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Defines |
| #define | ENDALN 127 |
| #define | MAX(a, b) ((a)>(b)?(a):(b)) |
| #define | MIN(a, b) ((a)<(b)?(a):(b)) |
Functions |
| static lint | pdiff (sint A, sint B, sint i, sint j, sint go1, sint go2) |
| static lint | prfscore (sint n, sint m) |
| static sint | gap_penalty1 (sint i, sint j, sint k) |
| static sint | open_penalty1 (sint i, sint j) |
| static sint | ext_penalty1 (sint i, sint j) |
| static sint | gap_penalty2 (sint i, sint j, sint k) |
| static sint | open_penalty2 (sint i, sint j) |
| static sint | ext_penalty2 (sint i, sint j) |
| static void | padd (sint k) |
| static void | pdel (sint k) |
| static void | palign (void) |
| static void | ptracepath (sint *alen) |
| static void | add_ggaps (void) |
| static char * | add_ggaps_mask (char *mask, int len, char *path1, char *path2) |
| lint | prfalign (sint *group, sint *aligned) |
Variables |
| double ** | tmat |
| float | gap_open |
| float | gap_extend |
| float | transition_weight |
| sint | gap_pos1 |
| sint | gap_pos2 |
| sint | max_aa |
| sint | nseqs |
| sint * | seqlen_array |
| sint * | seq_weight |
| sint | debug |
| Boolean | neg_matrix |
| sint | mat_avscore |
| short | blosum30mt [] |
| short | blosum40mt [] |
| short | blosum45mt [] |
| short | blosum62mt2 [] |
| short | blosum80mt [] |
| short | pam20mt [] |
| short | pam60mt [] |
| short | pam120mt [] |
| short | pam160mt [] |
| short | pam350mt [] |
| short | gon40mt [] |
| short | gon80mt [] |
| short | gon120mt [] |
| short | gon160mt [] |
| short | gon250mt [] |
| short | gon350mt [] |
| short | clustalvdnamt [] |
| short | swgapdnamt [] |
| short | idmat [] |
| short | usermat [] |
| short | userdnamat [] |
| Boolean | user_series |
| UserMatSeries | matseries |
| short | def_dna_xref [] |
| short | def_aa_xref [] |
| short | dna_xref [] |
| short | aa_xref [] |
| sint | max_aln_length |
| Boolean | distance_tree |
| Boolean | dnaflag |
| char | mtrxname [] |
| char | dnamtrxname [] |
| char ** | seq_array |
| char * | amino_acid_codes |
| char * | gap_penalty_mask1 |
| char * | gap_penalty_mask2 |
| char * | sec_struct_mask1 |
| char * | sec_struct_mask2 |
| sint | struct_penalties1 |
| sint | struct_penalties2 |
| Boolean | use_ss1 |
| Boolean | use_ss2 |
| Boolean | endgappenalties |
| static sint | print_ptr |
| static sint | last_print |
| static sint * | displ |
| static char ** | alignment |
| static sint * | aln_len |
| static sint * | aln_weight |
| static char * | aln_path1 |
| static char * | aln_path2 |
| static sint | alignment_len |
| static sint ** | profile1 |
| static sint ** | profile2 |
| static lint * | HH |
| static lint * | DD |
| static lint * | RR |
| static lint * | SS |
| static lint * | gS |
| static sint | matrix [NUMRES][NUMRES] |
| static sint | nseqs1 |
| static sint | nseqs2 |
| static sint | prf_length1 |
| static sint | prf_length2 |
| static sint * | gaps |
| static sint | gapcoef1 |
| static sint | gapcoef2 |
| static sint | lencoef1 |
| static sint | lencoef2 |
| static Boolean | switch_profiles |
