amenu.c

经典生物信息学多序列比对工具clustalw

		fprintf(stdout," ********* PAIRWISE ALIGNMENT PARAMETERS *********\n");
		fprintf(stdout,"\n\n");

		fprintf(stdout,"     Slow/Accurate alignments:\n\n");

		fprintf(stdout,"     1. Gap Open Penalty       :%4.2f\n",pw_go_penalty);
		fprintf(stdout,"     2. Gap Extension Penalty  :%4.2f\n",pw_ge_penalty);
		fprintf(stdout,"     3. Protein weight matrix  :%s\n" ,
                                        matrix_menu.opt[pw_matnum-1].title);
		fprintf(stdout,"     4. DNA weight matrix      :%s\n" ,
                                        dnamatrix_menu.opt[pw_dnamatnum-1].title);
		fprintf(stdout,"\n");

		fprintf(stdout,"     Fast/Approximate alignments:\n\n");

		fprintf(stdout,"     5. Gap penalty            :%d\n",(pint)wind_gap);
		fprintf(stdout,"     6. K-tuple (word) size    :%d\n",(pint)ktup);
		fprintf(stdout,"     7. No. of top diagonals   :%d\n",(pint)signif);
		fprintf(stdout,"     8. Window size            :%d\n\n",(pint)window);

                fprintf(stdout,"     9. Toggle Slow/Fast pairwise alignments ");
                if(quick_pairalign)
                      fprintf(stdout,"= FAST\n\n");
                else
                      fprintf(stdout,"= SLOW\n\n");


		fprintf(stdout,"     H. HELP\n\n\n");
		
		getstr("Enter number (or [RETURN] to exit)",lin2);
		if( *lin2 == EOS) {
                        if(dnaflag) {
                                dna_pw_go_penalty     = pw_go_penalty;
                                dna_pw_ge_penalty     = pw_ge_penalty;
                		dna_ktup       = ktup;
                		dna_window     = window;
                		dna_signif     = signif;
                		dna_wind_gap   = wind_gap;

                        }
                        else {
                                prot_pw_go_penalty     = pw_go_penalty;
                                prot_pw_ge_penalty     = pw_ge_penalty;
                		prot_ktup       = ktup;
                		prot_window     = window;
                		prot_signif     = signif;
                		prot_wind_gap   = wind_gap;

                        }
 
			return;
		}
		
		switch(toupper(*lin2)) {
			case '1':
				fprintf(stdout,"Gap Open Penalty Currently: %4.2f\n",pw_go_penalty);
				pw_go_penalty=(float)getreal("Enter number",(double)0.0,(double)100.0,(double)pw_go_penalty);
				break;
			case '2':
				fprintf(stdout,"Gap Extension Penalty Currently: %4.2f\n",pw_ge_penalty);
				pw_ge_penalty=(float)getreal("Enter number",(double)0.0,(double)10.0,(double)pw_ge_penalty);
				break;
                        case '3':
                                pw_matnum = read_matrix("PROTEIN",pw_matrix_menu,pw_mtrxname,pw_matnum,pw_usermat,pw_aa_xref);
                                break;
                        case '4':
                                pw_dnamatnum = read_matrix("DNA",dnamatrix_menu,pw_dnamtrxname,pw_dnamatnum,pw_userdnamat,pw_dna_xref);
                                break;
			case '5':
                                fprintf(stdout,"Gap Penalty Currently: %d\n",(pint)wind_gap);
                                wind_gap=getint("Enter number",1,500,wind_gap);
				break;
			case '6':
                                fprintf(stdout,"K-tuple Currently: %d\n",(pint)ktup);
                                if(dnaflag)
                                     ktup=getint("Enter number",1,4,ktup);
                                else
                                     ktup=getint("Enter number",1,2,ktup);                                     
				break;
			case '7':
                                fprintf(stdout,"Top diagonals Currently: %d\n",(pint)signif);
                                signif=getint("Enter number",1,50,signif);
				break;
			case '8':
                                fprintf(stdout,"Window size Currently: %d\n",(pint)window);
                                window=getint("Enter number",1,50,window);
				break;
                        case '9': quick_pairalign ^= TRUE;
                                break;
			case '?':
			case 'H':
				get_help('3');
				break;
			default:
				fprintf(stdout,"\n\nUnrecognised Command\n\n");
				break;
		}
	}
}





