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palign.cpp File Reference

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

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

Define Documentation

#define gap  )     ((k) <= 0 ? 0 : g + gh * (k))
 

#define MAX a,
 )     ((a)>(b)?(a):(b))
 

#define MIN a,
 )     ((a)<(b)?(a):(b))
 

#define pwint   int
 

#define tbgap  )     ((k) <= 0 ? 0 : tb + gh * (k))
 

#define tegap  )     ((k) <= 0 ? 0 : te + gh * (k))
 


Function Documentation

static void add sint  v  )  [static]
 

static sint calc_score sint  iat,
sint  jat,
sint  v1,
sint  v2
[static]
 

static void del sint  k  )  [static]
 

static int diff sint  A,
sint  B,
sint  M,
sint  N,
sint  tb,
sint  te
[static]
 

static void forward_pass char *  ia,
char *  ib,
sint  n,
sint  m
[static]
 

sint pairalign sint  istart,
sint  iend,
sint  jstart,
sint  jend
 

static void reverse_pass char *  ia,
char *  ib
[static]
 

static float tracepath sint  tsb1,
sint  tsb2
[static]
 


Variable Documentation

char* amino_acid_codes
 

short blosum30mt[]
 

short clustalvdnamt[]
 

pwint * DD [static]
 

sint debug
 

short def_aa_xref[]
 

short def_dna_xref[]
 

sint* displ [static]
 

Boolean dnaflag
 

sint g [static]
 

sint gap_pos1
 

sint gap_pos2
 

sint gh [static]
 

short gon250mt[]
 

pwint* HH [static]
 

short idmat[]
 

sint int_scale [static]
 

sint last_print [static]
 

sint mat_avscore
 

sint matrix[NUMRES][NUMRES] [static]
 

sint max_aa
 

sint max_aln_length
 

pwint maxscore [static]
 

float mm_score [static]
 

sint nseqs
 

short pam350mt[]
 

sint print_ptr [static]
 

short pw_aa_xref[]
 

short pw_dna_xref[]
 

char pw_dnamtrxname[]
 

float pw_ge_penalty
 

float pw_go_penalty
 

char pw_mtrxname[]
 

short pw_userdnamat[]
 

short pw_usermat[]
 

pwint * RR [static]
 

sint sb1 [static]
 

sint sb2 [static]
 

sint se1 [static]
 

sint se2 [static]
 

sint seq1 [static]
 

sint seq2 [static]
 

char** seq_array
 

sint* seqlen_array
 

pwint * SS [static]
 

short swgapdnamt[]
 

double** tmat
 

float transition_weight
 


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