source: tags/initial/GDE/MOLPHY/Nucst.c

/*
 * protst.c   Adachi, J.   1996.03.12
 * Copyright (C) 1993-1996 J. Adachi & M. Hasegawa, All rights reserved.
 */

#define MAIN_MODULE 1
#include "protst.h"


void
copyright()
{
#ifndef NUC
        fprintf(stderr, "ProtST %s (%s) ", VERSION, DATE );
        fprintf(stderr, "Basic Statistics of Protein Sequences\n");
#else
        fprintf(stderr, "NucST %s (%s) ", VERSION, DATE );
        fprintf(stderr, "Basic Statistics of Nucleic Acid Sequences\n");
#endif
        fprintf(stderr, "Copyright (C) 1993-1996 J. Adachi & M. Hasegawa. ");
        fprintf(stderr, "All rights reserved.\n");
/*      fprintf(stderr, "  ProtST comes with NO WARRANTY\n"); */
}


void
usage()
{
        copyright();
        fprintf(stderr, "Usage: %s [-%s] sequence_file\n", Prog_name, SWITCHES);
        fprintf(stderr, " Help: %s -h\n", Prog_name);
}


void
helpinfo()
{
        copyright();
        fprintf(stderr,
                "Usage: %s [switches] sequence_file\n",Prog_name);
        fprintf(stderr, "Switches:\n");
        fprintf(stderr, "-a      Alignments viewer\n");
        fprintf(stderr, "-c num  column size\n");
        fprintf(stderr, "-S      Sequential input format (PHYLIP)\n");
        fprintf(stderr, "-I      Interleaved input format (other packages)\n");
}

static void prologue();
static void pml();


main(argc, argv)
int argc;
char **argv;
{
        FILE *seqfp;
        int i, ch;
        char **cpp;
        extern int Optindex;   /* index of next argument */
        extern char *Optargp;  /* pointer to argument of current option */

        Tpmradix = TPMRADIX;
        Ct0 = time(NULL);
        if((Prog_name = strrchr(argv[0], DIR_CHAR)) != NULL )
                Prog_name++;
        else
                Prog_name = argv[0];

        while((ch = mygetopt(argc, argv, SWITCHES)) != -1 ) {
                switch(ch) {
                case 'a': Align_optn  = TRUE;  break;
                case 'c': Colmn_optn = TRUE;
                                cpp = &Optargp;
                                if (i = strtol(Optargp, cpp, 10)) Maxcolumn = i;
                                break;
                case 'i': Info_optn   = TRUE;  break;
                case 'I': Inlvd_optn  = TRUE;
                          Seque_optn  = FALSE; break;
                case 'L': Logfl_optn  = TRUE;  break;
                case 'S': Seque_optn  = TRUE;
                          Inlvd_optn  = FALSE; break;
                case 'v': Verbs_optn  = TRUE;  break;
                case 'w': Write_optn  = TRUE;  break;
                case 'z': Debug_optn  = TRUE;  break;
                case 'Z': Debug       = TRUE;  break;
                case 'h':
                case 'H': helpinfo(); exit(1);
                default : usage(); exit(1);
                }
        }
        if (Colmn_optn) {
                Linesites  = ((Maxcolumn - 10) / 11) * 10;
                Maxelement = ((Maxcolumn -  9) /  5);
        } else {
                Linesites  = LINESITES;
                Maxelement = MAXELEMENT;
        }

#ifdef DEBUG
        if (Debug) {
                printf("argc = %d\n",argc);
                for(i = 0; i < argc; i++) printf("argv[%d] = %s\n",i,argv[i]);
                putchar('\n');
                printf("\nOptindex = %d\n",Optindex);
                printf("Optargp = %s\n",Optargp);
        }
#endif

        if (Optindex == argc) {
                seqfp = stdin;
        } else if (Optindex + 1 == argc) {
                if ((seqfp = fopen(argv[Optindex++], "r")) == NULL) {
                        fprintf(stderr,"%s: can't open %s\n",Prog_name,argv[--Optindex]);
                        exit(1);
                }
        } else {
                fprintf(stderr, "%s: Inconsistent number of file in command line\n",
                        Prog_name);
                usage();
                exit(1);
        }
        if (Logfl_optn) {
                if ((Logfp = fopen(LOGFILE, "w")) == NULL) {
                        fprintf(stderr,
                                "%s: can't open log file: %s\n",Prog_name,LOGFILE);
                        exit(1);
                }
        }

        if (Verbs_optn) copyright();
        prologue(seqfp, stdout);
        if (seqfp != stdin) fclose(seqfp);
        if (Logfl_optn) fclose(Logfp);

        return 0;
}

/*  */
/* #if 0 */
/* void */
/* header(ofp, maxspc, numsite, commentp) */
/* FILE *ofp; */
/* int *maxspc; */
/* int *numsite; */
/* char **commentp; */
/* { */
/*      time_t ct; */
/*      char *datetime, *ip, *jp; */

