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clustalw.cpp File Reference

#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include "clustalw.h"
#include <wx/wx.h>

Functions

void * ckalloc (size_t)
void init_amenu (void)
void init_interface (void)
void init_matrix (void)
void fill_chartab (void)
void parse_params (Boolean)
void main_menu (void)
int clustalw_main (int argc, char **argv)

Variables

double ** tmat
char revision_level [] = "W (1.83)"
Boolean interactive = FALSE
char * help_file_name = "clustalw.hlp"
sint max_names
float gap_open
float gap_extend
float pw_go_penalty
float pw_ge_penalty
FILE * tree
FILE * clustal_outfile
FILE * gcg_outfile
FILE * nbrf_outfile
FILE * phylip_outfile
FILE * gde_outfile
FILE * nexus_outfile
FILE * fasta_outfile
sint * seqlen_array
sint max_aln_length
short usermat [NUMRES][NUMRES]
short pw_usermat [NUMRES][NUMRES]
short def_aa_xref [NUMRES+1]
short aa_xref [NUMRES+1]
short pw_aa_xref [NUMRES+1]
short userdnamat [NUMRES][NUMRES]
short pw_userdnamat [NUMRES][NUMRES]
short def_dna_xref [NUMRES+1]
short dna_xref [NUMRES+1]
short pw_dna_xref [NUMRES+1]
sint nseqs
sint nsets
sint * output_index
sint ** sets
sint * seq_weight
sint max_aa
sint gap_pos1
sint gap_pos2
sint mat_avscore
sint profile_no
Boolean usemenu
Boolean dnaflag
Boolean distance_tree
char ** seq_array
char ** names
char ** titles
char ** args
char seqname [FILENAMELEN+1]
char * gap_penalty_mask1 = NULL
char * gap_penalty_mask2 = NULL
char * sec_struct_mask1 = NULL
char * sec_struct_mask2 = NULL
sint struct_penalties
char * ss_name1 = NULL
char * ss_name2 = NULL
Boolean user_series = FALSE
UserMatSeries matseries
short usermatseries [MAXMAT][NUMRES][NUMRES]
short aa_xrefseries [MAXMAT][NUMRES+1]

Function Documentation

void* ckalloc size_t   ) 
 

int clustalw_main int  argc,
char **  argv
 

void fill_chartab void   ) 
 

void init_amenu void   ) 
 

void init_interface void   ) 
 

void init_matrix void   ) 
 

void main_menu void   ) 
 

void parse_params Boolean   ) 
 


Variable Documentation

short aa_xref[NUMRES+1]
 

short aa_xrefseries[MAXMAT][NUMRES+1]
 

char** args
 

FILE* clustal_outfile
 

short def_aa_xref[NUMRES+1]
 

short def_dna_xref[NUMRES+1]
 

Boolean distance_tree
 

short dna_xref[NUMRES+1]
 

Boolean dnaflag
 

FILE* fasta_outfile
 

float gap_extend
 

float gap_open
 

char* gap_penalty_mask1 = NULL
 

char * gap_penalty_mask2 = NULL
 

sint gap_pos1
 

sint gap_pos2
 

FILE * gcg_outfile
 

FILE * gde_outfile
 

char* help_file_name = "clustalw.hlp"
 

Boolean interactive = FALSE
 

sint mat_avscore
 

UserMatSeries matseries
 

sint max_aa
 

sint max_aln_length
 

sint max_names
 

char** names
 

FILE * nbrf_outfile
 

FILE * nexus_outfile
 

sint nseqs
 

sint nsets
 

sint* output_index
 

FILE * phylip_outfile
 

sint profile_no
 

short pw_aa_xref[NUMRES+1]
 

short pw_dna_xref[NUMRES+1]
 

float pw_ge_penalty
 

float pw_go_penalty
 

short pw_userdnamat[NUMRES][NUMRES]
 

short pw_usermat[NUMRES][NUMRES]
 

char revision_level[] = "W (1.83)"
 

char* sec_struct_mask1 = NULL
 

char * sec_struct_mask2 = NULL
 

char** seq_array
 

sint* seq_weight
 

sint* seqlen_array
 

char seqname[FILENAMELEN+1]
 

sint** sets
 

char* ss_name1 = NULL
 

char * ss_name2 = NULL
 

sint struct_penalties
 

char ** titles
 

double** tmat
 

FILE* tree
 

Boolean usemenu
 

Boolean user_series = FALSE
 

short userdnamat[NUMRES][NUMRES]
 

short usermat[NUMRES][NUMRES]
 

short usermatseries[MAXMAT][NUMRES][NUMRES]
 


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