source: tags/arb_5.1/CONVERTALN/gcg.c

#include <stdio.h>
#include "convert.h"
#include "global.h"

/* ------------------------------------------------------------------
 *   Function to_gcg().
 *       Convert from whatever to GCG format.
 */
void
to_gcg(intype, inf)
     int    intype;
     char *inf;
{
    FILE        *IFP1, *IFP2, *IFP3, *ofp;
    FILE_BUFFER  ifp1 = 0, ifp2 = 0, ifp3 = 0;
    char         temp[TOKENNUM], *eof, line[LINENUM], key[TOKENNUM];
    char         line1[LINENUM], line2[LINENUM], line3[LINENUM], name[LINENUM];
    char        *eof1, *eof2, *eof3;
    char         outf[TOKENNUM];
    int          seqdata;

    if(intype==MACKE)   {
        if((IFP1=fopen(inf, "r"))==NULL||(IFP2=fopen(inf, "r"))==NULL ||(IFP3=fopen(inf, "r"))==NULL)   {
            sprintf(temp, "Cannot open input file %s\n", inf);
            error(38, temp);
        }
        ifp1 = create_FILE_BUFFER(inf, IFP1);
        ifp2 = create_FILE_BUFFER(inf, IFP2);
        ifp3 = create_FILE_BUFFER(inf, IFP3);
    }
    else {
        if((IFP1=fopen(inf, "r")) == NULL)  {
            sprintf(temp, "CANNOT open input file %s, exit.\n", inf);
            error(37, temp);
        }
        ifp1 = create_FILE_BUFFER(inf, IFP1);
    }
    if(intype==MACKE)   {
        /* skip to #=; where seq. first appears */
        for(eof1=Fgetline(line1, LINENUM, ifp1); eof1!=NULL&&(line1[0]!='#'||line1[1]!='=') ;
            eof1=Fgetline(line1, LINENUM, ifp1)) ;
        /* skip to #:; where the seq. information is */
        for(eof2=Fgetline(line2, LINENUM, ifp2); eof2!=NULL&&(line2[0]!='#'||line2[1]!=':');
            eof2=Fgetline(line2, LINENUM, ifp2)) ;
        /* skip to where seq. data starts */
        for(eof3=Fgetline(line3,LINENUM, ifp3); eof3!=NULL&&line3[0]=='#';
            eof3=Fgetline(line3, LINENUM, ifp3)) ;
        /* for each seq. print out one gcg file. */
        for(; eof1!=NULL&&(line1[0]=='#'&&line1[1]=='=');
            eof1=Fgetline(line1, LINENUM, ifp1))    {
            macke_abbrev(line1, key, 2);
            Cpystr(temp, key);
            gcg_output_filename(temp, outf);
            if((ofp=fopen(outf, "w"))==NULL) {
                sprintf(temp, "CANNOT open file %s, exit.\n", outf);
                error(39, temp);
            }
            for(macke_abbrev(line2, name, 2);
                eof2!=NULL&&line2[0]=='#'&&line2[1]==':'&&Cmpstr(name, key)==EQ;
                eof2=Fgetline(line2, LINENUM, ifp2), macke_abbrev(line2, name, 2))
                gcg_doc_out(line2, ofp);
            eof3 = macke_origin(key, line3, ifp3);
            gcg_seq_out(ofp, key);
            fclose(ofp);
            init_seq_data();
        }
    } else  {
        seqdata=0;  /* flag of doc or data */
        eof = Fgetline(line, LINENUM, ifp1);
        while(eof!=NULL)    {
            if(intype==GENBANK) {
                genbank_key_word(line, 0, temp, TOKENNUM);
                if((Cmpstr(temp, "LOCUS"))==EQ) {
                    genbank_key_word(line+12, 0, key, TOKENNUM);
                    gcg_output_filename(key, outf);
                    if((ofp=fopen(outf, "w"))==NULL) {
                        sprintf(temp, "CANNOT open file %s, exit.\n", outf);
                        error(40, temp);
                    }
                } else if(Cmpstr(temp, "ORIGIN")==EQ)   {
                    gcg_doc_out(line, ofp);
                    seqdata = 1;
                    eof = genbank_origin(line, ifp1);
                }
            } else { /* EMBL or SwissProt */
                if(Lenstr(line)>2&&line[0]=='I'&&line[1]=='D')
                {
                    embl_key_word(line, 5, key, TOKENNUM);
                    gcg_output_filename(key, outf);
                    if((ofp=fopen(outf, "w"))==NULL) {
                        sprintf(temp, "CANNOT open file %s, exit.\n", outf);
                        error(41, temp);
                    }
                } else if(Lenstr(line)>1&&line[0]=='S'
                          &&line[1]=='Q') {
                    gcg_doc_out(line, ofp);
                    seqdata = 1;
                    eof = embl_origin(line, ifp1);
                }
            }
            if(seqdata) {
                gcg_seq_out(ofp, key);
                init_seq_data();
                seqdata=0;
                fclose(ofp);
            } else {
                gcg_doc_out(line, ofp);
                eof = Fgetline(line, LINENUM, ifp1);
            }
        }
    }
}
/* ----------------------------------------------------------------
 *   Function gcg_seq_out().
 *       Output sequence data in gcg format.
 */
void
gcg_seq_out(ofp, key)
     FILE    *ofp;
     char    *key;
{
    /*  int indi, indj, indk; */
    /*  char    *today_date(), *gcg_date(); */
    /*  void    gcg_out_origin(); */

