amenu.c

经典生物信息学多序列比对工具clustalw

			fprintf(stdout,"= NO\n");
		fprintf(stdout,"\n");
		fprintf(stdout,"     3. Output in alignment  ");
		fprintf(stdout,"= %s\n",secstroutput_txt[output_struct_penalties]);
		fprintf(stdout,"\n");

		fprintf(stdout,"     4. Helix gap penalty                     :%d\n",(pint)helix_penalty);
		fprintf(stdout,"     5. Strand gap penalty                    :%d\n",(pint)strand_penalty);
		fprintf(stdout,"     6. Loop gap penalty                      :%d\n",(pint)loop_penalty);

		fprintf(stdout,"     7. Secondary structure terminal penalty  :%d\n",(pint)helix_end_penalty);
		fprintf(stdout,"     8. Helix terminal positions       within :%d      outside :%d\n",
		                                 (pint)helix_end_minus,(pint)helix_end_plus);
		fprintf(stdout,"     9. Strand terminal positions      within :%d      outside :%d\n",
		                                 (pint)strand_end_minus,(pint)strand_end_plus);

		fprintf(stdout,"\n\n");
		fprintf(stdout,"     H. HELP\n\n\n");
		
		getstr("Enter number (or [RETURN] to exit)",lin2);
		if( *lin2 == EOS) { 
			return;
		}
		
		switch(toupper(*lin2)) {
			case '1': use_ss1 ^= TRUE;
				break;
			case '2': use_ss2 ^= TRUE;
				break;
			case '3': output_struct_penalties = secstroutput_options();
				break;
			case '4':
				fprintf(stdout,"Helix Penalty Currently: %d\n",(pint)helix_penalty);
				helix_penalty=getint("Enter number",1,9,helix_penalty);
				break;
			case '5':
				fprintf(stdout,"Strand Gap Penalty Currently: %d\n",(pint)strand_penalty);
				strand_penalty=getint("Enter number",1,9,strand_penalty);
				break;
			case '6':
				fprintf(stdout,"Loop Gap Penalty Currently: %d\n",(pint)loop_penalty);
				loop_penalty=getint("Enter number",1,9,loop_penalty);
				break;
			case '7':
				fprintf(stdout,"Secondary Structure Terminal Penalty Currently: %d\n",
				          (pint)helix_end_penalty);
				helix_end_penalty=getint("Enter number",1,9,helix_end_penalty);
				strand_end_penalty = helix_end_penalty;
				break;
			case '8':
				fprintf(stdout,"Helix Terminal Positions Currently: \n");
				fprintf(stdout,"        within helix: %d     outside helix: %d\n",
				                            (pint)helix_end_minus,(pint)helix_end_plus);
				helix_end_minus=getint("Enter number of residues within helix",0,3,helix_end_minus);
				helix_end_plus=getint("Enter number of residues outside helix",0,3,helix_end_plus);
				break;
			case '9':
				fprintf(stdout,"Strand Terminal Positions Currently: \n");
				fprintf(stdout,"        within strand: %d     outside strand: %d\n",
				                            (pint)strand_end_minus,(pint)strand_end_plus);
				strand_end_minus=getint("Enter number of residues within strand",0,3,strand_end_minus);
				strand_end_plus=getint("Enter number of residues outside strand",0,3,strand_end_plus);
				break;
			case '?':
			case 'H':
				get_help('B');
				break;
			default:
				fprintf(stdout,"\n\nUnrecognised Command\n\n");
				break;
		}
	}
}


static sint secstroutput_options(void)
{

        while(TRUE)
        {
                fprintf(stdout,"\n\n\n");
                fprintf(stdout," ********* Secondary Structure Output Menu *********\n");
                fprintf(stdout,"\n\n");


                fprintf(stdout,"     1. %s\n",secstroutput_txt[0]);
                fprintf(stdout,"     2. %s\n",secstroutput_txt[1]);
                fprintf(stdout,"     3. %s\n",secstroutput_txt[2]);
                fprintf(stdout,"     4. %s\n",secstroutput_txt[3]);
                fprintf(stdout,"     H. HELP\n\n");
                fprintf(stdout,
"     -- Current output is %s ",secstroutput_txt[output_struct_penalties]);
                fprintf(stdout,"--\n");


                getstr("\n\nEnter number (or [RETURN] to exit)",lin2);
                if(*lin2 == EOS) return(output_struct_penalties);

        	switch(toupper(*lin2))
        	{
       	 		case '1': return(0);
        		case '2': return(1);
      			case '3': return(2);
        		case '4': return(3);
			case '?': 
        		case 'H': get_help('C');
            		case 'Q':
        		case 'X': return(0);

        		default: fprintf(stdout,"\n\nUnrecognised Command\n\n");
            		break;
        	}
        }
}







static void phylogenetic_tree_menu(void)
{
        int catchint;

