il_opts il_opt_parse(int argc, char **argv)
{
il_opts opts;
memset(&opts, 0, sizeof(il_opts));
for (int i = 1; i < argc; i++) {\
if (argv[i][0] != '-') {
il_string s = il_string_new(argv[i]);
IL_APPEND(opts.args, s);
continue;
}
il_opt opt;
char *dot, *start = argv[i] + 1, *equals = strchr(start, '='), *namestart = start, *nameend = argv[i] + strlen(argv[i]);
il_string modname = {NULL, 0};
il_string name = {NULL, 0};
il_string arg = {NULL, 0};
if (((dot = strchr(start, '.'))) && (!equals || dot < equals)) {
modname = il_string_bin(start, dot - start);
namestart = dot+1;
}
if (equals) {
arg = il_string_new(equals+1);
nameend = equals;
}
name = il_string_bin(namestart, nameend - namestart);
opt = (il_opt){name, arg};
do_opt(&opts, modname, opt);
}
return opts;
}
int main(int argc, char *argv[])
{
char command[GPATH_MAX];
int err, ret;
struct Option *opt1;
struct Option *opt2;
struct Option *opt3;
struct Option *opt4;
struct Option *opt5;
struct Option *opt6;
struct Option *opt7;
struct Option *opt8;
struct Option *opt9;
struct Option *opt10;
struct Option *opt11;
struct Option *opt12;
struct Option *opt13;
struct Option *opt14;
struct Option *opt15;
struct Option *opt16;
struct Flag *flag_sfd;
struct Flag *flag_flow;
struct Flag *flag_seg;
struct Flag *flag_abs;
struct Flag *flag_flat;
struct GModule *module;
G_gisinit(argv[0]);
/* Set description */
module = G_define_module();
G_add_keyword(_("raster"));
G_add_keyword(_("hydrology"));
module->description = _("Calculates hydrological parameters and RUSLE factors.");
opt1 = G_define_standard_option(G_OPT_R_ELEV);
opt1->guisection = _("Inputs");
opt2 = G_define_standard_option(G_OPT_R_INPUT);
opt2->key = "depression";
opt2->label = _("Name of input depressions raster map");
opt2->description = _("All non-NULL and non-zero cells are considered as real depressions");
opt2->required = NO;
opt2->guisection = _("Inputs");
opt3 = G_define_standard_option(G_OPT_R_INPUT);
opt3->key = "flow";
opt3->description = _("Name of input raster representing amount of overland flow per cell");
opt3->required = NO;
opt3->guisection = _("Inputs");
opt4 = G_define_standard_option(G_OPT_R_INPUT);
opt4->key = "disturbed_land";
opt4->label = _("Name of input raster map percent of disturbed land");
opt4->description = _("For USLE");
opt4->required = NO;
opt4->guisection = _("Inputs");
opt5 = G_define_standard_option(G_OPT_R_INPUT);
opt5->key = "blocking";
opt5->label =
_("IName of input raster map blocking overland surface flow");
opt5->description =
_("For USLE. All non-NULL and non-zero cells are considered as blocking terrain.");
opt5->required = NO;
opt5->guisection = _("Inputs");
opt6 = G_define_option();
opt6->key = "threshold";
opt6->description =
_("Minimum size of exterior watershed basin");
opt6->required = NO;
opt6->type = TYPE_INTEGER;
opt6->guisection = _("Inputs");
opt7 = G_define_option();
opt7->key = "max_slope_length";
opt7->label =
_("Maximum length of surface flow in map units");
opt7->description = _("For USLE");
opt7->required = NO;
opt7->type = TYPE_DOUBLE;
opt7->guisection = _("Inputs");
opt8 = G_define_standard_option(G_OPT_R_OUTPUT);
opt8->key = "accumulation";
opt8->label =
_("Name for output accumulation raster map");
opt8->description =
_("Number of cells that drain through each cell");
opt8->required = NO;
opt8->guisection = _("Outputs");
opt9 = G_define_standard_option(G_OPT_R_OUTPUT);
opt9->key = "drainage";
opt9->description = _("Name for output drainage direction raster map");
opt9->required = NO;
opt9->guisection = _("Outputs");
opt10 = G_define_standard_option(G_OPT_R_OUTPUT);
opt10->key = "basin";
opt10->description =
_("Name for basins raster map");
opt10->description = _("Unique label for each watershed basin");
opt10->required = NO;
opt10->guisection = _("Outputs");
opt11 = G_define_standard_option(G_OPT_R_OUTPUT);
opt11->key = "stream";
opt11->description = _("Name for output stream segments raster map");
opt11->required = NO;
opt11->guisection = _("Outputs");
opt12 = G_define_standard_option(G_OPT_R_OUTPUT);
opt12->key = "half_basin";
opt12->label = _("Name for output half basins raster map");
opt12->description =
_("Each half-basin is given a unique value");
opt12->required = NO;
opt12->guisection = _("Outputs");
opt13 = G_define_standard_option(G_OPT_R_OUTPUT);
opt13->key = "length_slope";
opt13->label = _("Name for output slope length raster map");
opt13->description =
_("Slope length and steepness (LS) factor for USLE");
opt13->required = NO;
opt13->guisection = _("Outputs");
opt14 = G_define_standard_option(G_OPT_R_OUTPUT);
opt14->key = "slope_steepness";
opt14->label = _("Name for output slope steepness raster map");
opt14->description = _("Slope steepness (S) factor for USLE");
