cawlign 0.0.1
Codon-aware pairwise sequence alignment
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CawalignCodonScores Member List

This is the complete list of members for CawalignCodonScores, including all inherited members.

_init_alphabet(long not_found=-1)CawalignSimpleScores
alphabet (defined in CawalignSimpleScores)CawalignSimpleScores
amino_acids (defined in CawalignCodonScores)CawalignCodonScores
CawalignCodonScores(ConfigParser *)CawalignCodonScores
CawalignSimpleScores(const char *_alphabet, const cawlign_fp *_scoring_matrix, const cawlign_fp _open_gap_reference, const cawlign_fp _open_gap_query, const cawlign_fp _extend_gap_reference, const cawlign_fp _extend_gap_query)CawalignSimpleScores
CawalignSimpleScores(ConfigParser *)CawalignSimpleScores
CawalignSimpleScores(void) (defined in CawalignSimpleScores)CawalignSimpleScoresinline
char_map (defined in CawalignSimpleScores)CawalignSimpleScores
D (defined in CawalignSimpleScores)CawalignSimpleScores
extend_gap_query (defined in CawalignSimpleScores)CawalignSimpleScores
extend_gap_reference (defined in CawalignSimpleScores)CawalignSimpleScores
frameshift_cost (defined in CawalignCodonScores)CawalignCodonScores
gap_char (defined in CawalignSimpleScores)CawalignSimpleScores
mismatch_index (defined in CawalignCodonScores)CawalignCodonScores
nucleotide_diff(long, long)CawalignCodonScoresstatic
open_gap_query (defined in CawalignSimpleScores)CawalignSimpleScores
open_gap_reference (defined in CawalignSimpleScores)CawalignSimpleScores
s3x1 (defined in CawalignCodonScores)CawalignCodonScores
s3x2 (defined in CawalignCodonScores)CawalignCodonScores
s3x4 (defined in CawalignCodonScores)CawalignCodonScores
s3x5 (defined in CawalignCodonScores)CawalignCodonScores
scoring_matrix (defined in CawalignSimpleScores)CawalignSimpleScores
stop_codon_index (defined in CawalignCodonScores)CawalignCodonScores
synonymous_penalty (defined in CawalignCodonScores)CawalignCodonScores
translation_table (defined in CawalignCodonScores)CawalignCodonScores
~CawalignCodonScores(void) (defined in CawalignCodonScores)CawalignCodonScoresinlinevirtual
~CawalignSimpleScores(void) (defined in CawalignSimpleScores)CawalignSimpleScoresinlinevirtual