void showbest (FILE *fp,
#ifndef PCOMPLIB
unsigned char **aa0, unsigned char *aa1, int maxn,
#endif
struct beststr **bptr,int nbest,
int qlib, struct mngmsg *m_msg,
struct pstruct *ppst, struct db_str db,
char **info_gstring2
#ifndef PCOMPLIB
,void **f_str
#endif
)
{
int i, j, k, rel_tot;
int irelv;
int unf_num0, relm_num0;
int unf_num01,relm_num01;
int unf_num02, relm_num02;
int unf_num05, relm_num05;
int unf_num100, relm_num100;
int equ_num, rel_3_num, rel_1_num;
double unf_score0, unf_score01, unf_score02 ,unf_score05;
double unf_score100, equ_score, rel_3_score, rel_1_score;
double unf_score0_b, unf_score01_b, unf_score02_b ,unf_score05_b;
double unf_score100_b, equ_score_b, rel_3_score_b, rel_1_score_b;
char *bp;
#ifdef PCOMPLIB
int qsfnum[10],qsfnum_n[10],isf,nsf,nsf_n;
char *bp1, *bpn, *tp;
char sfstr[MAX_FN];
#endif
#ifdef PCOMPLIB
/* not done here because done in pvcomplib.c */
if ((bp=strchr(m_msg->qtitle,SFCHAR))!=NULL) {
strncpy(sfstr,bp+1,sizeof(sfstr));
sfstr[sizeof(sfstr)-1]='\0';
if ((bp1=strchr(sfstr,SFCHAR)) != NULL) { /* look for second | */
if ((bpn=strchr(sfstr,NSFCHAR))!=NULL) *bpn = '\0';
*bp1='\0';
tp = strtok(sfstr," \t");
qsfnum[0]=atoi(tp);
isf = 1;
while ((tp=strtok(NULL," \t"))!=NULL) {
qsfnum[isf++] = atoi(tp);
if (isf >= 10) {
fprintf(stderr," error - too many superfamilies: %d\n %s\n",
isf,m_msg->qtitle);
break;
}
}
qsfnum[nsf=isf]=0;
sf_sort(qsfnum,nsf);
/* now get negatives */
qsfnum_n[0]= nsf_n = 0;
if (bpn != NULL) {
tp = strtok(bpn+1," \t");
qsfnum_n[0]=atoi(tp);
isf = 1;
while ((tp=strtok(NULL," \t"))!=NULL) {
qsfnum_n[isf++] = atoi(tp);
if (isf >= 10) {
fprintf(stderr,
" error - too many negative superfamilies: %d\n %s\n",
isf,m_msg->qtitle);
break;
}
}
qsfnum[nsf_n=isf]=0;
sf_sort(qsfnum_n,nsf_n);
}
}
else { /* only one sfnum */
sscanf(bp+1,"%d",qsfnum);
qsfnum[1]=0;
qsfnum_n[0]= nsf_n = 0;
}
}
else {
fprintf(stderr," no query superfamily number\n %s\n",m_msg->qtitle);
return;
}
#endif
if (m_msg->qframe > 1 || m_msg->nframe > 1) {
/* this code is included for cases where there are several scores -
forward and reverse, or six in the case of tfastf33s, for each
sequence
lnum_sort sorts the library by lseek position, which will be
the same for the same sequence
*/
lnum_sort(bptr,nbest);
/* merge, saving the best score */
i = j = 0;
/* i has the source position we are currently examining
k has the adjacent alternative scores ( k > i)
j has the destination
*/
while (i<nbest) {
for (k=i+1; k < nbest && bptr[i]->seq->lseek == bptr[k]->seq->lseek; k++) {
if (bptr[i]->zscore < bptr[k]->zscore) bptr[i] = bptr[k];
}
bptr[j++]=bptr[i];
i = k;
}
if (j != m_msg->nbr_seq) {
fprintf(stderr,"*** warning ***, nbest (%d/%d) != nbr_seq (%d)\n",
