source: tags/arb_5.5/CONVERTALN/printable.c

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

#define PRTLENGTH   62

/* ---------------------------------------------------------------
 *   Function to_printable()
 *       Convert from some format to PRINTABLE format.
 */
void
to_printable(inf, outf, informat)
     char   *inf, *outf;
     int    informat;
{
    FILE        *IFP, *ofp;
    FILE_BUFFER  ifp;
    int          maxsize, current, total_seq, length;
    int          out_of_memory, indi, index, *base_nums, base_count, start;
    char         temp[TOKENNUM], eof;
    char        *name;

    if((IFP=fopen(inf, "r"))==NULL) {
        sprintf(temp, "Cannot open input file %s, exit\n", inf);
        error(64, temp);
    }
    ifp              = create_FILE_BUFFER(inf, IFP);
    if(Lenstr(outf) <= 0)   ofp = stdout;
    else if((ofp=fopen(outf, "w"))==NULL)   {
        sprintf(temp, "Cannot open output file %s, exit\n", outf);
        error(117, temp);
    }
    maxsize = 1;
    out_of_memory = 0;
    name = NULL;
    init();
    total_seq = 0;
    base_nums=NULL;
    do  {
        if(informat==ALMA)  {
            init_alma();
            eof=alma_in(ifp);
        } else if(informat==GENBANK)    {
            init_genbank();
            eof=genbank_in_locus(ifp);
        } else if(informat==EMBL||informat==PROTEIN)    {
            init_embl();
            eof=embl_in_id(ifp);
        } else if(informat==MACKE)  {
            init_macke();
            eof=macke_in_name(ifp);
        } else error(48,
                     "UNKNOW input format when converting to PRINABLE format.");
        if(eof==EOF) break;
        if(informat==ALMA)  {
            alma_key_word(data.alma.id, 0, temp, TOKENNUM);
        } else if(informat==GENBANK)    {
            genbank_key_word(data.gbk.locus, 0, temp, TOKENNUM);
        } else if(informat==EMBL||informat==PROTEIN)    {
            embl_key_word(data.embl.id, 0, temp, TOKENNUM);
        } else if(informat==MACKE)  {
            Cpystr(temp, data.macke.seqabbr);
        } else error(120,
                     "UNKNOW input format when converting to PRINABLE format.");
        total_seq++;

        if((name = Dupstr(temp))==NULL&&temp!=NULL) { out_of_memory=1; break; }
        if(data.seq_length>maxsize) maxsize = data.seq_length;

        if (!realloc_sequence_data(total_seq)) { out_of_memory = 1; break; }

        base_nums=(int*)Reallocspace((char *)base_nums, sizeof(int)*total_seq);
        if(base_nums==NULL) { out_of_memory=1; break; }

        data.ids[total_seq-1]     = name;
        data.seqs[total_seq-1]    = (char*)Dupstr(data.sequence);
        data.lengths[total_seq-1] = Lenstr(data.sequence);
        base_nums[total_seq-1]    = 0;

    } while(!out_of_memory);

    if(out_of_memory)   {   /* cannot hold all seqs into mem. */
        fprintf(stderr,
                "Rerun the conversion throught one seq. by one seq. base.\n");
        destroy_FILE_BUFFER(ifp); fclose(ofp);
        to_printable_1x1(inf, outf, informat);
        return;
    }
    current = 0;
    while(maxsize>current)  {
        for(indi=0; indi<total_seq; indi++) {
            length = Lenstr(data.seqs[indi]);
            for(index=base_count=0;
                index<PRTLENGTH&&(current+index)<length; index++)
                if(data.seqs[indi][index+current]!='~'&&
                   data.seqs[indi][index+current]!='-'&&
                   data.seqs[indi][index+current]!='.')
                    base_count++;

            /* check if the first char is base or not */
            if(current<length&&data.seqs[indi][current]!='~'&&
               data.seqs[indi][current]!='-'&&
               data.seqs[indi][current]!='.')
                start = base_nums[indi]+1;
            else start = base_nums[indi];

            printable_print_line(data.ids[indi],
                                 data.seqs[indi], current, start, ofp);
            base_nums[indi] += base_count;
        }
        current += PRTLENGTH;
        if(maxsize>current) fprintf(ofp, "\n\n");
    }

    Freespace((char **)&(base_nums));