        catchint = signal(SIGINT, SIG_IGN) != SIG_IGN;
        if (catchint) {
                if (setjmp(jmpbuf) != 0)
                        fprintf(stdout,"\n.. Interrupt\n");
#ifdef UNIX
                if (signal(SIGINT,jumper) == BADSIG)
                        fprintf(stdout,"Error: signal\n");
#else
                if (signal(SIGINT,SIG_DFL) == BADSIG)
                        fprintf(stdout,"Error: signal\n");
#endif
        }


    while(TRUE)
    {
        fprintf(stdout,"\n\n\n");
        fprintf(stdout,"****** PHYLOGENETIC TREE MENU ******\n");
        fprintf(stdout,"\n\n");

        fprintf(stdout,"    1.  Input an alignment\n");
        fprintf(stdout,"    2.  Exclude positions with gaps?        ");
	if(tossgaps)
		fprintf(stdout,"= ON\n");
	else
		fprintf(stdout,"= OFF\n");
        fprintf(stdout,"    3.  Correct for multiple substitutions? ");
	if(kimura)
		fprintf(stdout,"= ON\n");
	else
		fprintf(stdout,"= OFF\n");
        fprintf(stdout,"    4.  Draw tree now\n");
        fprintf(stdout,"    5.  Bootstrap tree\n");
	fprintf(stdout,"    6.  Output format options\n");
        fprintf(stdout,"\n");
        fprintf(stdout,"    S.  Execute a system command\n");
        fprintf(stdout,"    H.  HELP\n");
        fprintf(stdout,"    or press [RETURN] to go back to main menu\n\n\n");

        getstr("Your choice",lin1);
        if(*lin1 == EOS) return;

        switch(toupper(*lin1))
        {
       	 	case '1': seq_input(FALSE);
				phylip_name[0]=EOS;
				clustal_name[0]=EOS;
				dist_name[0]=EOS;
				nexus_name[0]=EOS;
         	   	break;
        	case '2': tossgaps ^= TRUE;
          	  	break;
      		case '3': kimura ^= TRUE;;
            		break;
        	case '4': phylogenetic_tree(phylip_name,clustal_name,dist_name,nexus_name,"amenu.pim");
            		break;
        	case '5': bootstrap_tree(phylip_name,clustal_name,nexus_name);
            		break;
		case '6': tree_format_options_menu();
			break;
        	case 'S': do_system();
            		break;
            	case '?':
        	case 'H': get_help('7');
            		break;
            	case 'Q':
        	case 'X': return;

        	default: fprintf(stdout,"\n\nUnrecognised Command\n\n");
            	break;
        }
    }
}






static void tree_format_options_menu(void)      /* format of tree output */
{	
        int catchint;

        catchint = signal(SIGINT, SIG_IGN) != SIG_IGN;
        if (catchint) {
                if (setjmp(jmpbuf) != 0)
                        fprintf(stdout,"\n.. Interrupt\n");
#ifdef UNIX
                if (signal(SIGINT,jumper) == BADSIG)
                        fprintf(stdout,"Error: signal\n");
#else
                if (signal(SIGINT,SIG_DFL) == BADSIG)
                        fprintf(stdout,"Error: signal\n");
#endif
        }


	while(TRUE) {
	fprintf(stdout,"\n\n\n");
	fprintf(stdout," ****** Format of Phylogenetic Tree Output ******\n");
	fprintf(stdout,"\n\n");
	fprintf(stdout,"     1. Toggle CLUSTAL format tree output    =  %s\n",
					(!output_tree_clustal)  ? "OFF" : "ON");
	fprintf(stdout,"     2. Toggle Phylip format tree output     =  %s\n",
					(!output_tree_phylip)   ? "OFF" : "ON");
	fprintf(stdout,"     3. Toggle Phylip distance matrix output =  %s\n",
					(!output_tree_distances)? "OFF" : "ON");
	fprintf(stdout,"     4. Toggle Nexus format tree output      =  %s\n\n",
					(!output_tree_nexus)? "OFF" : "ON");
	fprintf(stdout,"     5. Toggle Phylip bootstrap positions    =  %s\n\n",
(bootstrap_format==BS_NODE_LABELS) ? "NODE LABELS" : "BRANCH LABELS");
	fprintf(stdout,"\n");
	fprintf(stdout,"     H. HELP\n\n\n");	
	
		getstr("Enter number (or [RETURN] to exit)",lin2);
		if(*lin2 == EOS) return;
		
		switch(toupper(*lin2)) {
			case '1':
				output_tree_clustal   ^= TRUE;
				break;
			case '2':
              			output_tree_phylip    ^= TRUE;
			  	break;
			case '3':
              			output_tree_distances ^= TRUE;
			  	break;
			case '4':
              			output_tree_nexus ^= TRUE;
			  	break;
			case '5':
              			if (bootstrap_format == BS_NODE_LABELS)
					bootstrap_format = BS_BRANCH_LABELS;
				else
					bootstrap_format = BS_NODE_LABELS;
			  	break;
			case '?':
			case 'H':
				get_help('0');
				break;
			default:
				fprintf(stdout,"\n\nUnrecognised Command\n\n");
				break;
		}
	}
}


