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prfalign.cpp File Reference

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

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

Define Documentation

#define ENDALN   127
 

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

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


Function Documentation

static void add_ggaps void   )  [static]
 

static char * add_ggaps_mask char *  mask,
int  len,
char *  path1,
char *  path2
[static]
 

static sint ext_penalty1 sint  i,
sint  j
[static]
 

static sint ext_penalty2 sint  i,
sint  j
[static]
 

static sint gap_penalty1 sint  i,
sint  j,
sint  k
[static]
 

static sint gap_penalty2 sint  i,
sint  j,
sint  k
[static]
 

static sint open_penalty1 sint  i,
sint  j
[static]
 

static sint open_penalty2 sint  i,
sint  j
[static]
 

static void padd sint  k  )  [static]
 

static void palign void   )  [static]
 

static void pdel sint  k  )  [static]
 

static lint pdiff sint  A,
sint  B,
sint  i,
sint  j,
sint  go1,
sint  go2
[static]
 

lint prfalign sint *  group,
sint *  aligned
 

static lint prfscore sint  n,
sint  m
[static]
 

static void ptracepath sint *  alen  )  [static]
 


Variable Documentation

short aa_xref[]
 

char** alignment [static]
 

sint alignment_len [static]
 

sint* aln_len [static]
 

char* aln_path1 [static]
 

char * aln_path2 [static]
 

sint* aln_weight [static]
 

char* amino_acid_codes
 

short blosum30mt[]
 

short blosum40mt[]
 

short blosum45mt[]
 

short blosum62mt2[]
 

short blosum80mt[]
 

short clustalvdnamt[]
 

lint * DD [static]
 

sint debug
 

short def_aa_xref[]
 

short def_dna_xref[]
 

sint* displ [static]
 

Boolean distance_tree
 

short dna_xref[]
 

Boolean dnaflag
 

char dnamtrxname[]
 

Boolean endgappenalties
 

float gap_extend
 

float gap_open
 

char* gap_penalty_mask1
 

char * gap_penalty_mask2
 

sint gap_pos1
 

sint gap_pos2
 

sint gapcoef1 [static]
 

sint gapcoef2 [static]
 

sint* gaps [static]
 

short gon120mt[]
 

short gon160mt[]
 

short gon250mt[]
 

short gon350mt[]
 

short gon40mt[]
 

short gon80mt[]
 

lint* gS [static]
 

lint* HH [static]
 

short idmat[]
 

sint last_print [static]
 

sint lencoef1 [static]
 

sint lencoef2 [static]
 

sint mat_avscore
 

sint matrix[NUMRES][NUMRES] [static]
 

UserMatSeries matseries
 

sint max_aa
 

sint max_aln_length
 

char mtrxname[]
 

Boolean neg_matrix
 

sint nseqs
 

sint nseqs1 [static]
 

sint nseqs2 [static]
 

short pam120mt[]
 

short pam160mt[]
 

short pam20mt[]
 

short pam350mt[]
 

short pam60mt[]
 

sint prf_length1 [static]
 

sint prf_length2 [static]
 

sint print_ptr [static]
 

sint** profile1 [static]
 

sint ** profile2 [static]
 

lint * RR [static]
 

char* sec_struct_mask1
 

char * sec_struct_mask2
 

char** seq_array
 

sint* seq_weight
 

sint* seqlen_array
 

lint * SS [static]
 

sint struct_penalties1
 

sint struct_penalties2
 

short swgapdnamt[]
 

Boolean switch_profiles [static]
 

double** tmat
 

float transition_weight
 

Boolean use_ss1
 

Boolean use_ss2
 

Boolean user_series
 

short userdnamat[]
 

short usermat[]
 


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