/* 把 in 压缩成 out */
int huffman_encode_file(FILE *in, FILE *out)
{
symfreq sf;
symcode *sc;
node *root = NULL;
int rc;
unsigned int syms;
/* 获取输入文件中符号出现频率 */
syms = get_symfreq(&sf, in);
/* 生成编码表 */
sc = calc_code(&sf);
root = sf[0];
/* 再次扫描文件，使用之前生成的编码表来编码 */
rewind(in);
rc = write_code_table(out, sc, syms);
if (rc == 0)
rc = do_file_encode(in, out, sc);
/* 释放空间 */
free_tree(root);
free_encoder(sc);
return rc;
}
void showbest (FILE *fp,
#ifndef PCOMPLIB
unsigned char **aa0, unsigned char *aa1save, int maxn,
#endif
struct beststr **bptr,int nbest,
int qlib, struct mngmsg *m_msp,
struct pstruct *ppst, struct db_str db,
char **info_gstring2
#ifndef PCOMPLIB
,void **f_str
#endif
)
{
unsigned char *aa1, *aa1a;
int ntmp = 0;
char bline[MAX_BLINE], fmt[40], pad[MAX_BLINE], rline[40];
char l_name[128];
int istart = 0, istop, ib;
int nshow;
int quiet;
int r_margin;
struct beststr *bbp;
int n1tot;
char *bp;
char rel_label[12];
char tmp_str[20], *seq_code, *ann_code;
int seq_code_len, ann_code_len;
long loffset; /* loffset is offset from beginning of real sequence */
long l_off; /* l_off is the the virtual coordinate of residue 1 */
int n0, n1;
struct rstruct rst;
int lc, seqc_max, annc_max, nident, ngap;
float percent, gpercent;
struct a_struct *aln_p;
int *tres;
int gi_num;
char html_pre_E[120], html_post_E[120];
#ifndef PCOMPLIB
struct lmf_str *m_fptr;
#endif
strncpy(rel_label,"\0",2);
#ifdef SHOWREL
strncpy(rel_label," related",sizeof(rel_label));
#endif
#ifdef SHOWUN
strncpy(rel_label," unrelated",sizeof(rel_label));
#endif
rel_label[sizeof(rel_label)-1]='\0';
#ifdef PCOMPLIB
quiet = 1;
#else
quiet = m_msp->quiet;
#endif
n0 = m_msp->n0;
if (m_msp->aln.llen > MAX_BLINE) m_msp->aln.llen = MAX_BLINE;
if (ppst->zsflag < 0) r_margin = 10;
else if (ppst->zsflag>=0 && m_msp->srelv > 1 ) r_margin = 19;
else r_margin = 10;
if (m_msp->markx & MX_M9SUMM && m_msp->show_code == SHOW_CODE_ID) {
#ifdef SHOWSIM
r_margin += 15;
#else
r_margin += 10;
#endif
}
if (m_msp->markx & MX_HTML) {
strncpy(html_pre_E,"<font color=\"darkred\">",sizeof(html_pre_E));
strncpy(html_post_E,"</font>",sizeof(html_post_E));
}
else {
html_pre_E[0] = html_post_E[0] = '\0';
}
if (m_msp->nframe < 0) {
#ifndef SUPERFAMNUM
sprintf(fmt,"%%-%ds (%%4d)",m_msp->aln.llen-r_margin);
#else
sprintf(fmt,"%%-%ds [%%4d](%%4d)",m_msp->aln.llen-(r_margin+4));
#endif
}
else { sprintf(fmt,"%%-%ds (%%4d)",m_msp->aln.llen-(r_margin+4)); }
memset(pad,' ',m_msp->aln.llen-(r_margin+6));
pad[m_msp->aln.llen-(r_margin+12)]='\0';
if (quiet != -1) { /* quiet is set to -1 in comp_lib2.c to force
all significant hits to be shown */
nshow = 20;
if (m_msp->mshow == -1) {nshow = nbest;} /* show all */
/* show specified number */
else if (m_msp->mshow_flg) {
nshow = min (m_msp->mshow, nshow);
}
}
else nshow = m_msp->nshow;
if (quiet==0) istop = 20;
else istop = nshow;
if (quiet==0) {
printf(" How many scores would you like to see? [%d] ",m_msp->nshow);
fflush(stdout);
if (fgets(rline,20,stdin)==NULL) exit(0);