j,nbest,m_msg->nbr_seq);
fprintf(stdout,"*** warning ***, nbest (%d/%d) != nbr_seq (%d)\n",
j,nbest,m_msg->nbr_seq);
}
nbest = j;
if (ppst->zsflag >=0) sortbeste(bptr, nbest);
else sortbest(bptr,nbest,ppst->score_ix);
}
/* fprintf(stderr," %1d label is %s (%s)\n",irelv,labptr,label); */
/* get the query superfamily */
for (i=0; i<nbest; i++) {
/* if (sfn_cmp(BSFNUM(i),NQSFNUM)) continue; */
if (sfn_cmp(BSFNUM(i),QSFNUM)==0 && sfn_cmp(BSFNUM(i),NQSFNUM)==0) {
unf_num0=i;
unf_score0=bptr[i]->zscore;
unf_score0_b=zs_to_bit(bptr[i]->zscore,m_msg->n0,bptr[i]->seq->n1);
break;
}
}
if (i>=nbest) {
fprintf(stderr," %s: %d\n error - no unrelated sequences\n",
m_msg->qtitle,QSFNUM[0]);
return;
}
for (i=rel_tot=relm_num0=0; i<nbest; i++) {
/* if (sfn_cmp(BSFNUM(i),NQSFNUM)) continue; */
if (sfn_cmp(BSFNUM(i),QSFNUM)>0 ) {
rel_tot++; /* total related */
if (bptr[i]->zscore <= unf_score0) relm_num0++;
#ifdef DEBUG
if (ppst->debug_lib)
fprintf(stderr,"%d\t%l\t%.1f\n",i,bptr[i]->seq->lseek,bptr[i]->zscore);
#endif
}
}
/* relm_num0, unf_num0, unf_score0 done */
/* now calculate number missed at various expectation value cutoffs */
/* calculate z-score cutoff for E()=0.01, 0.02, 0.05 */
unf_score01 = E_to_zs(0.01,db.entries);
unf_score02 = E_to_zs(0.02,db.entries);
unf_score05 = E_to_zs(0.05,db.entries);
unf_score100 = E_to_zs(1.00,db.entries);
/* relm_num01, unf_num01, unf_score01 done */
for (i=unf_num01=0,relm_num01=rel_tot;
i<nbest && bptr[i]->zscore >= unf_score01; i++) {
/* if (sfn_cmp(BSFNUM(i),NQSFNUM)) continue; */
if (sfn_cmp(BSFNUM(i),QSFNUM)==0) {
if (sfn_cmp(BSFNUM(i),NQSFNUM)==0) unf_num01++;
}
else relm_num01--;
}
unf_score01_b=zs_to_bit(bptr[i]->zscore,m_msg->n0,bptr[i]->seq->n1);
for (i=unf_num02=0,relm_num02=rel_tot;
i<nbest && bptr[i]->zscore >= unf_score02; i++) {
/* if (sfn_cmp(BSFNUM(i),NQSFNUM)) continue; */
if (sfn_cmp(BSFNUM(i),QSFNUM)==0) {
if (sfn_cmp(BSFNUM(i),NQSFNUM)==0) unf_num02++;
}
else relm_num02--;
}
unf_score02_b=zs_to_bit(bptr[i]->zscore,m_msg->n0,bptr[i]->seq->n1);
for (i=unf_num05=0,relm_num05=rel_tot;
i<nbest && bptr[i]->zscore >= unf_score05; i++) {
/* if (sfn_cmp(BSFNUM(i),NQSFNUM)) continue; */
if (sfn_cmp(BSFNUM(i),QSFNUM)==0) {
if (sfn_cmp(BSFNUM(i),NQSFNUM)==0) unf_num05++;
}
else relm_num05--;
}
unf_score05_b=zs_to_bit(bptr[i]->zscore,m_msg->n0,bptr[i]->seq->n1);
for (i=unf_num100=0,relm_num100=rel_tot;
i<nbest && bptr[i]->zscore >= unf_score100; i++) {
/* if (sfn_cmp(BSFNUM(i),NQSFNUM)) continue; */
if (sfn_cmp(BSFNUM(i),QSFNUM)==0) {
if (sfn_cmp(BSFNUM(i),NQSFNUM)==0) unf_num100++;
}
else relm_num100--;
}
unf_score100_b=zs_to_bit(bptr[i]->zscore,m_msg->n0,bptr[i]->seq->n1);
/* the final criterion finds the score and the number of sequences
