}					}				info("No. of seqs in profile=%d",(pint)local_nseqs);                nseqs = profile1_nseqs + local_nseqs;                info("Total no. of seqs     =%d",(pint)nseqs);				profile2_empty=FALSE;				empty = FALSE;	   }      }	if (sec_struct_mask != NULL) sec_struct_mask=ckfree(sec_struct_mask);	if (gap_penalty_mask != NULL) gap_penalty_mask=ckfree(gap_penalty_mask);	if (ss_name != NULL) ss_name=ckfree(ss_name);	if(local_nseqs<=0) return local_nseqs;		info("Sequences assumed to be %s",		dnaflag?"DNA":"PROTEIN");	if (usemenu) fprintf(stdout,"\n\n");        for(i=profile2_empty?1:profile1_nseqs+1; i<=nseqs; 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;	}	return nseqs;}static void calc_gap_penalty_mask(int prf_length, char *mask, char *gap_mask){	int i,j;	char *struct_mask;	struct_mask = (char *)ckalloc((prf_length+1) * sizeof(char));/*    calculate the gap penalty mask from the secondary structures*/	i=0;	while (i<prf_length) {		if (tolower(mask[i]) == 'a' || mask[i] == '$') {			for (j = -helix_end_plus; j<0; j++) {				if ((i+j>=0) && (tolower(struct_mask[i+j]) != 'a')				             && (tolower(struct_mask[i+j]) != 'b'))					struct_mask[i+j] = 'a';			}			for (j = 0; j<helix_end_minus; j++) {				if (i+j>=prf_length || (tolower(mask[i+j]) != 'a'				                    && mask[i+j] != '$')) break;				struct_mask[i+j] = 'a';			}			i += j;			while (tolower(mask[i]) == 'a'				                    || mask[i] == '$') {				if (i>=prf_length) break;				if (mask[i] == '$') {					struct_mask[i] = 'A';					i++;					break;				}				else struct_mask[i] = mask[i];				i++;			}			for (j = 0; j<helix_end_minus; j++) {				if ((i-j-1>=0) && (tolower(mask[i-j-1]) == 'a'				                    || mask[i-j-1] == '$'))					struct_mask[i-j-1] = 'a';			}			for (j = 0; j<helix_end_plus; j++) {				if (i+j>=prf_length) break;				struct_mask[i+j] = 'a';			}		}	 	else if (tolower(mask[i]) == 'b' || mask[i] == '%') {			for (j = -strand_end_plus; j<0; j++) {				if ((i+j>=0) && (tolower(struct_mask[i+j]) != 'a')				             && (tolower(struct_mask[i+j]) != 'b'))					struct_mask[i+j] = 'b';			}			for (j = 0; j<strand_end_minus; j++) {				if (i+j>=prf_length || (tolower(mask[i+j]) != 'b'				                    && mask[i+j] != '%')) break;				struct_mask[i+j] = 'b';			}			i += j;			while (tolower(mask[i]) == 'b'				                    || mask[i] == '%') {				if (i>=prf_length) break;				if (mask[i] == '%') {					struct_mask[i] = 'B';					i++;					break;				}				else struct_mask[i] = mask[i];				i++;			}			for (j = 0; j<strand_end_minus; j++) {				if ((i-j-1>=0) && (tolower(mask[i-j-1]) == 'b'				                    || mask[i-j-1] == '%'))				struct_mask[i-j-1] = 'b';			}			for (j = 0; j<strand_end_plus; j++) {				if (i+j>=prf_length) break; 				struct_mask[i+j] = 'b';			}		}	else i++;	}	for(i=0;i<prf_length;i++) {		switch (struct_mask[i]) {			case 'A':				gap_mask[i] = helix_penalty+'0';				break;			case 'a':				gap_mask[i] = helix_end_penalty+'0';				break;			case 'B':				gap_mask[i] = strand_penalty+'0';				break;			case 'b':				gap_mask[i] = strand_end_penalty+'0';				break;			default:				gap_mask[i] = loop_penalty+'0';				break;		}	}	struct_mask=ckfree(struct_mask);	}void print_sec_struct_mask(int prf_length, char *mask, char *struct_mask){	int i,j;/*    calculate the gap penalty mask from the secondary structures*/	i=0;	while (i<prf_length) {		if (tolower(mask[i]) == 'a' || mask[i] == '$') {			for (j = 0; j<helix_end_minus; j++) {				if (i+j>=prf_length || (tolower(mask[i+j]) != 