internal module provides code to support dynamic programming code. Do not use this module unless you know what you are doing!

Functions: rint Round a floating point up a few digits.

calc_affine_penalty Calculate an affine gap penalty. find_global_start Find the starting positions for a global alignment. find_local_start Find the starting positions for a local alignment. find_global_best Find the best score from a global alignment. find_local_best Find the best score from a local alignment.

pad_until_equal Pad two strings with chars until they're equal length. lpad_until_equal Left pad two strings until they're equal length. pad Pad a string with a characters. lpad Left pad a string with characters.

Classes: identity_match Calculate match scores based on identity. dictionary_match Calculate match scores from a dictionary lookup. affine_penalty Calculate a linear gap penalty. no_penalty No gap penalty.

_find_best ( positions )

calc_affine_penalty (
        length,
        open,
        extend,
        count_first,
        )

clean_alignments ( alignments )

find_global_best (
        sequenceA,
        sequenceB,
        score_matrix,
        penalize_end_gaps,
        gap_A_fn,
        gap_B_fn,
        )

find_global_start (
        sequenceA,
        sequenceB,
        score_matrix,
        penalize_end_gaps,
        gap_A_fn,
        gap_B_fn,
        )

find_local_best ( score_matrix )

find_local_start ( score_matrix )

lpad (
        s,
        char,
        n,
        )

lpad_until_equal (
        s1,
        s2,
        char,
        )

pad (
        s,
        char,
        n,
        )

pad_until_equal (
        s1,
        s2,
        char,
        )

print_matrix ( matrix )

rint ( x,  precision=_PRECISION )

safe_rint ( x,  precision=_PRECISION )