where the number of unrelated sequences found == the number of
related sequences missed. */
equ_num=0;
i = 0; j=nbest-1;
/* j is counting up the list of scores (actually down the array) from
the lowest scoring related sequence
i is counting down the list of scores (actually up the array)
from the highest scoring unrelated sequence */
for (i=0, j=nbest-1; j>=0 && i<nbest; i++,j--) {
/* i++ while sequences are related, stop at next unrelated */
while (i<nbest && (sfn_cmp(BSFNUM(i),QSFNUM) || sfn_cmp(BSFNUM(i),NQSFNUM))) i++;
/* j-- while sequences are unrelated, stop at next related */
while (j>=0 && ( sfn_cmp(BSFNUM(j),QSFNUM)==0)) j--;
/*
fprintf(stderr,"i: %3d %3d %4d; j: %3d %3d %4d\n",i,bptr[i]->zscore,
BSFNUM(i),j,bptr[j]->zscore,BSFNUM(j));
*/
/* if unrelated [i] score <= related [j] score, quit */
if (bptr[i]->zscore <= bptr[j]->zscore) break;
equ_num++;
}
equ_score = 0.0;
if (i>=nbest || j<0) {
#ifndef PCOMPLIB
if (ppst->debug_lib)
#endif
fprintf(stderr," i (%3d), j (%3d) off end\n %s\n", i, j,m_msg->qtitle);
equ_num = rel_tot+1; equ_score = 0.0;
}
else {
equ_score=bptr[i]->zscore;
equ_score_b =zs_to_bit(bptr[i]->zscore,m_msg->n0,bptr[i]->seq->n1);
}
/* get the lowest scoring related */
for (i=0,rel_1_num=rel_tot-1; i<nbest && rel_1_num > 0; i++) {
/* if (sfn_cmp(BSFNUM(i),NQSFNUM)) continue; */
if (sfn_cmp(BSFNUM(i),QSFNUM)) rel_1_num--;
}
rel_1_num = i;
rel_1_score = bptr[i]->zscore;
rel_1_score_b=zs_to_bit(bptr[i]->zscore,m_msg->n0,bptr[i]->seq->n1);
/* get the 3rd lowest scoring related */
for (i=0,rel_3_num=rel_tot-3; i<nbest && rel_3_num > 0; i++) {
/* if (sfn_cmp(BSFNUM(i),NQSFNUM)) continue; */
if (sfn_cmp(BSFNUM(i),QSFNUM)) rel_3_num--;
}
rel_3_num = i;
rel_3_score = bptr[i]->zscore;
rel_3_score_b=zs_to_bit(bptr[i]->zscore,m_msg->n0,bptr[i]->seq->n1);
fprintf(fp,"%3d>%s - %d (%d/%d)\n",
qlib,m_msg->qtitle, QSFNUM[0],rel_tot,nbest);
fprintf(fp," 0.0 criterion- relm: %3d pos: %3d score: %5.1f exp: %6.4g\n",
relm_num0, unf_num0+1, unf_score0_b,
zs_to_E(unf_score0,m_msg->n0,ppst->dnaseq,ppst->zdb_size,db));
fprintf(fp," 0.01 criterion- relm: %3d unf: %3d score: %5.1f exp: %6.4g\n",
relm_num01, unf_num01, unf_score01_b,
zs_to_E(unf_score01,m_msg->n0,ppst->dnaseq,ppst->zdb_size,db));
fprintf(fp," 0.02 criterion- relm: %3d unf: %3d score: %5.1f exp: %6.4g\n",
relm_num02, unf_num02, unf_score02_b,
zs_to_E(unf_score02,m_msg->n0,ppst->dnaseq,ppst->zdb_size,db));
fprintf(fp," 0.05 criterion- relm: %3d unf: %3d score: %5.1f exp: %6.4g\n",
relm_num05, unf_num05, unf_score05_b,
zs_to_E(unf_score05,m_msg->n0,ppst->dnaseq,ppst->zdb_size,db));
fprintf(fp," 1.00 criterion- relm: %3d unf: %3d score: %5.1f exp: %6.4g\n",
relm_num100, unf_num100, unf_score100_b,