/*      fprintf(ofp, "%s %s  ", Prog_name, VERSION); */

/*      ct = time(NULL); */
/*      datetime = ctime(&ct); */
/*      for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++; */
/*      *ip = '\0'; */
/*      fputs(datetime + 4, ofp); */
/*      fputs("  ", ofp); */
/*      fprintf(ofp, "  %d OTUs %d sites  %s\n", *maxspc, *numsite, *commentp); */
/*      free_cvector(*commentp); */
/* } /*_ header */ */
/* #endif */

 void
header(ofp, maxspc, numsite, commentp)
FILE *ofp;
int *maxspc;
int *numsite;
char **commentp;
{
        char date[32];

        strftime(date, 32, "%x", localtime(&Ct0));
        fprintf(ofp, "%s %s(%s)", Prog_name, VERSION, date);
        fprintf(ofp, " %d OTUs %d sites. %s\n", *maxspc, *numsite, *commentp);
} /*_ header */


static void
prologue(ifp, ofp)
FILE *ifp;
FILE *ofp;
{
        ivector alias;
        char *comment;

        getsize(ifp, &Maxspc, &Maxsite, &comment);

        header(ofp, &Maxspc, &Maxsite, &comment);
        Identif = (char **)malloc((unsigned)Maxspc * sizeof(char *));
        if (Identif == NULL) maerror("in prologue, Identif");
        Sciname = (char **)malloc((unsigned)Maxspc * sizeof(char *));
        if (Sciname == NULL) maerror("in prologue, Sciname");
        Engname = (char **)malloc((unsigned)Maxspc * sizeof(char *));
        if (Engname == NULL) maerror("in prologue, Engname");
        Seqchar = new_cmatrix(Maxspc, Maxsite);
        if (Seque_optn)
                getseqs(ifp, Identif, Seqchar, Maxspc, Maxsite);
        else if (Inlvd_optn)
                getseqi(ifp, Identif, Seqchar, Maxspc, Maxsite);
        else
                getseq(ifp, Identif, Sciname, Engname, Seqchar, Maxspc, Maxsite);

        getfreqepm(Seqchar, Freqemp, Maxspc, Maxsite);
        alias = new_ivector(Maxsite);
        radixsort(Seqchar, alias, Maxspc, Maxsite, &Numptrn);
        Seqconint = new_imatrix(Maxspc, Numptrn);
        Weight = new_ivector(Numptrn);
        condenceseq(Seqchar, alias, Seqconint, Weight, Maxspc, Maxsite, Numptrn);
        convseq(Seqconint, Maxspc, Numptrn);
        free_ivector(alias);

        Insdel = new_ivector(Maxsite);
        seqinsdel(Seqchar, Maxspc, Maxsite, Insdel, &Numnoindel);

        seqdiff(Seqchar, Maxspc, Maxsite, Insdel, Numnoindel);
        if (!Align_optn && Maxspc > 28) putchar('\f');

        seqfreq(Seqchar, Maxspc, Maxsite, Insdel, Numnoindel);
/*      if (!Align_optn && Maxspc > 28) putchar('\f'); */

        if (Info_optn) seqtran(Seqchar, Maxspc, Maxsite, Insdel, Numnoindel);
/*      if (!Align_optn && Info_optn && Maxspc > 14) putchar('\f'); */

        if (Align_optn) prsequence(ofp, Identif, Seqchar, Maxspc, Maxsite);
        if (Write_optn && Info_optn && (Maxspc * Maxsite > 3600)) putchar('\f');

        if (Write_optn && Info_optn)
                prcondenceseq(Identif, Seqconint, Weight, Maxspc, Maxsite, Numptrn);

        free_ivector(Insdel);
}