#include "bz_all.h"#ifndef __lintstatic const char rcsid[] ="$Id: bz_terse.c,v 1.1 2001/08/26 09:21:08 schwartz Exp $";#endifstatic int isrev(SEQ *s){        return (s->flags & SEQ_IS_REVCOMP);}void print_job_footer(){	printf("#:eof\n");}void print_job_header (ss_t ss, gap_scores_t *ds, int K, int L){	int i, j;	uchar b[] = "ACGT";	printf("#:laf\n");	printf("J {\n");	ck_argc("print_align_header");	fprintf_argv(stdout);	printf("\n     A    C    G    T\n ");	for (i = 0; i < 4; ++i) {		for (j = 0; j < 4; ++j)			printf("%5d", ss[b[i]][b[j]]);		printf("\n ");	}	if (ds->O)	    printf(" O = %d, E = %d, K = %d, L = %d", ds->O, ds->E, K, L);	printf("\n}\n");}/* print_align_header  ------------  print the top part of an alignment file */void print_align_header (SEQ * seq1, SEQ * seq2, ss_t ss, gap_scores_t * ds,   int K, int L){	printf("#:lav\n");	printf("S {\n  \"%s\" %d %d %d %d\n  \"%s\" %d %d %d %d\n}\n",		SEQ_NAME(seq1), SEQ_FROM(seq1), SEQ_TO(seq1), isrev(seq1), seq1->count,		SEQ_NAME(seq2), SEQ_FROM(seq2), SEQ_TO(seq2), isrev(seq2), seq2->count);	printf("H {\n   \"%s%s\"\n   \"%s%s\"\n}\n", 		SEQ_HEAD(seq1), revlabel(seq1), SEQ_HEAD(seq2), revlabel(seq2));}static void print_align_lav(int score, const uchar *seq1, const uchar *seq2, int beg1, int end1, int beg2, int end2, edit_script_t *S){        int M, N, i, j, o, nG = 0, lG = 0;	int total_run = 0, total_match = 0;         M = end1 - beg1 + 1;        N = end2 - beg2 + 1;	printf("A {\n s %d\n b %d %d\n e %d %d\n",		score, beg1, beg2, end1, end2);        for (o = i = j = 0; i < M || j < N; ) {                int start_i = i;                int start_j = j;                 int match = 0;		int run;	        run = es_rep_len(S, &o, seq1+beg1+i-1, seq2+beg2+j-1, &match);		i += run; j += run;		total_match += match;		total_run += run;		printf(" l %d %d %d %d\n",			    beg1+start_i, beg2+start_j, run, match);                if (i < M || j < N) {		  nG++;		  lG += es_indel_len(S, &o, &i, &j);		}		         }	printf("}\n");}void print_align_list(align_t *a) {	while (a) {		print_align_lav(a->score, a->seq1, a->seq2, a->beg1, a->end1,			a->beg2, a->end2, a->script);		a = a->next_align;	}}void free_align_list(align_t *a){	align_t *b;	while (a) {		edit_script_free(a->script);		b = a->next_align;		ckfree(a);		a = b;	}}static int percent_match(SEQ *sf1, SEQ *sf2, int len, int pos1, int pos2){	uchar *p = SEQ_CHARS(sf1) + pos1;	uchar *q = SEQ_CHARS(sf2) + pos2;	int m = 0, i = len;	while (i-- > 0)		m += (*p++ == *q++);	return align_match_percent (len, m);}void print_msp_list(SEQ *sf1, SEQ *sf2, struct msp_table *mt){	int len, beg1, beg2, end1, end2, score, pm;	msp_t *mp;	/* print each maximal segment pair */	for (mp=MSP_TAB_FIRST(mt); MSP_TAB_MORE(mt,mp); mp=MSP_TAB_NEXT(mp)) {		beg1 = mp->pos1 + 1;		beg2 = mp->pos2 + 1;		len = mp->len - 1;		end1 = beg1 + len;		end2 = beg2 + len;		score = mp->score;		pm = percent_match(sf1, sf2, len, beg1 - 1, beg2 - 1);		printf("a {\n  s %d\n  b %d %d\n  e %d %d\n",		  score, beg1, beg2, end1, end2);		printf("  l %d %d %d %d %d\n}\n", beg1, beg2, end1, end2, pm);	}}