exit(1);		}		strcpy(seqname, param_arg[setprofile2]);		profile_no = 2;		profile_input();		if(nseqs > profile1_nseqs) 			do_something = do_profile = TRUE;		else {			if(nseqs<0) cl_error_code=2;			else if(nseqs==0) cl_error_code=3;			error("No sequences read from profile 2");			exit(cl_error_code);		}		strcpy(profile2_name,seqname);	}/*************************************************************************//* Look for /tree or /bootstrap or /align or /usetree ******************//*************************************************************************/	if (setbatch != -1)		interactive=FALSE;	if (setinteractive != -1)		interactive=TRUE;	if (interactive) {		settree = -1;		setbootstrap = -1;		setalign = -1;		setusetree = -1;		setusetree1 = -1;		setusetree2 = -1;		setnewtree = -1;		setconvert = -1;	}	if(settree != -1 )		if(empty) {			error("Cannot draw tree.  No input alignment file");			exit(1);		}		else 			do_tree = TRUE;	if(setbootstrap != -1)		if(empty) {			error("Cannot bootstrap tree. No input alignment file");			exit(1);		}		else {			temp = 0;			if(param_arg[setbootstrap] != NULL)				 if (sscanf(param_arg[setbootstrap],"%d",&temp)!=1) {                         fprintf(stdout,"Bad option for /bootstrap (must be integer)\n");                         temp = 0;                    };			if(temp > 0)          boot_ntrials = temp;			do_boot = TRUE;		}	if(setalign != -1)		if(empty) {			error("Cannot align sequences.  No input file");			exit(1);		}		else 			do_align = TRUE;	if(setconvert != -1)		if(empty) {			error("Cannot convert sequences.  No input file");			exit(1);		}		else 			do_convert = TRUE; 	if(setusetree != -1)		if(empty) {			error("Cannot align sequences.  No input file");			exit(1);		}		else  {		        if(strlen(param_arg[setusetree]) == 0) {				error("Cannot align sequences.  No tree file specified");				exit(1);		        }                        else {			        strcpy(phylip_tree_name, param_arg[setusetree]);		        }		        use_tree_file = TRUE;		        do_align_only = TRUE;		}	if(setnewtree != -1)		if(empty) {			error("Cannot align sequences.  No input file");			exit(1);		}		else  {		        if(strlen(param_arg[setnewtree]) == 0) {				error("Cannot align sequences.  No tree file specified");				exit(1);		        }                        else {			        strcpy(phylip_tree_name, param_arg[setnewtree]);		        }		    new_tree_file = TRUE;			do_tree_only = TRUE;		} 	if(setusetree1 != -1)		if(profile1_empty) {			error("Cannot align profiles.  No input file");			exit(1);		}		else if(profile_type == SEQUENCE) {			error("Invalid option /usetree1.");			exit(1);		}		else  {		        if(strlen(param_arg[setusetree1]) == 0) {				error("Cannot align profiles.  No tree file specified");				exit(1);		        }                        else {			        strcpy(p1_tree_name, param_arg[setusetree1]);		        }		        use_tree1_file = TRUE;		        do_align_only = TRUE;		}	if(setnewtree1 != -1)		if(profile1_empty) {			error("Cannot align profiles.  No input file");			exit(1);		}		else if(profile_type == SEQUENCE) {			error("Invalid option /newtree1.");			exit(1);		}		else  {		        if(strlen(param_arg[setnewtree1]) == 0) {				error("Cannot align profiles.  No tree file specified");				exit(1);		        }                        else {			        strcpy(p1_tree_name, param_arg[setnewtree1]);		        }		    new_tree1_file = TRUE;		} 	if(setusetree2 != -1)		if(profile2_empty) {			error("Cannot align profiles.  No input file");			exit(1);		}		else if(profile_type == SEQUENCE) {			error("Invalid option /usetree2.");			exit(1);		}		else  {		        if(strlen(param_arg[setusetree2]) == 0) {				error("Cannot align profiles.  No tree file specified");				exit(1);		        }                        else {			        strcpy(p2_tree_name, param_arg[setusetree2]);		        }		        use_tree2_file = TRUE;		        do_align_only = TRUE;		}	if(setnewtree2 != -1)		if(profile2_empty) {			error("Cannot align profiles.  No input file");			exit(1);		}		else if(profile_type == SEQUENCE) {			error("Invalid option /newtree2.");			exit(1);		}		else  {		        if(strlen(param_arg[setnewtree2]) == 0) {				error("Cannot align profiles.  