256 lines
6.3 KiB
C
256 lines
6.3 KiB
C
/*
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Title: writeSCF
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File: writeSCF.c
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Purpose: Output of Standard Chromatogram Format sequences
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Last update: 23 November 1992
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Change log:
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4 Feb 1992, Now draft proposal version 2
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23 Nov 92, SCF 2.0 + LaDeana's changes
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*/
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/*
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** makeSCF version number
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*/
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#define VERSION_NO "2.00"
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/* ---- Imports ---- */
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#include "scf.h" /* IMPORT: scf structures */
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#include "seq.h" /* IMPORT: Seq, BasesAndTraces, NULLSeq,
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newSeq, freeSeq */
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#include "mach-io.h" /* IMPORT: be_write_int_1, be_write_int_2, be_write_int_4 */
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#include <ctype.h>
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#include <stdio.h> /* IMPORT: fopen, fclose, fseek, ftell, fgetc,
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EOF */
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/* ---- Internal functions ---- */
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static int write_scf_header(FILE *fp, Header *h)
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{
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int i;
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if (be_write_int_4(fp,&h->magic_number)==False) return (False);
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if (be_write_int_4(fp,&h->samples)==False) return (False);
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if (be_write_int_4(fp,&h->samples_offset)==False) return (False);
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if (be_write_int_4(fp,&h->bases)==False) return (False);
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if (be_write_int_4(fp,&h->bases_left_clip)==False) return (False);
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if (be_write_int_4(fp,&h->bases_right_clip)==False) return (False);
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if (be_write_int_4(fp,&h->bases_offset)==False) return (False);
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if (be_write_int_4(fp,&h->comments_size)==False) return (False);
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if (be_write_int_4(fp,&h->comments_offset)==False) return (False);
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if (fwrite(h->version,sizeof(h->version),1,fp)!=1) return (False);
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if (be_write_int_4(fp,&h->sample_size)==False) return (False);
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if (be_write_int_4(fp,&h->code_set)==False) return (False);
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for (i=0;i<20;i++)
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if (be_write_int_4(fp,&h->spare[i])==False) return (False);
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return (True);
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}
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static int write_scf_sample1(FILE *fp, Samples1 *s)
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{
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if (be_write_int_1(fp,&s->sample_A)==False) return (False);
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if (be_write_int_1(fp,&s->sample_C)==False) return (False);
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if (be_write_int_1(fp,&s->sample_G)==False) return (False);
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if (be_write_int_1(fp,&s->sample_T)==False) return (False);
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return (True);
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}
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static int write_scf_sample2(FILE *fp, Samples2 *s)
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{
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if (be_write_int_2(fp,&s->sample_A)==False) return (False);
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if (be_write_int_2(fp,&s->sample_C)==False) return (False);
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if (be_write_int_2(fp,&s->sample_G)==False) return (False);
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if (be_write_int_2(fp,&s->sample_T)==False) return (False);
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return (True);
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}
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static int write_scf_base(FILE *fp, Bases *b)
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{
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if (be_write_int_4(fp,&b->peak_index)==False) return (False);
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if (be_write_int_1(fp,&b->prob_A)==False) return (False);
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if (be_write_int_1(fp,&b->prob_C)==False) return (False);
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if (be_write_int_1(fp,&b->prob_G)==False) return (False);
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if (be_write_int_1(fp,&b->prob_T)==False) return (False);
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if (be_write_int_1(fp,(uint_1 *)&b->base)==False) return (False);
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if (be_write_int_1(fp,&b->spare[0])==False) return (False);
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if (be_write_int_1(fp,&b->spare[1])==False) return (False);
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if (be_write_int_1(fp,&b->spare[2])==False) return (False);
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return (True);
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}
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static int write_scf_comment(FILE *fp, Comments *c, size_t l)
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{
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if (fwrite(c, l, 1, fp) !=1) return (False);
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return (True);
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}
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/* ---- Exports ---- */
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Boolean writeSeqSCF(Seq seq, char *fn)
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/*
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** Write Seq out as a .scf file
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*/
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{
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FILE *fp;
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Header header;
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Bases base;
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Comments comments[1024];
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Comments default_comments[] = "conversion_program = makeSCF " VERSION_NO "\n";
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char *src;
