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sequence.cpp 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,
 )     ((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"}

char* gap_penalty_mask
 

sint gap_pos2
 

Boolean interactive
 

sint max_aln_length
 

sint max_names
 

char** names
 

sint nseqs
 

sint* output_index
 

Boolean profile1_empty
 

Boolean profile2_empty
 

sint profile_no
 

char * sec_struct_mask
 

char** seq_array
 

sint seqFormat [static]
 

sint* seqlen_array
 

char seqname[]
 

char* ss_name
 

sint struct_penalties
 

char ** titles
 

Boolean usemenu
 


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