zs_to_E(unf_score100,m_msg->n0,ppst->dnaseq,ppst->zdb_size,db));
fprintf(fp," equ num: %3d score: %5.1f exp: %6.4g\n",equ_num,equ_score_b,
zs_to_E(equ_score,m_msg->n0,ppst->dnaseq,ppst->zdb_size,db));
fprintf(fp," rel[-1]: %3d score: %5.1f exp: %6.4g\n",rel_1_num+1,rel_1_score_b,
zs_to_E(rel_1_score,m_msg->n0,ppst->dnaseq,ppst->zdb_size,db));
fprintf(fp," rel[-3]: %3d score: %5.1f exp: %6.4g\n",rel_3_num+1,rel_3_score_b,
zs_to_E(rel_3_score,m_msg->n0,ppst->dnaseq,ppst->zdb_size,db));
/*
fprintf(fp,"/ ** %s ** /\n",info_gstring2);
fflush(fp);
*/
m_msg->nshow = m_msg->ashow;
}
void showbest (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
struct beststr **bptr,int nbest,
int qlib, struct mngmsg *m_msp,
struct pstruct *ppst, struct db_str db,
char **info_gstring2
,void **f_str
)
{
unsigned char *aa1;
int best_align_done = 0;
int ntmp = 0;
char bline[MAX_BLINE], fmt[40], pad[MAX_BLINE], fmt2[40], rline[40];
char l_name[128], link_name[140];
int istart = 0, istop, ib;
int nshow; /* number of sequences shown before prompt,
and ultimately displayed */
int first_line, link_shown;
int quiet;
int r_margin;
struct beststr *bbp;
int n1tot;
char *bp, *bline_p;
char rel_label[12];
char score_label[120];
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 n1, ranlib_done;
struct rstruct rst;
int l_score0, ngap;
double lzscore, lzscore2, lbits;
float percent, gpercent;
struct a_struct *aln_p;
struct a_res_str *cur_ares_p;
struct rstruct *rst_p;
int gi_num;
char html_pre_E[120], html_post_E[120];
int have_lalign = 0;
struct lmf_str *m_fptr;
/* for lalign alignments, only show stuff when -m != 11 */
if (m_msp->markx & MX_M11OUT) return;
if (strcmp(m_msp->label,"ls-w")==0) {
have_lalign = 1;
if ((m_msp->markx & MX_M9SUMM) == 0) return;
}
rel_label[0]='\0';
SAFE_STRNCPY(score_label,"scores", sizeof(score_label));
quiet = m_msp->quiet;
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
}
else if (m_msp->markx & MX_MBLAST2) {
r_margin -= 10;
}
else if (m_msp->markx & (MX_M9SUMM + MX_M8OUT)) {
r_margin = 0;
}
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) {
sprintf(fmt,"%%-%ds (%%4d)",m_msp->aln.llen-r_margin);
}
else {
sprintf(fmt,"%%-%ds (%%4d)",m_msp->aln.llen-(r_margin+4));
}
sprintf(fmt2,"%%-%ds",m_msp->aln.llen-r_margin+8);
memset(pad,' ',m_msp->aln.llen-(r_margin+6));
pad[m_msp->aln.llen-(r_margin+12)]='\0';
if (have_lalign) {
if (ppst->show_ident) {
SAFE_STRNCPY(score_label,"alignments", sizeof(score_label));
pad[m_msp->aln.llen-(r_margin+16)]='\0';
}
else {
SAFE_STRNCPY(score_label,"non-identical alignments", sizeof(score_label));
pad[m_msp->aln.llen-(r_margin+30)]='\0';
}
}
nshow = min(m_msp->nshow,nbest);
if ((bp = strchr (m_msp->qtitle, '\n')) != NULL) *bp = '\0';