nshow = m_msp->nshow;
if (rline[0]!='\n' && rline[0]!=0) sscanf(rline,"%d",&nshow);
if (nshow<=0) nshow = min(20,nbest);
}
if ((bp = strchr (m_msp->qtitle, '\n')) != NULL) *bp = '\0';
/* fprintf (fp, "%3d %s\n", qlib,m_msp->qtitle); */
if (m_msp->markx & MX_HTML) fprintf(fp,"<p><tt><pre>\n");
if (ppst->zsflag >= 0) {
if (bptr[0]->rst.escore < m_msp->e_cut) {
if (m_msp->z_bits==1) {/* show bit score */
fprintf(fp,"\nThe best%s scores are:%s%s bits %sE(%ld)%s",
rel_label,pad,m_msp->label,html_pre_E,ppst->zdb_size,html_post_E);
}
else {/* show z-score */
fprintf(fp,"\nThe best%s scores are:%s%s z-sc %sE(%ld)%s",
rel_label,pad,m_msp->label,html_pre_E,ppst->zdb_size,html_post_E);
}
header_aux(fp);
if (m_msp->markx & MX_M9SUMM) {
if (m_msp->show_code == SHOW_CODE_ID) {
#ifdef SHOWSIM
fprintf(fp," %%_id %%_sim alen");
#else
fprintf(fp," %%_id alen");
#endif
}
else {
if (m_msp->markx & MX_HTML && m_msp->show_code !=1) { fprintf(fp,"<!-- ");}
#ifndef SHOWSIM
fprintf(fp,"\t%%_id %%_gid %4s alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs ",m_msp->f_id1);
#else
fprintf(fp,"\t%%_id %%_sim %4s alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs ",m_msp->f_id1);
#endif
}
if (m_msp->show_code == SHOW_CODE_ALIGN) { fprintf(fp," aln_code"); }
if (m_msp->markx & MX_HTML && m_msp->show_code!=1) { fprintf(fp," -->");}
}
fprintf(fp,"\n");
}
else {
fprintf(fp,"!! No library sequences with E() < %.2g\n",m_msp->e_cut);
m_msp->nshow = 0;
if (m_msp->markx & MX_HTML) fprintf(fp,"<p></tt></pre>\n");
return;
}
}
else {
fprintf(fp,"\nThe best%s scores are:%s%s",rel_label,pad,m_msp->label);
header_aux(fp);
if (m_msp->markx & MX_M9SUMM) {
if (m_msp->show_code == SHOW_CODE_ID) {
#ifdef SHOWSIM
fprintf(fp," %%_id %%_sm alen");
#else
fprintf(fp," %%_id alen");
#endif
}
else {
#ifndef SHOWSIM
fprintf(fp,"\t%%_id %%_gid %4s alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs ",m_msp->f_id1);
#else
fprintf(fp,"\t%%_id %%_sim %4s alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs ",m_msp->f_id1);
#endif /* SHOWSIM */
}
}
if (m_msp->show_code == SHOW_CODE_ALIGN) { fprintf(fp," aln_code"); }
fprintf(fp,"\n");
}
istart = 0;
l1:
istop = min(nbest,nshow);
for (ib=istart; ib<istop; ib++) {
bbp = bptr[ib];
#ifndef PCOMPLIB
#ifdef DEBUG
if (bbp->seq->n1 != bbp->n1 ) {
fprintf(stderr, " *** lib len error [%d!=%d] *** %s score %d\n",
bbp->seq->n1,bbp->n1, bbp->seq->libstr, bbp->rst.score[0]);
}
#endif
#endif
#ifdef SUPERFAMNUM
if (BBP_INFO(nsfnum) > 0 && sfn_cmp(m_msp->qsfnum_n,BBP_INFO(sfnum))) continue;
#ifdef SHOWUN
if (BBP_INFO(nsfnum) > 0 && sfn_cmp(m_msp->qsfnum,BBP_INFO(sfnum))) {
istop = min(istop+1,nbest);
/*
fprintf(stderr,"skipping %d: %d==%d\n",ib,m_msp->qsfnum,BBP_INFO(sfnum));
*/
continue;
}
#endif /* SHOWUN */
#ifdef SHOWREL
if (BBP_INFO(nsfnum) == 0 || (BBP_INFO(nsfnum) > 0 && !sfn_cmp(m_msp->qsfnum,BBP_INFO(sfnum)))) {
istop = min(istop+1,nbest);
continue;
}
#endif /* SHOWREL */
#endif /* SUPERFAMNUM */
if (quiet==1 && ppst->zsflag>=0) {
