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Defines |
| #define | MIN(a, b) ((a)<(b)?(a):(b)) |
| #define | MAX(a, b) ((a)>(b)?(a):(b)) |
| #define | gap(k) ((k) <= 0 ? 0 : g + gh * (k)) |
| #define | tbgap(k) ((k) <= 0 ? 0 : tb + gh * (k)) |
| #define | tegap(k) ((k) <= 0 ? 0 : te + gh * (k)) |
| #define | pwint int |
Functions |
| static void | add (sint v) |
| static sint | calc_score (sint iat, sint jat, sint v1, sint v2) |
| static float | tracepath (sint tsb1, sint tsb2) |
| static void | forward_pass (char *ia, char *ib, sint n, sint m) |
| static void | reverse_pass (char *ia, char *ib) |
| static sint | diff (sint A, sint B, sint M, sint N, sint tb, sint te) |
| static void | del (sint k) |
| sint | pairalign (sint istart, sint iend, sint jstart, sint jend) |
Variables |
| static sint | int_scale |
| double ** | tmat |
| float | pw_go_penalty |
| float | pw_ge_penalty |
| float | transition_weight |
| sint | nseqs |
| sint | max_aa |
| sint | gap_pos1 |
| sint | gap_pos2 |
| sint | max_aln_length |
| sint * | seqlen_array |
| sint | debug |
| sint | mat_avscore |
| short | blosum30mt [] |
| short | pam350mt [] |
| short | idmat [] |
| short | pw_usermat [] |
| short | pw_userdnamat [] |
| short | clustalvdnamt [] |
| short | swgapdnamt [] |
| short | gon250mt [] |
| short | def_dna_xref [] |
| short | def_aa_xref [] |
| short | pw_dna_xref [] |
| short | pw_aa_xref [] |
| Boolean | dnaflag |
| char ** | seq_array |
| char * | amino_acid_codes |
| char | pw_mtrxname [] |
| char | pw_dnamtrxname [] |
| static float | mm_score |
| static sint | print_ptr |
| static sint | last_print |
| static sint * | displ |
| static pwint * | HH |
| static pwint * | DD |
| static pwint * | RR |
| static pwint * | SS |
| static sint | g |
| static sint | gh |
| static sint | seq1 |
| static sint | seq2 |
| static sint | matrix [NUMRES][NUMRES] |
| static pwint | maxscore |
| static sint | sb1 |
| static sint | sb2 |
| static sint | se1 |
| static sint | se2 |