static void multi_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) {
		gap_open   = dna_gap_open;
		gap_extend = dna_gap_extend;
	}
	else {
		gap_open   = prot_gap_open;
		gap_extend = prot_gap_extend;
	}

	while(TRUE) {

		fprintf(stdout,"\n\n\n");
		fprintf(stdout," ********* MULTIPLE ALIGNMENT PARAMETERS *********\n");
		fprintf(stdout,"\n\n");
		
		fprintf(stdout,"     1. Gap Opening Penalty              :%4.2f\n",gap_open);
		fprintf(stdout,"     2. Gap Extension Penalty            :%4.2f\n",gap_extend);

		fprintf(stdout,"     3. Delay divergent sequences        :%d %%\n\n",(pint)divergence_cutoff);

                fprintf(stdout,"     4. DNA Transitions Weight           :%1.2f\n\n",transition_weight);
                fprintf(stdout,"     5. Protein weight matrix            :%s\n"
                                        	,matrix_menu.opt[matnum-1].title);
                fprintf(stdout,"     6. DNA weight matrix                :%s\n"
                                        	,dnamatrix_menu.opt[dnamatnum-1].title);
		fprintf(stdout,"     7. Use negative matrix              :%s\n\n",(!neg_matrix) ? "OFF" : "ON");
                fprintf(stdout,"     8. Protein Gap Parameters\n\n");
		fprintf(stdout,"     H. HELP\n\n\n");		

		getstr("Enter number (or [RETURN] to exit)",lin2);

		if(*lin2 == EOS) {
			if(dnaflag) {
				dna_gap_open    = gap_open;
				dna_gap_extend  = gap_extend;
			}
			else {
				prot_gap_open   = gap_open;
				prot_gap_extend = gap_extend;
			}
			return;
		}
		
		switch(toupper(*lin2)) {
			case '1':
			fprintf(stdout,"Gap Opening Penalty Currently: %4.2f\n",gap_open);
				gap_open=(float)getreal("Enter number",(double)0.0,(double)100.0,(double)gap_open);
				break;
			case '2':
				fprintf(stdout,"Gap Extension Penalty Currently: %4.2f\n",gap_extend);
				gap_extend=(float)getreal("Enter number",(double)0.0,(double)10.0,(double)gap_extend);
				break;
			case '3':
				fprintf(stdout,"Min Identity Currently: %d\n",(pint)divergence_cutoff);
				divergence_cutoff=getint("Enter number",0,100,divergence_cutoff);
				break;
			case '4':
				fprintf(stdout,"Transition Weight Currently: %1.2f\n",(pint)transition_weight);
				transition_weight=(float)getreal("Enter number",(double)0.0,(double)1.0,(double)transition_weight);
				break;
			case '5':
                                matnum = read_matrix("PROTEIN",matrix_menu,mtrxname,matnum,usermat,aa_xref);
				break;
			case '6':
                                dnamatnum = read_matrix("DNA",dnamatrix_menu,dnamtrxname,dnamatnum,userdnamat,dna_xref);
				break;
			case '7':
				neg_matrix ^= TRUE;
				break;
			case '8':
                                gap_penalties_menu();
				break;
			case '?':
			case 'H':
				get_help('4');
				break;
			default:
				fprintf(stdout,"\n\nUnrecognised Command\n\n");
				break;
		}
	}
}






static void gap_penalties_menu(void)
{
	char c;
	sint i;
        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," ********* PROTEIN GAP PARAMETERS *********\n");
		fprintf(stdout,"\n\n\n");

		fprintf(stdout,"     1. Toggle Residue-Specific Penalties :%s\n\n",(no_pref_penalties) ? "OFF" : "ON");
		fprintf(stdout,"     2. Toggle Hydrophilic Penalties      :%s\n",(no_hyd_penalties) ? "OFF" : "ON");
		fprintf(stdout,"     3. Hydrophilic Residues              :%s\n\n"
					,hyd_residues);
		fprintf(stdout,"     4. Gap Separation Distance           :%d\n",(pint)gap_dist);
		fprintf(stdout,"     5. Toggle End Gap Separation         :%s\n\n",(!use_endgaps) ? "OFF" : "ON");
		fprintf(stdout,"     H. HELP\n\n\n");		

		getstr("Enter number (or [RETURN] to exit)",lin2);

		if(*lin2 == EOS) return;
		