opt14->required = NO;
opt14->guisection = _("Outputs");
opt15 = G_define_option();
opt15->key = "convergence";
opt15->type = TYPE_INTEGER;
opt15->required = NO;
opt15->answer = "5";
opt15->label = _("Convergence factor for MFD (1-10)");
opt15->description =
_("1 = most diverging flow, 10 = most converging flow. Recommended: 5");
opt16 = G_define_option();
opt16->key = "memory";
opt16->type = TYPE_INTEGER;
opt16->required = NO;
opt16->answer = "300"; /* 300MB default value, please keep r.terraflow in sync */
opt16->description = _("Maximum memory to be used with -m flag (in MB)");
flag_sfd = G_define_flag();
flag_sfd->key = 's';
flag_sfd->label = _("SFD (D8) flow (default is MFD)");
flag_sfd->description =
_("SFD: single flow direction, MFD: multiple flow direction");
flag_flow = G_define_flag();
flag_flow->key = '4';
flag_flow->description =
_("Allow only horizontal and vertical flow of water");
flag_seg = G_define_flag();
flag_seg->key = 'm';
flag_seg->label =
_("Enable disk swap memory option: Operation is slow");
flag_seg->description =
_("Only needed if memory requirements exceed available RAM; see manual on how to calculate memory requirements");
flag_abs = G_define_flag();
flag_abs->key = 'a';
flag_abs->label =
_("Use positive flow accumulation even for likely underestimates");
flag_abs->description =
_("See manual for a detailed description of flow accumulation output");
flag_flat = G_define_flag();
flag_flat->key = 'b';
flag_flat->label =
_("Beautify flat areas");
flag_flat->description =
_("Flow direction in flat areas is modified to look prettier");
if (G_parser(argc, argv))
exit(EXIT_FAILURE);
/* Check option combinations */
/* Check for some output map */
if ((opt8->answer == NULL)
&& (opt9->answer == NULL)
&& (opt10->answer == NULL)
&& (opt11->answer == NULL)
&& (opt12->answer == NULL)
&& (opt14->answer == NULL)
&& (opt15->answer == NULL)) {
G_fatal_error(_("Sorry, you must choose an output map."));
}
err = 0;
/* basin and basin threshold */
err += (opt10->answer != NULL && opt6->answer == NULL);
/* stream and basin threshold */
err += (opt11->answer != NULL && opt6->answer == NULL);
/* half_basin and basin threshold */
err += (opt12->answer != NULL && opt6->answer == NULL);
/* LS factor and basin threshold */
err += (opt13->answer != NULL && opt6->answer == NULL);
/* S factor and basin threshold */
err += (opt14->answer != NULL && opt6->answer == NULL);
if (err) {
G_message(_("Sorry, if any of the following options are set:\n"
" basin, stream, half_basin, length_slope, or slope_steepness\n"
" you MUST provide a value for the basin "
"threshold parameter."));
G_usage();
exit(EXIT_FAILURE);
}
/* Build command line */
sprintf(command, "%s/etc/r.watershed.%s",
G_gisbase(),
flag_seg->answer ? "seg" : "ram");
new_argv[new_argc++] = command;
if (flag_sfd->answer)
new_argv[new_argc++] = "-s";
if (flag_flow->answer)
new_argv[new_argc++] = "-4";
if (flag_abs->answer)
new_argv[new_argc++] = "-a";
if (flag_flat->answer && !flag_seg->answer)
new_argv[new_argc++] = "-b";
if (flag_flat->answer && flag_seg->answer)
G_message(_("Beautify flat areas is not yet supported for disk swap mode"));
do_opt(opt1);
do_opt(opt2);
do_opt(opt3);
do_opt(opt4);
do_opt(opt5);
do_opt(opt6);
do_opt(opt7);
do_opt(opt8);
do_opt(opt9);
do_opt(opt10);
do_opt(opt11);
do_opt(opt12);
do_opt(opt13);
do_opt(opt14);
do_opt(opt15);
if (flag_seg->answer)
do_opt(opt16);
new_argv[new_argc++] = NULL;
G_debug(1, "Mode: %s", flag_seg->answer ? "Segmented" : "All in RAM");
ret = G_vspawn_ex(new_argv[0], new_argv);
if (ret != EXIT_SUCCESS)
G_warning(_("Subprocess failed with exit code %d"), ret);
/* record map metadata/history info */
if (opt8->answer)
write_hist(opt8->answer,
"Watershed accumulation: overland flow that traverses each cell",
opt1->answer, flag_seg->answer, flag_sfd->answer);
if (opt9->answer)
write_hist(opt9->answer,
"Watershed drainage direction (CCW from East divided by 45deg)",
opt1->answer, flag_seg->answer, flag_sfd->answer);
if (opt10->answer)
write_hist(opt10->answer,
"Watershed basins", opt1->answer, flag_seg->answer,
flag_sfd->answer);
if (opt11->answer)
write_hist(opt11->answer,
"Watershed stream segments", opt1->answer,
flag_seg->answer, flag_sfd->answer);
if (opt12->answer)
write_hist(opt12->answer,
"Watershed half-basins", opt1->answer, flag_seg->answer,
flag_sfd->answer);
if (opt13->answer)
write_hist(opt13->answer,
"Watershed slope length and steepness (LS) factor",
opt1->answer, flag_seg->answer, flag_sfd->answer);
if (opt14->answer)
write_hist(opt14->answer,
"Watershed slope steepness (S) factor",
opt1->answer, flag_seg->answer, flag_sfd->answer);
exit(ret);
}
/*
* Handle initial connection protocol.