if (bbp->rst.escore > m_msp->e_cut) {
nshow = ib;
goto done;
}
else if (bbp->rst.escore < m_msp->e_low) continue;
}
#ifndef PCOMPLIB
if ((m_fptr=re_openlib(bbp->seq->m_file_p,!m_msp->quiet))==NULL) {
fprintf(stderr,"*** cannot re-open %s\n",bbp->seq->m_file_p->lb_name);
exit(1);
}
RANLIB(bline,m_msp->aln.llen,bbp->seq->lseek,bbp->seq->libstr,m_fptr);
#else /* PCOMPLIB */
strncpy(bline,BBP_INFO(bline),m_msp->aln.llen-r_margin);
bline[m_msp->aln.llen]='\0';
#endif
/* l_name is used to build an HTML link from the bestscore line to
the alignment. It can also be used to discriminate multiple hits
from the same long sequence. This requires that fast_pan use -m 6. */
strncpy(l_name,bline,sizeof(l_name)); /* get rid of text after second "|" */
l_name[sizeof(l_name)-1]='\0';
if ((bp=strchr(l_name,' '))!=NULL) *bp=0;
if ((bp=strchr(&l_name[3],'|'))!=NULL) *bp='\0';
if (m_msp->nframe > 2) sprintf(&l_name[strlen(l_name)],"_%d",bbp->frame+1);
else if (m_msp->nframe > 0 && bbp->frame == 1)
strncat(l_name,"_r",sizeof(l_name));
if (bbp->seq->cont-1 > 0) {
sprintf(tmp_str,":%d",bbp->seq->cont-1);
strncat(l_name,tmp_str,sizeof(l_name)-strlen(l_name));
}
#ifndef PCOMPLIB
aln_p = &(m_msp->aln);
if (m_msp->stages>1 || m_msp->markx & MX_M9SUMM) {
if (bbp->seq->aa1b == NULL || (m_msp->ann_flg && bbp->seq->aa1_ann==NULL)) {
/* get the sequence but don't save it */
n1 = re_getlib(aa1save,
m_msp->ann_flg ? &(bbp->seq->aa1_ann) : NULL,
maxn,m_msp->maxt3,
m_msp->l_overlap,bbp->seq->cont,m_msp->term_code,
&loffset,&l_off,bbp->seq->m_file_p);
aa1 = aa1save;
aa1a = bbp->seq->aa1_ann;
}
else {
n1 = bbp->seq->n1;
aa1 = bbp->seq->aa1b;
aa1a = bbp->seq->aa1_ann;
loffset = bbp->seq->l_offset;
l_off = bbp->seq->l_off;
}
if (! m_msp->markx & MX_M9SUMM) {
do_opt (aa0[bbp->frame], m_msp->n0, aa1, n1, bbp->frame, ppst, f_str[bbp->frame], &rst);
bbp->rst.score[2]=rst.score[2];
}
else {
if (!bbp->have_ares) { /* showbest() can be called more than once */
do_walign(aa0[bbp->frame],m_msp->n0, aa1, n1, bbp->frame,
ppst, f_str[bbp->frame],
&bbp->a_res, &bbp->have_ares);
/* if do_walign does not provide a fresh a_res,
then copy the re-used a_res to a new location */
if (bbp->have_ares && !(bbp->have_ares & 0x2)) {
if ((tres = calloc(bbp->a_res.nres+1,sizeof(int)))!=NULL) {
memcpy(tres,bbp->a_res.res,sizeof(int)*bbp->a_res.nres);
bbp->a_res.res = tres;
bbp->have_ares |= 0x2; /* set 0x2 if has local copy */
}
else {
bbp->have_ares = 0; /* could not allocate memory */
}
}
}
else {
pre_cons(aa1,n1,bbp->frame,f_str[bbp->frame]);
}
aln_func_vals(bbp->frame, aln_p);
seqc_max = bbp->a_res.nres + 4*m_msp->aln.llen+4;
seq_code = NULL;
seq_code_len = 0;
if (m_msp->show_code == SHOW_CODE_ALIGN) {
seq_code=(char *)calloc(seqc_max,sizeof(char));
/* if we have an annotation string, allocate space for the encoded annotation */
if (m_msp->ann_arr[0] != '\0') {
/* the annotation encoding can be considerably longer than the alignment encoding */
annc_max = 4*seqc_max;
ann_code=(char *)calloc(annc_max,sizeof(char));