#ifdef log
    fprintf(stderr, "Total %d sequences have been processed\n", total_seq);
#endif

    destroy_FILE_BUFFER(ifp); fclose(ofp);
}
/* ---------------------------------------------------------------
 *   Function to_printable_1x1()
 *       Convert from one foramt to PRINTABLE format, one seq by one seq.
 */
void
to_printable_1x1(inf, outf, informat)
     char   *inf, *outf;
     int    informat;
{
    FILE        *IFP, *ofp;
    FILE_BUFFER  ifp;
    int          maxsize, current, total_seq;
    int          base_count, index;
    char         temp[TOKENNUM], eof;
    char        *name;

    if((IFP=fopen(inf, "r"))==NULL) {
        sprintf(temp, "Cannot open input file %s, exit\n", inf);
        error(125, temp);
    }
    ifp              = create_FILE_BUFFER(inf, IFP);
    if(Lenstr(outf) <= 0)   ofp = stdout;
    else if((ofp=fopen(outf, "w"))==NULL)   {
        sprintf(temp, "Cannot open output file %s, exit\n", outf);
        error(126, temp);
    }
    maxsize = 1; current = 0;
    name = NULL;
    while(maxsize>current)  {
        init();
        FILE_BUFFER_rewind(ifp);
        total_seq = 0;
        do  {   /* read in one sequence */
            if(informat==ALMA)  {
                init_alma();
                eof=alma_in(ifp);
            } else if(informat==GENBANK)    {
                init_genbank();
                eof=genbank_in_locus(ifp);
            } else if(informat==EMBL||informat==PROTEIN)    {
                init_embl();
                eof=embl_in_id(ifp);
            } else if(informat==MACKE)  {
                init_macke();
                eof=macke_in_name(ifp);
            } else error(129,
                         "UNKNOW input format when converting to PRINTABLE format.");
            if(eof==EOF) break;
            if(informat==ALMA)  {
                alma_key_word(data.alma.id, 0, temp, TOKENNUM);
            } else if(informat==GENBANK)    {
                genbank_key_word(data.gbk.locus, 0, temp, TOKENNUM);
            } else if(informat==EMBL||informat==PROTEIN)    {
                embl_key_word(data.embl.id, 0, temp, TOKENNUM);
            } else if(informat==MACKE)  {
                macke_key_word(data.macke.name, 0, temp, TOKENNUM);
            } else error(131,
                         "UNKNOW input format when converting to PRINTABLE format.");
            Freespace(&name);
            name = Dupstr(temp);
            if(data.seq_length>maxsize)
                maxsize = data.seq_length;
            for(index=base_count=0;
                index<current&&index<data.seq_length; index++) {
                if(data.sequence[index]!='~'
                   &&data.sequence[index]!='.'
                   &&data.sequence[index]!='-') base_count++;
            }
            /* check if the first char is a base or not */
            if(current<data.seq_length&&data.sequence[current]!='~'
               &&data.sequence[current]!='.'
               &&data.sequence[current]!='-') base_count++;

            /* find if there any non-gap char in the next 62
             * char of the seq. data
             * #### count no need to be the first base num
             for(index=current, count=0;
             count==0&&index<data.seq_length
             &&index<(current+PRTLENGTH); index++)
             if(data.sequence[index]!='~'
             &&data.sequence[index]!='.'
             &&data.sequence[index]!='-')
             { base_count++; count++; }
            */

            printable_print_line(name, data.sequence, current,
                                 base_count, ofp);
            total_seq++;
        } while(1);
        current += PRTLENGTH;
        if(maxsize>current) fprintf(ofp, "\n\n");
    }   /* print block by block */

    destroy_FILE_BUFFER(ifp); fclose(ofp);

#ifdef log
    fprintf(stderr, "Total %d sequences have been processed\n", total_seq);
#endif

}
/* ------------------------------------------------------------
 *   Function printable_print_line().
 *       print one printable line.
 */
void
printable_print_line(id, sequence, start, base_count, fp)
     char    *id, *sequence;
     int start;
     int base_count;
     FILE    *fp;
{
    int indi, index, count, bnum, /*length,*/ seq_length;

    fprintf(fp, " ");
    if((bnum=Lenstr(id))>10)    {
        /* truncate if length of id is greater than 10 */
        for(indi=0; indi<10; indi++)
            fprintf(fp, "%c", id[indi]);
        bnum = 1;
    } else  {
        fprintf(fp, "%s", id);
        bnum = 10 - bnum + 1;
    }
    /* fill in the blanks to make up 10 chars id spaces */
    seq_length = Lenstr(sequence);
    if(start<seq_length)
        for(indi=0; indi<bnum; indi++)
            fprintf(fp, " ");
    else {  fprintf(fp, "\n"); return;  }
    fprintf(fp, "%4d ", base_count);
    for(index=start, count=0; count<PRTLENGTH&&index<seq_length; index++)   {
        fprintf(fp, "%c", sequence[index]);
        count++;
    }   /* printout sequence data */
    fprintf(fp, "\n");
}