		switch(toupper(*lin2)) {
			case '1':
				no_pref_penalties ^= TRUE;
				break;
			case '2':
				no_hyd_penalties ^= TRUE;
				break;
			case '3':
				fprintf(stdout,"Hydrophilic Residues Currently: %s\n",hyd_residues);

				getstr("Enter residues (or [RETURN] to quit)",lin1);
                                if (*lin1 != EOS) {
                                        for (i=0;i<strlen(hyd_residues) && i<26;i++) {
                                        c = lin1[i];
                                        if (isalpha(c))
                                                hyd_residues[i] = (char)toupper(c);
                                        else
                                                break;
                                        }
                                        hyd_residues[i] = EOS;
                                }
                                break;
			case '4':
				fprintf(stdout,"Gap Separation Distance Currently: %d\n",(pint)gap_dist);
				gap_dist=getint("Enter number",0,100,gap_dist);
				break;
			case '5':
				use_endgaps ^= TRUE;
				break;
			case '?':
			case 'H':
				get_help('A');
				break;
			default:
				fprintf(stdout,"\n\nUnrecognised Command\n\n");
				break;
		}
	}
}




static sint read_matrix(char *title,MatMenu menu, char *matnam, sint matn, short *mat, short *xref)
{       static char userfile[FILENAMELEN+1];
	int i;

        while(TRUE)
        {
                fprintf(stdout,"\n\n\n");
                fprintf(stdout," ********* %s WEIGHT MATRIX MENU *********\n",title);
                fprintf(stdout,"\n\n");

		for(i=0;i<menu.noptions;i++)
                	fprintf(stdout,"     %d. %s\n",i+1,menu.opt[i].title);
                fprintf(stdout,"     H. HELP\n\n");
                fprintf(stdout,
"     -- Current matrix is the %s ",menu.opt[matn-1].title);
                if(matn == menu.noptions) fprintf(stdout,"(file = %s)",userfile);
                fprintf(stdout,"--\n");


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

                i=toupper(*lin2)-'0';
		if(i>0 && i<menu.noptions) {
                        strcpy(matnam,menu.opt[i-1].string);
                        matn=i;
		} else if (i==menu.noptions) {
                        if(user_mat(userfile, mat, xref)) {
                              strcpy(matnam,userfile);
                              matn=i;
                        }
		}
		else
                switch(toupper(*lin2))  {
                        case '?':
                        case 'H':
                                get_help('8');
                                break;
                        default:
                                fprintf(stdout,"\n\nUnrecognised Command\n\n");
                                break;
                }
        }
}


char prompt_for_yes_no(char *title,char *prompt)
{
	char line[80];
	char lin2[80];

	fprintf(stdout,"\n%s\n",title);
	strcpy(line,prompt);
	strcat(line, "(y/n) ? [y]");
	getstr(line,lin2);
	if ((*lin2 != 'n') && (*lin2 != 'N'))
		return('y');
	else
		return('n');

}


/*
*	fatal()
*
*	Prints error msg to stdout and exits.
*	Variadic parameter list can be passed.
*
*	Return values:
*		none
*/

void fatal( char *msg,...)
{
	va_list ap;
	
	va_start(ap,msg);
	fprintf(stdout,"\n\nFATAL ERROR: ");
	vfprintf(stdout,msg,ap);
	fprintf(stdout,"\n\n");
	va_end(ap);
	exit(1);
}

/*
*	error()
*
*	Prints error msg to stdout.
*	Variadic parameter list can be passed.
*
*	Return values:
*		none
*/

void error( char *msg,...)
{
	va_list ap;
	
	va_start(ap,msg);
	fprintf(stdout,"\n\nERROR: ");
	vfprintf(stdout,msg,ap);
	fprintf(stdout,"\n\n");
	va_end(ap);
}

/*
*	warning()
*
*	Prints warning msg to stdout.
*	Variadic parameter list can be passed.
*
*	Return values:
*		none
*/

void warning( char *msg,...)
{
	va_list ap;
	
	va_start(ap,msg);
	fprintf(stdout,"\n\nWARNING: ");
	vfprintf(stdout,msg,ap);
	fprintf(stdout,"\n\n");
	va_end(ap);
}

/*
*	info()
*
*	Prints info msg to stdout.
*	Variadic parameter list can be passed.
*
*	Return values:
*		none
*/

void info( char *msg,...)
{
	va_list ap;
	
	va_start(ap,msg);
	fprintf(stdout,"\n");
	vfprintf(stdout,msg,ap);
	va_end(ap);
}