'a'				                    && mask[i+j] != '$')) break;				struct_mask[i+j] = 'a';			}			i += j;			while (tolower(mask[i]) == 'a'				                    || mask[i] == '$') {				if (i>=prf_length) break;				if (mask[i] == '$') {					struct_mask[i] = 'A';					i++;					break;				}				else struct_mask[i] = mask[i];				i++;			}			for (j = 0; j<helix_end_minus; j++) {				if ((i-j-1>=0) && (tolower(mask[i-j-1]) == 'a'				                    || mask[i-j-1] == '$'))					struct_mask[i-j-1] = 'a';			}		}	 	else if (tolower(mask[i]) == 'b' || mask[i] == '%') {			for (j = 0; j<strand_end_minus; j++) {				if (i+j>=prf_length || (tolower(mask[i+j]) != 'b'				                    && mask[i+j] != '%')) break;				struct_mask[i+j] = 'b';			}			i += j;			while (tolower(mask[i]) == 'b'				                    || mask[i] == '%') {				if (i>=prf_length) break;				if (mask[i] == '%') {					struct_mask[i] = 'B';					i++;					break;				}				else struct_mask[i] = mask[i];				i++;			}			for (j = 0; j<strand_end_minus; j++) {				if ((i-j-1>=0) && (tolower(mask[i-j-1]) == 'b'				                    || mask[i-j-1] == '%'))				struct_mask[i-j-1] = 'b';			}		}	else i++;	}}FILE *  open_output_file(char *prompt,      char *path, 				char *file_name,   char *file_extension) {	static char temp[FILENAMELEN+1];	static char local_prompt[MAXLINE];	FILE * file_handle;/*	if (*file_name == EOS) {*/		strcpy(file_name,path);		strcat(file_name,file_extension);/*	}*/	if(strcmp(file_name,seqname)==0) {		warning("Output file name is the same as input file.");		if (usemenu) {			strcpy(local_prompt,"\n\nEnter new name to avoid overwriting ");			strcat(local_prompt," [%s]: ");          			fprintf(stdout,local_prompt,file_name);			gets(temp);			if(*temp != EOS) strcpy(file_name,temp);		}	}	else if (usemenu) {		strcpy(local_prompt,prompt);		strcat(local_prompt," [%s]: ");          		fprintf(stdout,local_prompt,file_name);		gets(temp);		if(*temp != EOS) strcpy(file_name,temp);	}#ifdef VMS	if((file_handle=fopen(file_name,"w","rat=cr","rfm=var"))==NULL) {#else	if((file_handle=fopen(file_name,"w"))==NULL) {#endif		error("Cannot open output file [%s]",file_name);		return NULL;	}	return file_handle;}FILE *  open_explicit_file(char *file_name){ 	FILE * file_handle;	if (*file_name == EOS) {		error("Bad output file [%s]",file_name);		return NULL;	}#ifdef VMS	if((file_handle=fopen(file_name,"w","rat=cr","rfm=var"))==NULL) {#else	if((file_handle=fopen(file_name,"w"))==NULL) {#endif		error("Cannot open output file [%s]",file_name);		return NULL;	}	return file_handle;}/* Ramu void */void align(char *phylip_name){ 	char path[FILENAMELEN+1];	FILE *tree;	sint count;		if(empty && usemenu) {		error("No sequences in memory. Load sequences first.");		return;	}	   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);        get_path(seqname,path);/* DES DEBUG 	fprintf(stdout,"\n\n Seqname = %s  \n Path = %s \n\n",seqname,path);*/	if(usemenu || !interactive) {        	if(!open_alignment_output(path)) return;	}	if (nseqs >= 2) {        	get_path(seqname,path);        	if (phylip_name[0]!