if (m_msp->markx & MX_M8OUT) {
if ((bp = strchr (m_msp->qtitle, ' ')) != NULL) *bp = '\0';
}
/* fprintf (fp, "%3d %s\n", qlib,m_msp->qtitle); */
if (m_msp->markx & MX_HTML) fprintf(fp,"<pre>");
/* **************************************************************** */
/* done with display format */
/* **************************************************************** */
/* **************************************************************** */
/* prompt for number of best scores if quiet == 0 */
/* **************************************************************** */
if (quiet == 0) { /* interactive */
nshow = min(m_msp->nshow, nbest);
printf(" How many scores would you like to see? [%d] ",nshow);
fflush(stdout);
if (fgets(rline,20,stdin)==NULL) exit(0);
if (rline[0]!='\n' && rline[0]!=0) sscanf(rline,"%d",&nshow);
if (nshow > nbest) nshow=nbest;
if (nshow<=0) nshow = min(20,nbest);
}
/* display number of hits for -m 8C (Blast Tab-commented format) */
if (m_msp->markx & MX_M8COMMENT) {
/* line below copied from BLAST+ output */
fprintf(fp,"# Fields: query id, subject id, %% identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score");
if (m_msp->show_code == SHOW_CODE_ALIGN || m_msp->show_code == SHOW_CODE_CIGAR) { fprintf(fp," aln_code");}
fprintf(fp,"\n");
fprintf(fp,"# %d hits found\n",nshow);
}
/* **************************************************************** */
/* have number of scores in interactive or quiet mode */
/* display "The best scores are" */
/* **************************************************************** */
if (m_msp->markx & MX_MBLAST2) {
fprintf(fp, "%81s\n"," Score E");
fprintf(fp, "Sequences producing significant alignments: (Bits) Value\n\n");
}
else if (!(m_msp->markx & MX_M8OUT)) {
if (ppst->zsflag >= 0) {
if (m_msp->z_bits==1) {/* show bit score */
fprintf(fp,"\nThe best%s %s are:%s%s bits %sE(%ld)%s",
rel_label,score_label,pad,m_msp->label,html_pre_E,ppst->zdb_size,html_post_E);
if (ppst->zsflag > 20) {
fprintf(fp," E2()");
}
}
else {/* show z-score */
fprintf(fp,"\nThe best%s %s are:%s%s z-sc %sE(%ld)%s",
rel_label,score_label,pad,m_msp->label,html_pre_E,ppst->zdb_size,html_post_E);
if (ppst->zsflag > 20) {
fprintf(fp," E2()");
}
}
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,"\nThe best%s %s are:%s%s",rel_label,score_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");
}
} /* !(m_msp->markx & MX_M8OUT) */
istart = 0;
l1:
istop = min(nshow, nbest);
for (ib=istart; ib<istop; ib++) {
bbp = bptr[ib];
if (ppst->do_rep) {
bbp->repeat_thresh =
min(E1_to_s(ppst->e_cut_r, m_msp->n0, bbp->seq->n1,ppst->zdb_size, m_msp->pstat_void),
bbp->rst.score[ppst->score_ix]);
}
#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->mseq->libstr, bbp->rst.score[0]);