}
else {
ann_code = NULL;
annc_max = 0;
}
if (seq_code != NULL) {
calc_astruct(aln_p, &bbp->a_res);
/* we need this for offset information for calc_code, but it is
incomplete so we must do it again */
cal_coord(m_msp->n0,BBP_INFO(n1),
m_msp->q_offset + (m_msp->q_off-1) + (m_msp->sq0off-1),
loffset + (l_off-1) + (m_msp->sq1off-1),
aln_p);
lc=calc_code(aa0[bbp->frame],m_msp->n0,
aa1,n1,
&m_msp->aln,&bbp->a_res,
ppst,seq_code,seqc_max,
m_msp->ann_arr,
m_msp->aa0a, aa1a,
ann_code, annc_max,
f_str[bbp->frame]);
seq_code_len = strlen(seq_code);
if (ann_code != NULL) ann_code_len = strlen(ann_code);
else ann_code_len = 0;
}
}
else {
lc=calc_id(aa0[bbp->frame],m_msp->n0,aa1,n1,
&m_msp->aln, &bbp->a_res,
ppst,f_str[bbp->frame]);
}
m_msp->aln.a_len = lc;
nident = m_msp->aln.nident;
if (lc > 0) percent = (100.0*(float)nident)/(float)lc;
else percent = -1.00;
ngap = m_msp->aln.ngap_q + m_msp->aln.ngap_l;
#ifndef SHOWSIM
if (lc-ngap > 0) gpercent = (100.0*(float)nident)/(float)(lc-ngap);
else gpercent = -1.00;
#else
if (lc-ngap > 0) gpercent = (100.0*(float)m_msp->aln.nsim)/(float)(lc);
else gpercent = -1.00;
#endif /* SHOWSIM */
}
}
#endif /* PCOMPLIB */
n1tot = (BBP_INFO(n1tot_p)) ? *BBP_INFO(n1tot_p) : BBP_INFO(n1);
bp = bline;
if ((m_msp->markx & MX_HTML) && !strncmp(bline,"gi|",3)) {
bp = strchr(bline+4,'|')+1;
*(bp-1) = 0;
gi_num = atoi(bline+3);
}
#ifndef SUPERFAMNUM
bp[m_msp->aln.llen-r_margin]='\0';
#else
bp[m_msp->aln.llen-r_margin-5]='\0';
#endif
if (m_msp->nframe == -1) bp[m_msp->aln.llen-r_margin]='\0';
else bp[m_msp->aln.llen-(r_margin+4)]='\0';
#ifndef SUPERFAMNUM
fprintf (fp, fmt,bp,n1tot);
#else
if (m_msp->nframe == -1) {
fprintf (fp, fmt,bp,BBP_INFO(sfnum[0]),n1tot);
}
else {fprintf (fp, fmt,bp,n1tot);}
#endif
if (m_msp->nframe > 2) fprintf (fp, " [%d]", bbp->frame+1);
else if (m_msp->nframe >= 0) fprintf(fp," [%c]",(bbp->frame > 0 ?'r':'f'));
if (m_msp->srelv == 1) fprintf (fp, " %4d", bbp->rst.score[ppst->score_ix]);
else {
if (m_msp->srelv-1 > 0) fprintf (fp, " %4d", bbp->rst.score[0]);
if (m_msp->srelv-1 > 1 || m_msp->stages>1)
fprintf (fp, " %4d", bbp->rst.score[1]);
fprintf (fp, " %4d", bbp->rst.score[ppst->score_ix]);
}
if (ppst->zsflag>=0) {
if (m_msp->z_bits==1) {
fprintf (fp, " %.1f %s%7.2g%s",zs_to_bit(bbp->zscore,m_msp->n0,BBP_INFO(n1)),html_pre_E,bbp->rst.escore,html_post_E);
}
else fprintf (fp, " %.1f %s%7.2g%s",bbp->zscore,html_pre_E,bbp->rst.escore,html_post_E);
}
show_aux(fp,bbp);
#ifdef PCOMPLIB
n1 = BBP_INFO(n1);
percent = bbp->percent;
gpercent = bbp->gpercent;
aln_p = &(bbp->aln_d);
seq_code = bbp->aln_code;
seq_code_len = bbp->aln_code_n;
ann_code = bbp->ann_code;
ann_code_len = bbp->ann_code_n;
loffset = bbp->seq->l_offset;
l_off = 0;
#endif
if (m_msp->markx & MX_M9SUMM) {
if (m_msp->show_code != SHOW_CODE_ID) {
/* we need the coordinates for annotated SHOW_CODE_ALIGN */
cal_coord(m_msp->n0,BBP_INFO(n1),
m_msp->q_offset + (m_msp->q_off-1) + (m_msp->sq0off-1),
loffset + (l_off-1) + (m_msp->sq1off-1),
