amenu.c

经典生物信息学多序列比对工具clustalw

/* Menus and command line interface for Clustal W  */
/* DES was here MARCH. 1994 */
/* DES was here SEPT.  1994 */
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include <stdlib.h>
#include <stdarg.h>
#include <signal.h>
#include <setjmp.h>
#include "clustalw.h"

static jmp_buf jmpbuf;
#ifndef VMS
#ifndef AIX
#define BADSIG (void (*)())-1
#endif
#endif

static void jumper(int);

static void jumper(int i)
{
        longjmp(jmpbuf,1);
}


/*
*	Prototypes
*/


static void pair_menu(void);
static void multi_menu(void);
static void gap_penalties_menu(void);
static void multiple_align_menu(void);          /* multiple alignments menu */
static void profile_align_menu(void);           /* profile       "      "   */
static void phylogenetic_tree_menu(void);       /* NJ trees/distances menu  */
static void format_options_menu(void);          /* format of alignment output */
static void tree_format_options_menu(void);     /* format of tree output */
static void ss_options_menu(void);
static sint secstroutput_options(void);
static sint read_matrix(char *title,MatMenu menu, char *matnam, sint matn, short *mat, short *xref);

/*
*	 Global variables
*/

extern float    gap_open,      gap_extend;
extern float  	dna_gap_open,  dna_gap_extend;
extern float 	prot_gap_open, prot_gap_extend;
extern float    pw_go_penalty,      pw_ge_penalty;
extern float  	dna_pw_go_penalty,  dna_pw_ge_penalty;
extern float 	prot_pw_go_penalty, prot_pw_ge_penalty;
extern float	transition_weight;
extern char 	revision_level[];
extern sint    wind_gap,ktup,window,signif;
extern sint    dna_wind_gap, dna_ktup, dna_window, dna_signif;
extern sint    prot_wind_gap,prot_ktup,prot_window,prot_signif;
extern sint	nseqs;
extern sint 	divergence_cutoff;
extern sint 	debug;
extern Boolean 	neg_matrix;
extern Boolean  quick_pairalign;
extern Boolean	reset_alignments_new;		/* DES */
extern Boolean	reset_alignments_all;		/* DES */
extern sint 	gap_dist;
extern Boolean 	no_var_penalties, no_hyd_penalties, no_pref_penalties;
extern sint 	output_order;
extern sint profile_no;
extern short 	usermat[], pw_usermat[];
extern short 	aa_xref[], pw_aa_xref[];
extern short 	userdnamat[], pw_userdnamat[];
extern short 	dna_xref[], pw_dna_xref[];

extern Boolean 	lowercase; /* Flag for GDE output - set on comm. line*/
extern Boolean 	cl_seq_numbers;
extern Boolean seqRange;  /* to append sequence range with seq names, Ranu */

extern Boolean 	output_clustal, output_nbrf, output_phylip, output_gcg, output_gde, output_nexus;
extern Boolean output_fasta; /* Ramu */

extern Boolean 	output_tree_clustal, output_tree_phylip, output_tree_distances,output_tree_nexus;
extern sint     bootstrap_format;
extern Boolean 	tossgaps, kimura;
extern Boolean  percent;
extern Boolean 	usemenu;
extern Boolean 	showaln, save_parameters;
extern Boolean	dnaflag;
extern Boolean  use_ambiguities;


extern char 	hyd_residues[];
extern char 	mtrxname[], pw_mtrxname[];
extern char 	dnamtrxname[], pw_dnamtrxname[];
extern char	seqname[];

extern sint output_struct_penalties;
extern Boolean use_ss1, use_ss2;

extern Boolean empty;
extern Boolean profile1_empty, profile2_empty;   /* whether or not profiles   */

extern char  	profile1_name[FILENAMELEN+1];
extern char  	profile2_name[FILENAMELEN+1];

extern Boolean         use_endgaps;
extern sint        matnum,pw_matnum;
extern sint        dnamatnum,pw_dnamatnum;

extern sint        helix_penalty;
extern sint        strand_penalty;
extern sint        loop_penalty;
extern sint        helix_end_minus;
extern sint        helix_end_plus;
extern sint        strand_end_minus;
extern sint        strand_end_plus;
extern sint        helix_end_penalty;
extern sint        strand_end_penalty;

extern MatMenu matrix_menu;
extern MatMenu pw_matrix_menu;
extern MatMenu dnamatrix_menu;

static char phylip_name[FILENAMELEN]="";
static char clustal_name[FILENAMELEN]="";
static char dist_name[FILENAMELEN]="";
static char nexus_name[FILENAMELEN]="";
static char fasta_name[FILENAMELEN]="";

static char p1_tree_name[FILENAMELEN]="";
static char p2_tree_name[FILENAMELEN]="";

static char *secstroutput_txt[] = {
				"Secondary Structure",
				"Gap Penalty Mask",
				"Structure and Penalty Mask",
				"None"	};
				                

static char *lin1, *lin2, *lin3;

static int firstres =0;	/* range of alignment for saving as ... */
static int lastres = 0;

void init_amenu(void)
{

	lin1 = (char *)ckalloc( (MAXLINE+1) * sizeof (char) );
	lin2 = (char *)ckalloc( (MAXLINE+1) * sizeof (char) );
	lin3 = (char *)ckalloc( (MAXLINE+1) * sizeof (char) );
}

void main_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," **************************************************************\n");
		fprintf(stdout," ******** CLUSTAL %s Multiple Sequence Alignments  ********\n",revision_level);
		fprintf(stdout," **************************************************************\n");
		fprintf(stdout,"\n\n");
		
		fprintf(stdout,"     1. Sequence Input From Disc\n");
		fprintf(stdout,"     2. Multiple Alignments\n");
		fprintf(stdout,"     3. Profile / Structure Alignments\n");
		fprintf(stdout,"     4. Phylogenetic trees\n");
		fprintf(stdout,"\n");
		fprintf(stdout,"     S. Execute a system command\n");
		fprintf(stdout,"     H. HELP\n");
		fprintf(stdout,"     X. EXIT (leave program)\n\n\n");
		
		getstr("Your choice",lin1);