}
#endif
/* this gets us a valid bline[] and the library for searching if necessary
do not read if we have a long enough bline or we don't need a sequence
*/
if (bbp->mseq->bline != NULL && bbp->mseq->bline_max >= m_msp->aln.llen) {
ranlib_done = 0;
/* copy m_msp->aln.llen, not llen-r_margin, because the r_margin
will be set later, possibly after the gi|12345 is removed */
strncpy(bline,bbp->mseq->bline,m_msp->aln.llen);
bline[m_msp->aln.llen]='\0';
}
else {
if ((m_fptr=re_openlib(bbp->mseq->m_file_p,!m_msp->quiet))==NULL) {
fprintf(stderr,"*** cannot re-open %s\n",bbp->mseq->m_file_p->lb_name);
exit(1);
}
RANLIB(bline,m_msp->aln.llen,bbp->mseq->lseek,bbp->mseq->libstr,m_fptr);
ranlib_done = 1;
}
/* get a valid cur_ares_p chain and put it in bbp->ares */
if (!m_msp->align_done && (m_msp->stages>1 || (m_msp->markx & MX_M9SUMM))) { /* we need a sequence */
if (bbp->seq->aa1b == NULL || (m_msp->ann_flg==1 && bbp->seq->annot_p==NULL)) {
if (!ranlib_done) { /* we didn't open the library already */
if ((m_fptr=re_openlib(bbp->mseq->m_file_p,!m_msp->quiet))==NULL) {
fprintf(stderr,"*** cannot re-open %s\n",bbp->mseq->m_file_p->lb_name);
exit(1);
}
RANLIB(bline,m_msp->aln.llen,bbp->mseq->lseek,bbp->mseq->libstr,m_fptr);
ranlib_done = 1;
}
n1 = re_getlib(aa1save,
(m_msp->ann_flg==1) ? &(bbp->seq->annot_p) : NULL,
maxn,m_msp->ldb_info.maxt3,
m_msp->ldb_info.l_overlap,bbp->mseq->cont,m_msp->ldb_info.term_code,
&bbp->seq->l_offset,&bbp->seq->l_off,bbp->mseq->m_file_p);
aa1 = aa1save;
if (m_msp->ann_flg==2 && bbp->seq->annot_p==NULL ) {
/* get information about this sequence from bline */
if (get_annot(m_msp->annot1_sname, m_msp, bline, bbp->seq->n1, &(bbp->seq->annot_p), 1, ppst->debug_lib) > 0) {
/* do something with annotation */
s_annot_to_aa1a(bbp->n1, bbp->seq->annot_p, m_msp->ann_arr);
}
}
}
else {
n1 = bbp->seq->n1;
aa1 = bbp->seq->aa1b;
}
if (n1 != bbp->n1) {
fprintf(stderr," *** sequence length conflict %d != %d: %s\n", n1, bbp->n1, bline);
continue;
}
if ( m_msp->stages > 1 && bbp->rst.score[2] == -BIGNUM) {
/* this is not typically done unless m_msp->stages > 1 */
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];
}
if (!bbp->have_ares & 0x1) {
bbp->a_res = build_ares_code(aa0[bbp->frame], m_msp->n0, aa1, bbp->seq,
bbp->frame, &bbp->have_ares,
bbp->repeat_thresh, m_msp, ppst, f_str[bbp->frame] );
best_align_done = 1;
}
} /* end stages > 1 || MX_M9SUMM9 */
n1tot = (bbp->mseq->n1tot_p) ? *bbp->mseq->n1tot_p : bbp->seq->n1;
bline_p = bline;
if (!(m_msp->markx & (MX_M8OUT)) && !strncmp(bline,"gi|",3)) {
bline_p = strchr(bline+4,'|')+1;
*(bline_p-1) = 0;
gi_num = atoi(bline+3);
}
/* 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.