aln_p);
if (m_msp->markx & MX_HTML) fprintf(fp,"<!-- ");
/* %_id %_sim s-w alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs */
/* alignment min max min max */
/* sequence coordinate min max min max */
fprintf(fp,"\t%5.3f %5.3f %4d %4d %4ld %4ld %4ld %4ld %4ld %4ld %4ld %4ld %3d %3d %3d",
percent/100.0,gpercent/100.0,
#ifndef PCOMPLIB
bbp->a_res.sw_score,
#else
bbp->sw_score,
#endif
aln_p->a_len,
aln_p->d_start0,aln_p->d_stop0,
aln_p->q_offset+1, aln_p->q_offset+m_msp->n0,
aln_p->d_start1,aln_p->d_stop1,
aln_p->l_offset+1, aln_p->l_offset+BBP_INFO(n1),
aln_p->ngap_q,aln_p->ngap_l,aln_p->nfs);
if (m_msp->show_code == SHOW_CODE_ALIGN
&& seq_code_len > 0 && seq_code != NULL) {
fprintf(fp,"\t%s",seq_code);
if (ann_code_len > 0 && ann_code != NULL) {
fprintf(fp,"\t%s",ann_code);
}
/* fprintf(fp," [%2d:%d]",bbp->wrkr,bbp->seqnm); */
/* if we are doing MX_M10FORM and -m 9c, then we want to keep
the alignment code string for the alignment output - otherwise, we
can free() it
If PCOMPLIB, then it is stored in bbp->ann_code*, otherwise, it's in a_res.
*/
#ifndef PCOMPLIB
if (m_msp->markx & MX_M10FORM) {
/* save encoded alignments in a_res */
if ((bbp->a_res.aln_code = (char *)calloc(seq_code_len+1,sizeof(char)))!=NULL) {
strncpy(bbp->a_res.aln_code,seq_code,seq_code_len+1);
bbp->a_res.aln_code[seq_code_len] = '\0';
bbp->a_res.aln_code_n = seq_code_len;
}
}
/* always free the originally allocated encoding */
free(seq_code);
seq_code = NULL;
seq_code_len = 0;
#else
/* only free it if not to be used */
if (!(m_msp->markx & MX_M10FORM)) {
free(bbp->aln_code);
bbp->aln_code_n = 0;
}
#endif
/* also clean up ann_code(_n) */
if (ann_code_len > 0 && ann_code != NULL) {
#ifndef PCOMPLIB
if (m_msp->markx & MX_M10FORM) {
/* save encoded annotations in a_res */
if ((bbp->a_res.ann_code = (char *)calloc(ann_code_len+1,sizeof(char)))!=NULL) {
strncpy(bbp->a_res.ann_code,ann_code,ann_code_len+1);
bbp->a_res.ann_code[ann_code_len] = '\0';
bbp->a_res.ann_code_n = ann_code_len;
}
else {
bbp->a_res.ann_code = NULL;
bbp->a_res.ann_code_n = 0;
}
}
free(ann_code);
ann_code = NULL;
ann_code_len = 0;
#else
if (!(m_msp->markx & MX_M10FORM)) {
free(bbp->ann_code);
bbp->ann_code_n = 0;
}
#endif
}
}
if (m_msp->markx & MX_HTML) fprintf(fp," -->");
}
else {
#ifdef SHOWSIM
fprintf(fp," %5.3f %5.3f %4d", percent/100.0,(float)aln_p->nsim/(float)aln_p->a_len,aln_p->a_len);
#else
fprintf(fp," %5.3f %4d", percent/100.0,aln_p->a_len);
#endif
}
}
if (m_msp->markx & MX_HTML) fprintf(fp," <A HREF=\"#%s\">align</A>",l_name);
fprintf (fp, "\n");
fflush(fp);
}
if (quiet==0) {
printf(" More scores? [0] ");
fflush(stdout);
if (fgets(rline,20,stdin)==NULL) exit(0);
ntmp = 0;
if (rline[0]!='\n' && rline[0]!=0) sscanf(rline,"%d",&ntmp);
if (ntmp<=0) ntmp = 0;
if (ntmp>0) {
istart = istop;
nshow += ntmp;
goto l1;
}
}
else if (quiet == 1)
if (ib < nbest && (ppst->zsflag>=0 && bbp->rst.escore < m_msp->e_cut)) {
if (m_msp->mshow_flg && istop >= m_msp->mshow) goto done;