		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': multiple_align_menu();
				break;
			case '3': profile_align_menu();
				break;
			case '4': phylogenetic_tree_menu();
				break;
			case 'S': do_system();
				break;
			case '?':
			case 'H': get_help('1');
				break;
			case 'Q':
			case 'X': exit(0);
				break;
			default: fprintf(stdout,"\n\nUnrecognised Command\n\n");
				break;
		}
	}
}









static void multiple_align_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,"****** MULTIPLE ALIGNMENT MENU ******\n");
        fprintf(stdout,"\n\n");


        fprintf(stdout,"    1.  Do complete multiple alignment now (%s)\n",
                        (!quick_pairalign) ? "Slow/Accurate" : "Fast/Approximate");
        fprintf(stdout,"    2.  Produce guide tree file only\n");
        fprintf(stdout,"    3.  Do alignment using old guide tree file\n\n");
        fprintf(stdout,"    4.  Toggle Slow/Fast pairwise alignments = %s\n\n",
                                        (!quick_pairalign) ? "SLOW" : "FAST");
        fprintf(stdout,"    5.  Pairwise alignment parameters\n");
        fprintf(stdout,"    6.  Multiple alignment parameters\n\n");
	fprintf(stdout,"    7.  Reset gaps before alignment?");
	if(reset_alignments_new)
		fprintf(stdout," = ON\n");
	else
		fprintf(stdout," = OFF\n");
        fprintf(stdout,"    8.  Toggle screen display          = %s\n",
                                        (!showaln) ? "OFF" : "ON");
        fprintf(stdout,"    9.  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': align(phylip_name);
            break;
        case '2': make_tree(phylip_name);
            break;
        case '3': get_tree(phylip_name);
            break;
        case '4': quick_pairalign ^= TRUE;
            break;
        case '5': pair_menu();
            break;
        case '6': multi_menu();
            break;
	case '7': reset_alignments_new ^= TRUE;
	    if(reset_alignments_new==TRUE)
		reset_alignments_all=FALSE;
            break;
        case '8': showaln ^= TRUE;
	    break;
        case '9': format_options_menu();
            break;
        case 'S': do_system();
            break;
        case '?':
        case 'H': get_help('2');
            break;
        case 'Q':
        case 'X': return;

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









static void profile_align_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,"****** PROFILE AND STRUCTURE ALIGNMENT MENU ******\n");
        fprintf(stdout,"\n\n");

        fprintf(stdout,"    1.  Input 1st. profile             ");
        if (!profile1_empty) fprintf(stdout,"(loaded)");
        fprintf(stdout,"\n");
        fprintf(stdout,"    2.  Input 2nd. profile/sequences   ");
        if (!profile2_empty) fprintf(stdout,"(loaded)");
        fprintf(stdout,"\n\n");
        fprintf(stdout,"    3.  Align 2nd. profile to 1st. profile\n");
        fprintf(stdout,"    4.  Align sequences to 1st. profile (%s)\n\n",
                        (!quick_pairalign) ? "Slow/Accurate" : "Fast/Approximate");
        fprintf(stdout,"    5.  Toggle Slow/Fast pairwise alignments = %s\n\n",
                                        (!quick_pairalign) ? "SLOW" : "FAST");
        fprintf(stdout,"    6.  Pairwise alignment parameters\n");
        fprintf(stdout,"    7.  Multiple alignment parameters\n\n");
        fprintf(stdout,"    8.  Toggle screen display                = %s\n",
                                        (!showaln) ? "OFF" : "ON");
        fprintf(stdout,"    9.  Output format options\n");
        fprintf(stdout,"    0.  Secondary structure 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': profile_no = 1;      /* 1 => 1st profile */ 
          profile_input();
		  strcpy(profile1_name, seqname);
            break;
        case '2': profile_no = 2;      /* 2 => 2nd profile */
          profile_input();
		  strcpy(profile2_name, seqname);
            break;
        case '3': profile_align(p1_tree_name,p2_tree_name);       /* align the 2 alignments now */
            break;
        case '4': new_sequence_align(phylip_name);  /* align new sequences to profile 1 */
            break;
        case '5': quick_pairalign ^= TRUE;
	    break;
        case '6': pair_menu();
            break;
        case '7': multi_menu();
            break;
        case '8': showaln ^= TRUE;
	    break;
        case '9': format_options_menu();
            break;
        case '0': ss_options_menu();
            break;
        case 'S': do_system();
            break;
        case '?':
        case 'H': get_help('6');
            break;
        case 'Q':
        case 'X': return;

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


static void ss_options_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," ********* SECONDARY STRUCTURE OPTIONS *********\n");
		fprintf(stdout,"\n\n");

		fprintf(stdout,"     1. Use profile 1 secondary structure / penalty mask  ");
		if(use_ss1)
			fprintf(stdout,"= YES\n");
		else
			fprintf(stdout,"= NO\n");
		fprintf(stdout,"     2. Use profile 2 secondary structure / penalty mask  ");
		if(use_ss2)
			fprintf(stdout,"= YES\n");
		else