No tree file specified");				exit(1);		        }                        else {			        strcpy(p2_tree_name, param_arg[setnewtree2]);		        }		    new_tree2_file = TRUE;		} 	if( (!do_tree) && (!do_boot) && (!empty) && (!do_profile) && (!do_align_only) && (!do_tree_only) && (!do_convert)) 		do_align = TRUE;/*** ? /quicktree  */        if(setquicktree != -1)		quick_pairalign = TRUE;	if(dnaflag) {		gap_open   = dna_gap_open;		gap_extend = dna_gap_extend;		pw_go_penalty  = dna_pw_go_penalty;		pw_ge_penalty  = dna_pw_ge_penalty;                ktup       = dna_ktup;                window     = dna_window;                signif     = dna_signif;                wind_gap   = dna_wind_gap;	}	else {		gap_open   = prot_gap_open;		gap_extend = prot_gap_extend;		pw_go_penalty  = prot_pw_go_penalty;		pw_ge_penalty  = prot_pw_ge_penalty;                ktup       = prot_ktup;                window     = prot_window;                signif     = prot_signif;                wind_gap   = prot_wind_gap;	}		if(interactive) {		if (!xmenus) usemenu = TRUE;		return;	}	if(!do_something) {		error("No input file(s) specified");		exit(1);	}/****************************************************************************//* Now do whatever has been requested ***************************************//****************************************************************************/	if(do_profile) {		if (profile_type == PROFILE) profile_align(p1_tree_name,p2_tree_name);		else new_sequence_align(phylip_tree_name);	}	else if(do_align)		align(phylip_tree_name);        else if(do_convert) {                get_path(seqname,path);                if(!open_alignment_output(path)) exit(1);                create_alignment_output(1,nseqs);        }        else if (do_align_only)                get_tree(phylip_tree_name);	else if(do_tree_only)		make_tree(phylip_tree_name);	else if(do_tree)		phylogenetic_tree(phylip_tree_name,clustal_tree_name,dist_tree_name,nexus_tree_name,pim_name);	else if(do_boot)		bootstrap_tree(phylip_tree_name,clustal_tree_name,nexus_tree_name);	fprintf(stdout,"\n");	exit(0);/*******whew!***now*go*home****/}Boolean user_mat(char *str, short *mat, short *xref){        sint maxres;        FILE *infile;        if(usemenu)                getstr("Enter name of the matrix file",lin2);        else                strcpy(lin2,str);        if(*lin2 == EOS) return FALSE;        if((infile=fopen(lin2,"r"))==NULL) {                error("Cannot find matrix file [%s]",lin2);                return FALSE;        }	strcpy(str, lin2);	maxres = read_user_matrix(str, mat, xref);        if (maxres <= 0) return FALSE;	return TRUE;}Boolean user_mat_series(char *str, short *mat, short *xref){        sint maxres;        FILE *infile;        if(usemenu)                getstr("Enter name of the matrix file",lin2);        else                strcpy(lin2,str);        if(*lin2 == EOS) return FALSE;        if((infile=fopen(lin2,"r"))==NULL) {                error("Cannot find matrix file [%s]",lin2);                return FALSE;        }	strcpy(str, lin2);	maxres = read_matrix_series(str, mat, xref);        if (maxres <= 0) return FALSE;	return TRUE;}sint seq_input(Boolean append){        sint i;	sint local_nseqs;	if(usemenu) {fprintf(stdout,"\n\nSequences should all be in 1 file.\n"); fprintf(stdout,"\n7 formats accepted: \n");fprintf(stdout,"NBRF/PIR, EMBL/SwissProt, Pearson (Fasta), GDE, Clustal, GCG/MSF, RSF.\n\n\n");/*fprintf(stdout,"\nGCG users should use TOPIR to convert their sequence files before use.\n\n\n");*/	}       if (append)          local_nseqs = readseqs(nseqs+(sint)1);       else          local_nseqs = readseqs((sint)1);  /*  1 is the first seq to be read */       if(local_nseqs < 0)               /* file could not be opened */           { 		return local_nseqs;           }       else if(local_nseqs == 0)         /* no sequences */           {	       error("No sequences in file!  