calcgap.cpp 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

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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 )

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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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