(6-April-2013) Add ability to specify additional alignments with
link_name;
*/
SAFE_STRNCPY(l_name,bline_p,sizeof(l_name)); /* get rid of text after second "|" */
if ((bp=strchr(l_name,' '))!=NULL) *bp=0;
if ((bp=strchr(&l_name[6],'|'))!=NULL) *bp='\0'; /* increase to [6] from [3] to allow longer db names "ref", "unk", */
if (m_msp->nframe > 2) sprintf(&l_name[strlen(l_name)],"_%d",bbp->frame+1);
else if (m_msp->nframe > 0 && bbp->frame == 1)
SAFE_STRNCAT(l_name,"_r",sizeof(l_name));
if (bbp->mseq->cont-1 > 0) {
sprintf(tmp_str,":%d",bbp->mseq->cont-1);
SAFE_STRNCAT(l_name,tmp_str,sizeof(l_name));
}
if (m_msp->markx & MX_M8OUT) {
if ((bp=strchr(bline_p,' '))!=NULL) *bp = '\0';
}
else {
bline_p[m_msp->aln.llen-r_margin]='\0';
/* check for translated frame info */
if (m_msp->nframe > -1) bline_p[m_msp->aln.llen-(r_margin+4)]='\0';
}
/* now its time to report the summary numbers for all the alignments */
/* in the next loop, cur_ares_p could be NULL if we haven't done do_walign() */
cur_ares_p = bbp->a_res;
first_line = 1;
do {
/* if cur_res_p != NULL, then we get rst from a_res->rst
Otherwise, it comes from bbp->rst
*/
if ((!first_line || (have_lalign && !ppst->show_ident)) && cur_ares_p ) {
rst_p = &cur_ares_p->rst;
}
else {
rst_p = &bbp->rst;
}
n1 = bbp->seq->n1;
l_score0 = rst_p->score[ppst->score_ix];
lzscore = find_z(l_score0, rst_p->escore, n1, rst_p->comp, m_msp->pstat_void);
if (ppst->zsflag > 20) {
lzscore2 = find_z(l_score0, rst_p->escore, n1, rst_p->comp, m_msp->pstat_void2);
}
lbits = zs_to_bit(lzscore, m_msp->n0, n1);
/* *********************************** */
/* standard "The best scores are" here */
/* *********************************** */
if (!(m_msp->markx & (MX_M8OUT + MX_MBLAST2))) {
if (first_line) {
first_line = 0;
fprintf (fp, fmt,bline_p,n1tot);
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'));
}
else {
fprintf (fp, fmt2,"\n+-");
}
if (m_msp->srelv == 1) fprintf (fp, " %4d", rst_p->score[ppst->score_ix]);
else {
if (m_msp->srelv-1 > 0) fprintf (fp, " %4d", rst_p->score[0]);
if (m_msp->srelv-1 > 1 || m_msp->stages>1)
fprintf (fp, " %4d", rst_p->score[1]);
fprintf (fp, " %4d", rst_p->score[ppst->score_ix]);
}
if (ppst->zsflag>=0) {
if (m_msp->z_bits==1) {
fprintf (fp, " %.1f %s%7.2g%s",lbits,html_pre_E,
zs_to_E(lzscore, n1, ppst->dnaseq, ppst->zdb_size, m_msp->db),
html_post_E);
if (ppst->zsflag > 20) {
fprintf (fp, " %7.2g",zs_to_E(lzscore2, n1, ppst->dnaseq, ppst->zdb_size, m_msp->db));
}
}
else {
fprintf (fp, " %.1f %s%7.2g%s",lzscore,html_pre_E,
zs_to_E(lzscore, n1, ppst->dnaseq, ppst->zdb_size, m_msp->db),
html_post_E);
if (ppst->zsflag > 20) {
fprintf (fp, " %7.2g",zs_to_E(lzscore2, n1, ppst->dnaseq, ppst->zdb_size, m_msp->db));
}
}
}
show_aux(fp,bbp);
}
else if (m_msp->markx & MX_M8OUT) { /* MX_M8OUT -- provide query, library */
if (first_line) {first_line = 0;}
fprintf (fp,"%s\t%s",m_msp->qtitle,bline_p);
}
else if (m_msp->markx & MX_MBLAST2) { /* blast "Sequences producing" */
if (first_line) {first_line = 0;}
fprintf (fp,"%-67s %6.1f %.1g", bline_p, lbits,