static void format_options_menu(void)      /* format of alignment output */
{	
	sint i;
	sint length = 0;
	char path[FILENAMELEN+1];
    int catchint;

        catchint = signal(SIGINT, SIG_IGN) != SIG_IGN;
        if (catchint) {
                if (setjmp(jmpbuf) != 0)
                        fprintf(stdout,"\n.. Interrupt\n");
#ifdef UNIX
                if (signal(SIGINT,jumper) == BADSIG)
                        fprintf(stdout,"Error: signal\n");
#else
                if (signal(SIGINT,SIG_DFL) == BADSIG)
                        fprintf(stdout,"Error: signal\n");
#endif
        }


	while(TRUE) {
	fprintf(stdout,"\n\n\n");
	fprintf(stdout," ********* Format of Alignment Output *********\n");
	fprintf(stdout,"\n\n");
	fprintf(stdout,"     F. Toggle FASTA format output       =  %s\n\n",
					(!output_fasta) ? "OFF" : "ON");
	fprintf(stdout,"     1. Toggle CLUSTAL format output     =  %s\n",
					(!output_clustal) ? "OFF" : "ON");
	fprintf(stdout,"     2. Toggle NBRF/PIR format output    =  %s\n",
					(!output_nbrf) ? "OFF" : "ON");
	fprintf(stdout,"     3. Toggle GCG/MSF format output     =  %s\n",
					(!output_gcg) ? "OFF" : "ON");
	fprintf(stdout,"     4. Toggle PHYLIP format output      =  %s\n",
					(!output_phylip) ? "OFF" : "ON");
	fprintf(stdout,"     5. Toggle NEXUS format output       =  %s\n",
					(!output_nexus) ? "OFF" : "ON");
	fprintf(stdout,"     6. Toggle GDE format output         =  %s\n\n",
					(!output_gde) ? "OFF" : "ON");
	fprintf(stdout,"     7. Toggle GDE output case           =  %s\n",
					(!lowercase) ? "UPPER" : "LOWER");

	fprintf(stdout,"     8. Toggle CLUSTALW sequence numbers =  %s\n",
					(!cl_seq_numbers) ? "OFF" : "ON");
	fprintf(stdout,"     9. Toggle output order              =  %s\n\n",
					(output_order==0) ? "INPUT FILE" : "ALIGNED");

	fprintf(stdout,"     0. Create alignment output file(s) now?\n\n");
	fprintf(stdout,"     T. Toggle parameter output          = %s\n",
					(!save_parameters) ? "OFF" : "ON");
	fprintf(stdout,"     R. Toggle sequence range numbers =  %s\n",
					(!seqRange) ? "OFF" : "ON");
	fprintf(stdout,"\n");
	fprintf(stdout,"     H. HELP\n\n\n");	
	
		getstr("Enter number (or [RETURN] to exit)",lin2);
		if(*lin2 == EOS) return;
		
		switch(toupper(*lin2)) {
			case '1':
				output_clustal ^= TRUE;
				break;
			case '2':
              			output_nbrf ^= TRUE;
			  	break;
			case '3':
              			output_gcg ^= TRUE;
			  	break;
			case '4':
              			output_phylip ^= TRUE;
			  	break;
			case '5':
              			output_nexus ^= TRUE;
			  	break;
			case '6':
              			output_gde ^= TRUE;
			  	break;
			case '7':
              			lowercase ^= TRUE;
			  	break;
			case '8':
              			cl_seq_numbers ^= TRUE;
			  	break;
			case '9':
                                if (output_order == INPUT) output_order = ALIGNED;
              			else output_order = INPUT;
			  	break;
			case 'F':
              			output_fasta ^= TRUE;
			  	break;
			case 'R':
              			seqRange ^= TRUE;
			  	break;

			case '0':		/* DES */
				if(empty) {
					error("No sequences loaded");
					break;
				}
				get_path(seqname,path);
				if(!open_alignment_output(path)) break;
				create_alignment_output(1,nseqs);
				break;
        		case 'T': save_parameters ^= TRUE;
	   			 break;
			case '?':
			case 'H':
				get_help('5');
				break;
			default:
				fprintf(stdout,"\n\nUnrecognised Command\n\n");
				break;
		}
	}
}












static void pair_menu(void)
{
        int catchint;

        catchint = signal(SIGINT, SIG_IGN) != SIG_IGN;
        if (catchint) {
                if (setjmp(jmpbuf) != 0)
                        fprintf(stdout,"\n.. Interrupt\n");
#ifdef UNIX
                if (signal(SIGINT,jumper) == BADSIG)
                        fprintf(stdout,"Error: signal\n");
#else
                if (signal(SIGINT,SIG_DFL) == BADSIG)
                        fprintf(stdout,"Error: signal\n");
#endif
        }


        if(dnaflag) {
                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 {
                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;

        }

	while(TRUE) {
	
		fprintf(stdout,"\n\n\n");