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if ((fp = fopen(fn,"wb"))==NULL)
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return (False);
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else {
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int i;
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int prec; /* precision to use */
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/* source dependant switches */
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prec = 1;
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switch (seq->format) {
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case ABIFormat:
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src = "ABI 373A";
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break;
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case ALFFormat:
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src = "Pharmacia A.L.F.";
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prec = 2;
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break;
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case SCFFormat:
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src = "SCF";
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if (seq->maxTraceVal > 255) prec=2; /* retain precision */
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break;
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default:
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src = "Unknown";
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break;
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}
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if (seq->info==NULL) {
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sprintf(comments,"%ssource = %s\n",
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default_comments,
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src);
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} else {
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sprintf(comments,"%s\n%ssource = %s\n",
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seq->info,
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default_comments,
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src);
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}
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header.magic_number = SCF_MAGIC;
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header.samples = seq->NPoints;
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header.samples_offset = (uint_4)sizeof(Header);
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header.bases = seq->NorigBases;
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header.bases_left_clip = seq->leftCutoff;
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header.bases_right_clip = seq->rightCutoff;
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header.bases_offset = (uint_4)(header.samples_offset + header.samples * ((prec==2)?sizeof(Samples2):sizeof(Samples1)));
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header.comments_size = (uint_4)strlen(comments)+1;
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header.comments_offset = (uint_4)(header.bases_offset + header.bases * sizeof(Bases));
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strncpy(header.version, VERSION_NO,4);
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header.sample_size = prec;
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header.code_set = CSET_DEFAULT;
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for(i=0;i<20;i++) header.spare[i]=0;
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if (write_scf_header(fp, &header)==False) return (False);
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switch(prec) {
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case 2:
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{
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Samples2 sample;
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for(i=0; i<header.samples; i++) {
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sample.sample_A = seq->traceA[i];
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sample.sample_C = seq->traceC[i];
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sample.sample_G = seq->traceG[i];
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sample.sample_T = seq->traceT[i];
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if (write_scf_sample2(fp, &sample)==False) return(False);
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}
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break;
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}
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default:
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{
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Samples1 sample;
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for(i=0; i<header.samples; i++) {
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#define scale(P,M) ( (byte) ((float)(P)*255.0/(float)(M)) )
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sample.sample_A = scale(seq->traceA[i],seq->maxTraceVal);
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sample.sample_C = scale(seq->traceC[i],seq->maxTraceVal);
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sample.sample_G = scale(seq->traceG[i],seq->maxTraceVal);
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sample.sample_T = scale(seq->traceT[i],seq->maxTraceVal);
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if (write_scf_sample1(fp, &sample)==False) return(False);
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}
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break;
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}
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}
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for(i=0; i<header.bases; i++) {
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base.peak_index = seq->basePos[i];
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base.base = seq->base[i];
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base.spare[0] = base.spare[1] = base.spare[2] = 0;
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base.prob_A = base.prob_C = base.prob_G = base.prob_T = 0;
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switch(base.base) {
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case 'A' : case 'a':
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base.prob_A = 1; break;
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case 'C' : case 'c':
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base.prob_C = 1; break;
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case 'G' : case 'g':
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base.prob_G = 1; break;
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case 'T' : case 't':
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base.prob_A = 1; break;
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default:
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base.prob_A = base.prob_C = base.prob_G = base.prob_T = 1;
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}
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if (write_scf_base(fp,&base)==False) return (False);
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}
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if (write_scf_comment(fp,comments,(size_t)header.comments_size)==False) return (False);
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fclose(fp);
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}
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return (True);
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}
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