istart=istop;
nshow += 10;
goto l1;
}
done:
m_msp->nshow = nshow;
if (m_msp->markx & MX_HTML) fprintf(fp,"</pre></tt><p><hr><p>\n");
if (fp!=stdout) fprintf(fp,"\n");
}
struct a_res_str *
build_ares_code(unsigned char *aa0, int n0,
unsigned char *aa1,
struct seq_record *seq,
int frame, int *have_ares, int repeat_thresh,
const struct mngmsg *m_msp, struct pstruct *ppst,
void *f_str
)
{
unsigned char *aa1_ann;
int n1;
struct rstruct rst;
struct a_res_str *my_ares_p, *cur_ares_p;
struct a_struct *aln_p;
long loffset; /* loffset is offset from beginning of real sequence */
long l_off; /* l_off is the the virtual coordinate of residue 1 */
int seqc_max, annc_max;
char *seq_code, *ann_code;
int seq_code_len, ann_code_len;
n1 = seq->n1;
aa1_ann = seq->aa1_ann;
loffset = seq->l_offset;
l_off = seq->l_off;
if (! (*have_ares & 0x1)) { /* we don't have an a_res, and we need one */
my_ares_p = do_walign(aa0, n0, aa1, n1, frame,
repeat_thresh, ppst, f_str,
have_ares);
}
else { /* we already have the a_res */
pre_cons(aa1,n1,frame,f_str);
}
/* here, we need to loop through all the alignments, and produce
the statistics/codes for each */
for (cur_ares_p = my_ares_p; cur_ares_p != NULL; cur_ares_p = cur_ares_p->next) {
seqc_max = my_ares_p->nres + 4*m_msp->aln.llen+4;
cur_ares_p->aln_code = seq_code = NULL;
cur_ares_p->aln_code_n = seq_code_len = 0;
cur_ares_p->ann_code = NULL;
cur_ares_p->ann_code_n = 0;
aln_p = &cur_ares_p->aln;
/* this sets a number of constants, from the alignment function
and frame, and only needs to be called once */
aln_func_vals(frame, aln_p);
if ((m_msp->show_code & SHOW_CODE_ALIGN) == SHOW_CODE_ALIGN) {
cur_ares_p->aln_code = seq_code=(char *)calloc(seqc_max,sizeof(char));
/* if we have an annotation string, allocate space for the
encoded annotation */
if (m_msp->ann_arr[0] != '\0') {
/* the annotation encoding can be considerably longer than
the alignment encoding */
annc_max = 4*seqc_max;
cur_ares_p->ann_code = ann_code=(char *)calloc(annc_max,sizeof(char));
}
else {
ann_code = NULL;
annc_max = 0;
}
if (seq_code != NULL) {
calc_astruct(aln_p, cur_ares_p);
/* we need this for offset information for calc_code, but it is
incomplete so we must do it again */
calc_coord(m_msp->n0,n1,
m_msp->q_offset + (m_msp->q_off-1) + (m_msp->sq0off-1),
loffset + (l_off-1) + (m_msp->sq1off-1),
aln_p);
aln_p->lc=calc_code(aa0, m_msp->n0,
aa1,n1,
aln_p,cur_ares_p,
ppst,seq_code,seqc_max,
m_msp->ann_arr,
m_msp->aa0a, aa1_ann,
ann_code, annc_max,
f_str, m_msp->show_code);
cur_ares_p->aln_code_n = seq_code_len = strlen(seq_code);
if (seq_code[1] == '0' && seq_code[0] == '=') {
fprintf(stderr," code begins with 0: %s\n", seq_code);
}
if (ann_code != NULL) ann_code_len = strlen(ann_code);
else ann_code_len = 0;
cur_ares_p->ann_code_n = ann_code_len;
}
}
else {
aln_p->lc=calc_id(aa0,m_msp->n0,aa1,n1,
aln_p, cur_ares_p,
ppst,f_str);
}
/* this should be all the information we need on the alignment */
} /* end for (cur_ares_p;) */
return my_ares_p;
}