zs_to_E(lzscore,n1,ppst->dnaseq,ppst->zdb_size,m_msp->db));
}
if (m_msp->markx & MX_M9SUMM || m_msp->markx & MX_M8OUT) {
loffset = bbp->seq->l_offset;
l_off = bbp->seq->l_off;
aln_p = &cur_ares_p->aln;
seq_code = cur_ares_p->aln_code;
seq_code_len = cur_ares_p->aln_code_n;
ann_code = cur_ares_p->ann_code;
ann_code_len = cur_ares_p->ann_code_n;
percent = calc_fpercent_id(100.0,aln_p->nident,aln_p->lc, m_msp->tot_ident, -100.0);
ngap = cur_ares_p->aln.ngap_q + cur_ares_p->aln.ngap_l;
#ifndef SHOWSIM
gpercent = calc_fpercent_id(100.0, aln_p->nident, aln_p->lc-ngap, m_msp->tot_ident, -100.0);
#else
gpercent = calc_fpercent_id(100.0, cur_ares_p->aln.nsim, aln_p->lc, m_msp->tot_ident, -100.0);
#endif /* SHOWSIM */
if (m_msp->show_code != SHOW_CODE_ID) { /* show more complete info than just identity */
/* calc_astruct(aln_p, cur_ares_p); -- this function
should not be used after calc_code or any other
alignment that calculates amax0/amax1 */
/* we need the coordinates for annotated SHOW_CODE_ALIGN */
calc_coord(m_msp->n0,bbp->seq->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 */
if (!(m_msp->markx & MX_M8OUT)) {
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,
cur_ares_p->sw_score,
aln_p->lc,
aln_p->d_start0,aln_p->d_stop0,
aln_p->q_start_off, aln_p->q_end_off,
aln_p->d_start1,aln_p->d_stop1,
aln_p->l_start_off, aln_p->l_end_off,
aln_p->ngap_q,aln_p->ngap_l,aln_p->nfs);
if ((m_msp->show_code & SHOW_CODE_ALIGN) == 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);
}
}
}
else { /* MX_M8OUT -- blast order, tab separated */
fprintf(fp,"\t%.2f\t%d\t%d\t%d\t%ld\t%ld\t%ld\t%ld\t%.2g\t%.1f",
percent,aln_p->lc,aln_p->nmismatch,
aln_p->ngap_q + aln_p->ngap_l+aln_p->nfs,
aln_p->d_start0, aln_p->d_stop0,
aln_p->d_start1, aln_p->d_stop1,
zs_to_E(lzscore,n1,ppst->dnaseq,ppst->zdb_size,m_msp->db),
lbits);
if ((m_msp->show_code & SHOW_CODE_ALIGN) == 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,"\n");
}
}
else { /* !SHOW_CODE */
#ifdef SHOWSIM
fprintf(fp," %5.3f %5.3f %4d",
percent/100.0,
(float)aln_p->nsim/(float)aln_p->lc,aln_p->lc);
#else
fprintf(fp," %5.3f %4d", percent/100.0,aln_p->lc);
#endif
if (m_msp->markx & MX_HTML) {
if (cur_ares_p->index > 0) {
sprintf(link_name,"%s_%d",l_name, cur_ares_p->index);
}
else {
SAFE_STRNCPY(link_name, l_name, sizeof(l_name));
}
fprintf(fp," <a href=\"#%s\">align</a>",link_name);
link_shown = 1;
}
if (cur_ares_p->annot_var_s) {
fprintf(fp," |Var: %s",cur_ares_p->annot_var_s);
}
else { link_shown = 0;}
}
}
} while ( cur_ares_p && (cur_ares_p = cur_ares_p->next));
/* if ((m_msp->markx & MX_HTML) && !link_shown) fprintf(fp," <a href=\"#%s\">align</a>",l_name); */
if (!(m_msp->markx & MX_M8OUT)) 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 = min(nshow+ntmp, nbest);
goto l1;
}
} /* end of for (ib) loop */
if (m_msp->markx & MX_MBLAST2) {fprintf(fp, "\n\n");}
m_msp->nshow = nshow; /* save the number of hits displayed for showalign */
if (best_align_done) { m_msp->align_done = 1;} /* note that alignments are done */
if (m_msp->markx & MX_HTML) fprintf(fp,"</pre><hr>\n");
}