=EOS) {                	if((tree = open_explicit_file(                	phylip_name))==NULL) return;        	}        	else {                 	if((tree = open_output_file(                	"\nEnter name for new GUIDE TREE           file  ",path,                	phylip_name,"dnd")) == NULL) return;        	}	}	if (save_parameters) create_parameter_output();	if(reset_alignments_new || reset_alignments_all) reset_align();        info("Start of Pairwise alignments");        info("Aligning...");        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 (quick_pairalign)           show_pair((sint)0,nseqs,(sint)0,nseqs);        else           pairalign((sint)0,nseqs,(sint)0,nseqs);	if (nseqs >= 2) {		guide_tree(tree,1,nseqs);		info("Guide tree        file created:   [%s]",                phylip_name);	}		count = malign((sint)0,phylip_name);		if (count <= 0) return;	if (usemenu) fprintf(stdout,"\n\n\n");		create_alignment_output(1,nseqs);        if (showaln && usemenu) show_aln();	phylip_name[0]=EOS;	return ;}void new_sequence_align(char *phylip_name){ 	char path[FILENAMELEN+1];	char tree_name[FILENAMELEN+1],temp[MAXLINE+1];	Boolean use_tree;	FILE *tree;	sint i,j,count;	float dscore;	Boolean save_ss2;		if(profile1_empty && usemenu) {		error("No profile in memory. Input 1st profile first.");		return;	}	if(profile2_empty && usemenu) {		error("No sequences in memory. Input sequences first.");		return;	}        get_path(profile2_name,path);        if(usemenu || !interactive) {        	if(!open_alignment_output(path)) return;	}	new_seq = profile1_nseqs+1;/* check for secondary structure information for list of sequences */	save_ss2 = use_ss2;	if (struct_penalties2 != NONE && use_ss2 == TRUE && (nseqs - profile1_nseqs >1)) {		if (struct_penalties2 == SECST) 			warning("Warning: ignoring secondary structure for a list of sequences");		else if (struct_penalties2 == GMASK)			warning("Warning: ignoring gap penalty mask for a list of sequences");		use_ss2 = FALSE;	}	for (i=1;i<=new_seq;i++) {     		for (j=i+1;j<=new_seq;j++) {       			dscore = countid(i,j);       			tmat[i][j] = ((double)100.0 - (double)dscore)/(double)100.0;       			tmat[j][i] = tmat[i][j];     		}   	}	tree_name[0] = EOS;	use_tree = FALSE;	if (nseqs >= 2) {		if (check_tree && usemenu) {			strcpy(tree_name,path);			strcat(tree_name,"dnd");#ifdef VMS        	if((tree=fopen(tree_name,"r","rat=cr","rfm=var"))!=NULL) {#else        	if((tree=fopen(tree_name,"r"))!=NULL) {#endif		if (usemenu)            	fprintf(stdout,"\nUse the existing GUIDE TREE file,  %s  (y/n) ? [y]: ",                                           tree_name);                gets(temp);                if(*temp != 'n' && *temp != 'N') {                    strcpy(phylip_name,tree_name);                    use_tree = TRUE;                }                fclose(tree);        	}		}		else if (!usemenu && use_tree_file) {			use_tree = TRUE;		}	}		if (save_parameters) create_parameter_output();	if(reset_alignments_new || reset_alignments_all) {/*		reset_prf1();*/		reset_prf2();	}	else fix_gaps();	if (struct_penalties1 == SECST)		calc_gap_penalty_mask(seqlen_array[1],sec_struct_mask1,gap_penalty_mask1);	if (struct_penalties2 == SECST)calc_gap_penalty_mask(seqlen_array[profile1_nseqs+1],sec_struct_mask2,gap_penalty_mask2);/* create the new tree file, if necessary */	if (use_tree == FALSE) {		if (nseqs >= 2) {        		get_path(profile2_name,path);        		if (phylip_name[0]!=EOS) {                		if((tree = open_explicit_file(                		phylip_name))==NULL) return;        		}        		else {                 		if((tree = open_output_file(                		"\nEnter name for new GUIDE TREE           file  ",path,                		phylip_name,"dnd")) == NULL) return;        		}		}        info("Start of Pairwise alignments");        info("Aligning...");        if(dnaflag) {                gap_open   = dna_gap_open;                gap_extend = dna_gap_extend;                pw_go_