Bad format?");               return local_nseqs;           }       else            {	   struct_penalties1 = struct_penalties2 = NONE;	   if (sec_struct_mask1 != NULL) sec_struct_mask1=ckfree(sec_struct_mask1);	   if (sec_struct_mask2 != NULL) sec_struct_mask2=ckfree(sec_struct_mask2);	   if (gap_penalty_mask1 != NULL) gap_penalty_mask1=ckfree(gap_penalty_mask1);	   if (gap_penalty_mask2 != NULL) gap_penalty_mask2=ckfree(gap_penalty_mask2);	   if (ss_name1 != NULL) ss_name1=ckfree(ss_name1);	   if (ss_name2 != NULL) ss_name2=ckfree(ss_name2);	   		if(append) nseqs+=local_nseqs;		else nseqs=local_nseqs;		info("Sequences assumed to be %s",			dnaflag?"DNA":"PROTEIN");		if (usemenu) {			fprintf(stdout,"\n\n");                	for(i=1; i<=nseqs; i++) {/* DES                         fprintf(stdout,"%s: = ",names[i]); */                        	info("Sequence %d: %-*s   %6.d %s",                        	(pint)i,max_names,names[i],(pint)seqlen_array[i],dnaflag?"bp":"aa");                	}	                }				if(dnaflag) {				gap_open   = dna_gap_open;				gap_extend = dna_gap_extend;			}			else {				gap_open   = prot_gap_open;				gap_extend = prot_gap_extend;			}			empty=FALSE;	   }	return local_nseqs;	}sint profile_input(void)   /* read a profile   */{                                           /* profile_no is 1 or 2  */        sint local_nseqs, i;	        if(profile_no == 2 && profile1_empty)            {             error("You must read in profile number 1 first");             return 0;           }    if(profile_no == 1)     /* for the 1st profile */      {       local_nseqs = readseqs((sint)1); /* (1) means 1st seq to be read = no. 1 */       if(local_nseqs < 0)               /* file could not be opened */           { 		return local_nseqs;           }       else if(local_nseqs == 0)         /* no sequences  */           {	       error("No sequences in file!  Bad format?");		return local_nseqs;           }       else if (local_nseqs > 0)           { 				/* success; found some seqs. */		struct_penalties1 = NONE;		if (sec_struct_mask1 != NULL) sec_struct_mask1=ckfree(sec_struct_mask1);		if (gap_penalty_mask1 != NULL) gap_penalty_mask1=ckfree(gap_penalty_mask1);		if (ss_name1 != NULL) ss_name1=ckfree(ss_name1);                if (struct_penalties != NONE) /* feature table / mask in alignment */                	{					struct_penalties1 = struct_penalties;					if (struct_penalties == SECST) {						sec_struct_mask1 = (char *)ckalloc((max_aln_length) * sizeof (char));						for (i=0;i<max_aln_length;i++)							sec_struct_mask1[i] = sec_struct_mask[i];					}					gap_penalty_mask1 = (char *)ckalloc((max_aln_length) * sizeof (char));					for (i=0;i<max_aln_length;i++)						gap_penalty_mask1[i] = gap_penalty_mask[i];        				ss_name1 = (char *)ckalloc( (MAXNAMES+1) * sizeof (char));					strcpy(ss_name1,ss_name);if (debug>0) {for (i=0;i<seqlen_array[1];i++)	fprintf(stdout,"%c",gap_penalty_mask1[i]);fprintf(stdout,"\n");}					}                nseqs = profile1_nseqs = local_nseqs;				info("No. of seqs=%d",(pint)nseqs);				profile1_empty=FALSE;				profile2_empty=TRUE;	   }      }    else      {			        /* first seq to be read = profile1_nseqs + 1 */       local_nseqs = readseqs(profile1_nseqs+(sint)1);        if(local_nseqs < 0)               /* file could not be opened */           { 		return local_nseqs;           }       else if(local_nseqs == 0)         /* no sequences */           {	       error("No sequences in file!  Bad format?");		return local_nseqs;           }       else if(local_nseqs > 0)           {		struct_penalties2 = NONE;		if (sec_struct_mask2 != NULL) sec_struct_mask2=ckfree(sec_struct_mask2);		if (gap_penalty_mask2 != NULL) gap_penalty_mask2=ckfree(gap_penalty_mask2);		if (ss_name2 != NULL) ss_name2=ckfree(ss_name2);                if (struct_penalties != NONE) /* feature table / mask in alignment */                	{					struct_penalties2 = struct_penalties;					if (struct_penalties == SECST) {						sec_struct_mask2 = (char *)ckalloc((max_aln_length) * sizeof (char));						for (i=0;i<max_aln_length;i++)							sec_struct_mask2[i] = sec_struct_mask[i];					}					gap_penalty_mask2 = (char *)ckalloc((max_aln_length) * sizeof (char));					for (i=0;i<max_aln_length;i++)						gap_penalty_mask2[i] = gap_penalty_mask[i];        				ss_name2 = (char *)ckalloc( (MAXNAMES+1) * sizeof (char));					strcpy(ss_name2,ss_name);if (debug>0) {for (i=0;i<seqlen_array[profile1_nseqs+1];i++)	fprintf(stdout,"%c",gap_penalty_mask2[i]);fprintf(stdout,"\n");