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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 |