Programme / Dev-Cpp / Mine / GENtle / clustalw

sequence.c File Reference

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


Defines
#define	MIN(a, b) ((a)<(b)?(a):(b))
Functions
static char *	get_seq (char , sint , char *)
static char *	get_clustal_seq (char , sint , char *, sint)
static char *	get_msf_seq (char , sint , char *, sint)
static void	check_infile (sint *)
static void	p_encode (char , char , sint)
static void	n_encode (char , char , sint)
static sint	res_index (char *, char)
static Boolean	check_dnaflag (char *, sint)
static sint	count_clustal_seqs (void)
static sint	count_pir_seqs (void)
static sint	count_msf_seqs (void)
static sint	count_rsf_seqs (void)
static void	get_swiss_feature (char *line, sint len)
static void	get_rsf_feature (char *line, sint len)
static void	get_swiss_mask (char *line, sint len)
static void	get_clustal_ss (sint length)
static void	get_embl_ss (sint length)
static void	get_rsf_ss (sint length)
static void	get_gde_ss (sint length)
static Boolean	cl_blankline (char *line)
void	fill_chartab (void)
sint	readseqs (sint first_seq)
Variables
sint	max_names
FILE *	fin
Boolean	usemenu
Boolean	dnaflag
Boolean	explicit_dnaflag
Boolean	interactive
char	seqname []
sint	nseqs
sint *	seqlen_array
sint *	output_index
char **	names
char **	titles
char **	seq_array
Boolean	profile1_empty
Boolean	profile2_empty
sint	gap_pos2
sint	max_aln_length
char *	gap_penalty_mask
char *	sec_struct_mask
sint	struct_penalties
char *	ss_name
sint	profile_no
sint	debug
char *	amino_acid_codes = "ABCDEFGHIKLMNPQRSTUVWXYZ-"
static sint	seqFormat
static char	chartab [128]
static char *	formatNames []

Define Documentation

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

Function Documentation

static Boolean check_dnaflag ( char * ,

sint

) [static]

static void check_infile ( sint * ) [static]

static Boolean cl_blankline ( char * line ) [static]

static sint count_clustal_seqs ( void ) [static]

static sint count_msf_seqs ( void ) [static]

static sint count_pir_seqs ( void ) [static]

static sint count_rsf_seqs ( void ) [static]

void fill_chartab ( void )

static char * get_clustal_seq ( char * ,

sint * ,

char * ,

sint

) [static]

static void get_clustal_ss ( sint length ) [static]

static void get_embl_ss ( sint length ) [static]

static void get_gde_ss ( sint length ) [static]

static char * get_msf_seq ( char * ,

sint * ,

char * ,

sint

) [static]

static void get_rsf_feature ( char * line,

sint len

) [static]

static void get_rsf_ss ( sint length ) [static]

static char * get_seq ( char * ,

sint * ,

char *

) [static]

static void get_swiss_feature ( char * line,

sint len

) [static]

static void get_swiss_mask ( char * line,

sint len

) [static]

static void n_encode ( char * ,

char * ,

sint

) [static]

static void p_encode ( char * ,

char * ,

sint

) [static]

sint readseqs ( sint first_seq )

static sint res_index ( char * ,

char

) [static]

Variable Documentation

char* amino_acid_codes = "ABCDEFGHIKLMNPQRSTUVWXYZ-"

char chartab[128] [static]

sint debug

Boolean dnaflag

Boolean explicit_dnaflag

FILE* fin

char* formatNames[] [static]

Initial value:
{"unknown","EMBL/Swiss-Prot","PIR", "Pearson","GDE","Clustal","Pileup/MSF","RSF","USER","PHYLIP","NEXUS"}