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calcgap.c File Reference

#include <stdio.h>
#include <ctype.h>
#include <stdlib.h>
#include <string.h>
#include "clustalw.h"

Functions

void calc_p_penalties (char **aln, sint n, sint fs, sint ls, sint *weight)
void calc_h_penalties (char **aln, sint n, sint fs, sint ls, sint *weight)
void calc_v_penalties (char **aln, sint n, sint fs, sint ls, sint *weight)
sint local_penalty (sint penalty, sint n, sint *pweight, sint *hweight, sint *vweight)
float percentid (char *s1, char *s2, sint length)
void calc_gap_coeff (char **alignment, sint *gaps, sint **profile, Boolean struct_penalties, char *gap_penalty_mask, sint first_seq, sint last_seq, sint prf_length, sint gapcoef, sint lencoef)

Variables

sint gap_dist
sint max_aa
sint debug
Boolean dnaflag
Boolean use_endgaps
Boolean endgappenalties
Boolean no_var_penalties
Boolean no_hyd_penalties
Boolean no_pref_penalties
char hyd_residues []
char * amino_acid_codes
int vll = 50
int vwindow = 5
sint vlut [26][26]
char pr []
sint pas_op []
sint pas_op2 []
sint pal_op []
float reduced_gap = 1.0
Boolean nvar_pen
Boolean nhyd_pen
Boolean npref_pen
sint gdist

Function Documentation

void calc_gap_coeff char **  alignment,
sint *  gaps,
sint **  profile,
Boolean  struct_penalties,
char *  gap_penalty_mask,
sint  first_seq,
sint  last_seq,
sint  prf_length,
sint  gapcoef,
sint  lencoef
 

void calc_h_penalties char **  aln,
sint  n,
sint  fs,
sint  ls,
sint *  weight
 

void calc_p_penalties char **  aln,
sint  n,
sint  fs,
sint  ls,
sint *  weight
 

void calc_v_penalties char **  aln,
sint  n,
sint  fs,
sint  ls,
sint *  weight
 

sint local_penalty sint  penalty,
sint  n,
sint *  pweight,
sint *  hweight,
sint *  vweight
 

float percentid char *  s1,
char *  s2,
sint  length
 


Variable Documentation

char* amino_acid_codes
 

sint debug
 

Boolean dnaflag
 

Boolean endgappenalties
 

sint gap_dist
 

sint gdist
 

char hyd_residues[]
 

sint max_aa
 

Boolean nhyd_pen
 

Boolean no_hyd_penalties
 

Boolean no_pref_penalties
 

Boolean no_var_penalties
 

Boolean npref_pen
 

Boolean nvar_pen
 

sint pal_op[]
 

Initial value:

 { 84, 69,128, 78, 88,176, 53, 95, 55, 49,
                    52,148,147,100, 91,129,105, 51,128, 88}

sint pas_op[]
 

Initial value:

 { 87, 87,104, 69, 80,139,100,104, 68, 79,
                    71,137,126, 93,128,124,111, 75,100, 77}

sint pas_op2[]
 

Initial value:

{ 88, 57,111, 98, 75,126, 95, 97, 70, 90,
                    60,122,110,107, 91,125,124, 81,106, 88}

char pr[]
 

Initial value:

     {'A' , 'C', 'D', 'E', 'F', 'G', 'H', 'K', 'I', 'L',
                   'M' , 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'Y', 'W'}

float reduced_gap = 1.0
 

Boolean use_endgaps
 

int vll = 50
 

sint vlut[26][26]
 

Initial value:

 {

          1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
          0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0,
          0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1
        }

int vwindow = 5
 


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