    fprintf(ofp, "\n%s  Length: %d  %s  Type: N  Check: %d  ..\n\n", key,
            gcg_seq_length(), gcg_date(today_date()),
            checksum(data.sequence, data.seq_length));
    gcg_out_origin(ofp);
}
/* --------------------------------------------------------------------
 *   Function gcg_doc_out().
 *       Output non-sequence data(document) of gcg format.
 */
void
gcg_doc_out(line, ofp)
     char    *line;
     FILE    *ofp;
{
    int indi, len;
    int previous_is_dot;

    for(indi=0, len=Lenstr(line), previous_is_dot=0; indi<len; indi++) {
        if(previous_is_dot) {
            if(line[indi]=='.') fprintf(ofp, " ");
            else previous_is_dot=0;
        }
        fprintf(ofp, "%c", line[indi]);
        if(line[indi]=='.') previous_is_dot=1;
    }
}
/* -----------------------------------------------------------------
 *   Function checksum().
 *       Calculate checksum for GCG format.
 */
int
checksum(string, numofstr)
     char    *string;
     int numofstr;
{
    int cksum=0, indi, count=0, charnum;

    for(indi=0; indi<numofstr; indi++)  {
        if(string[indi]=='.'||string[indi]=='-'||string[indi]=='~')
            continue;
        count++;
        if(string[indi]>='a'&&string[indi]<='z')
            charnum = string[indi]-'a'+'A';
        else charnum = string[indi];
        cksum = ((cksum+count*charnum) % 10000);
        if(count==57) count=0;
    }
    return(cksum);
}
/* --------------------------------------------------------------------
 *   Fcuntion gcg_out_origin().
 *       Output sequence data in gcg format.
 */
void
gcg_out_origin(fp)
     FILE    *fp;
{

    int indi, indj, indk;

    for(indi=0, indj=0, indk=1; indi<data.seq_length; indi++)   {
        if(data.sequence[indi]=='.'||data.sequence[indi]=='~'
           ||data.sequence[indi]=='-') continue;
        if((indk % 50)==1) fprintf(fp, "%8d  ", indk);
        fprintf(fp, "%c", data.sequence[indi]);
        indj++;
        if(indj==10) { fprintf(fp, " "); indj=0; }
        if((indk % 50)==0) fprintf(fp, "\n\n");
        indk++;
    }
    if((indk % 50)!=1) fprintf(fp, " \n");
}
/* --------------------------------------------------------------
 *   Function gcg_output_filename().
 *       Get gcg output filename, convert all '.' to '_' and
 *           append ".RDP" as suffix.
 */
void
gcg_output_filename(prefix, name)
     char    *prefix, *name;
{
    int indi, len;

    for(indi=0, len=Lenstr(prefix); indi<len; indi++)
        if(prefix[indi]=='.') prefix[indi]='_';
    sprintf(name, "%s.RDP", prefix);
}
/* ------------------------------------------------------------------
 *   Function gcg_seq_length().
 *       Calculate sequence length without gap.
 */
int
gcg_seq_length()    {

    int indi, len;

    for(indi=0, len=data.seq_length; indi<data.seq_length; indi++)
        if(data.sequence[indi]=='.'||data.sequence[indi]=='-'
           ||data.sequence[indi]=='~') len--;

    return(len);
}