#include <stdio.h>#include <string.h>#include <stdlib.h>#ifdef MAC#include <console.h>#endif#include "clustalw.h"/**	Prototypes*/#ifdef MACextern int ccommand(char ***);#endifextern void *ckalloc(size_t);extern void init_amenu(void);extern void init_interface(void);extern void init_matrix(void);extern void fill_chartab(void);extern void parse_params(Boolean);extern void main_menu(void);/**	Global variables*/double **tmat;char revision_level[] = "W (1.83)";  /* JULIE  feb 2001*/Boolean interactive=FALSE;#ifdef MSDOS        char *help_file_name = "clustalw.hlp";#else        char *help_file_name = "clustalw_help";#endifsint max_names; /* maximum length of names in current alignment file */float           gap_open,      gap_extend;float           pw_go_penalty, pw_ge_penalty;FILE *tree;FILE *clustal_outfile, *gcg_outfile, *nbrf_outfile, *phylip_outfile,     *gde_outfile, *nexus_outfile;FILE *fasta_outfile; /* Ramu */sint  *seqlen_array;sint max_aln_length;short usermat[NUMRES][NUMRES], pw_usermat[NUMRES][NUMRES];short def_aa_xref[NUMRES+1], aa_xref[NUMRES+1], pw_aa_xref[NUMRES+1];short userdnamat[NUMRES][NUMRES], pw_userdnamat[NUMRES][NUMRES];short def_dna_xref[NUMRES+1], dna_xref[NUMRES+1], 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,**titles;char **args;char seqname[FILENAMELEN+1];char *gap_penalty_mask1 = NULL, *gap_penalty_mask2 = NULL;char *sec_struct_mask1 = NULL, *sec_struct_mask2 = NULL;sint struct_penalties;char *ss_name1 = NULL, *ss_name2 = NULL;Boolean user_series = FALSE;UserMatSeries matseries;short usermatseries[MAXMAT][NUMRES][NUMRES];short aa_xrefseries[MAXMAT][NUMRES+1];int main(int argc,char **argv){	sint i;	#ifdef MAC	argc=ccommand(&argv);#endif    init_amenu();    init_interface();    init_matrix();		fill_chartab();	if(argc>1) {		args = (char **)ckalloc(argc * sizeof(char *));			for(i=1;i<argc;++i) 		{			args[i-1]=(char *)ckalloc((strlen(argv[i])+1) * sizeof(char));			strcpy(args[i-1],argv[i]);		}		usemenu=FALSE;		parse_params(FALSE);		for(i=0;i<argc-1;i++) 			ckfree(args[i]);		ckfree(args);	}	usemenu=TRUE;	interactive=TRUE;	main_menu();		exit(0);}