*/
int
tftp(struct tftphdr *tp, int size)
{
char *cp;
int argn, ecode;
struct formats *pf = NULL;
char *filename, *mode = NULL;
char *val = NULL, *opt = NULL;
char *ap = ackbuf + 2;
((struct tftphdr *)ackbuf)->th_opcode = ntohs(OACK);
filename = cp = tp->th_stuff;
// --> 2005/09/26 Ryan : using tmpfs for firmware upgrade to save run time memory
printf("filename[%s]\n",filename);
if (!strncmp(filename+5,"tmpfs",5))
{
mkdir("/tmp/tmpfs", 0777);
//TT mount("tmpfs", "/tmp/tmpfs", "tmpfs", MS_MGC_VAL, NULL);
}
// <--
argn = 0;
while ( cp < buf + size && *cp ) {
do {
cp++;
} while (cp < buf + size && *cp);
if ( *cp ) {
nak(EBADOP); /* Corrupt packet - no final NULL */
exit(0);
}
argn++;
if (argn == 1) {
mode = ++cp;
} else if (argn == 2) {
for (cp = mode; *cp; cp++)
*cp = tolower(*cp);
for (pf = formats; pf->f_mode; pf++) {
if (!strcmp(pf->f_mode, mode))
break;
}
if (!pf->f_mode) {
nak(EBADOP);
exit(0);
}
ecode = (*pf->f_validate)(filename, tp->th_opcode, pf);
if (ecode) {
nak(ecode);
exit(0);
}
opt = ++cp;
} else if ( argn & 1 ) {
val = ++cp;
} else {
do_opt(opt, val, &ap);
opt = ++cp;
}
}
if (!pf) {
nak(EBADOP);
exit(0);
}
if (strlen(filename) >= 128) {
nak(EBADOP);
exit(0);
}
strcpy(pf->filename, filename);
//printf("tftp filename=%s\n",filename);
if ( ap != (ackbuf+2) ) {
// doesn't come here
if ( tp->th_opcode == WRQ )
(*pf->f_recv)(pf, (struct tftphdr *)ackbuf, ap-ackbuf);
else
(*pf->f_send)(pf, (struct tftphdr *)ackbuf, ap-ackbuf);
} else {
if (tp->th_opcode == WRQ)
(*pf->f_recv)(pf, NULL, 0);
else
(*pf->f_send)(pf, NULL, 0);
}
exit(1);
}
/*
* Handle initial connection protocol.
*/
int tftp (struct tftphdr *tp, int size)
{
char *cp;
int argn, ecode;
struct formats *pf = NULL;
char *origfilename;
char *filename, *mode = NULL;
char *val = NULL, *opt = NULL;
char *ap = ackbuf + 2;
((struct tftphdr *) ackbuf)->th_opcode = ntohs (OACK);
origfilename = cp = (char *) &(tp->th_stuff);
argn = 0;
while (cp < buf + size && *cp)
{
do
{
cp++;
}
while (cp < buf + size && *cp);
if (*cp)
{
nak (EBADOP); /* Corrupt packet - no final NULL */
exit (0);
}
argn++;
if (argn == 1)
{
mode = ++cp;
}
else if (argn == 2)
{
for (cp = mode; *cp; cp++)
*cp = tolower (*cp);
for (pf = formats; pf->f_mode; pf++)
{
if (!strcmp (pf->f_mode, mode))
break;
}
if (!pf->f_mode)
{
nak (EBADOP);
exit (0);
}
if (!(filename = (*pf->f_rewrite) (origfilename, tp->th_opcode)))
{
nak (EACCESS); /* File denied by mapping rule */
exit (0);
}
if (verbosity >= 1)
{
if (filename == origfilename || !strcmp (filename, origfilename))
syslog (LOG_NOTICE, "%s from %s filename %s\n",
tp->th_opcode == WRQ ? "WRQ" : "RRQ", inet_ntoa (from.sin_addr), filename);
else
syslog (LOG_NOTICE, "%s from %s filename %s remapped to %s\n",
tp->th_opcode == WRQ ? "WRQ" : "RRQ", inet_ntoa (from.sin_addr), origfilename, filename);
}
ecode = (*pf->f_validate) (filename, tp->th_opcode, pf);
if (ecode)
{
nak (ecode);
exit (0);
}
opt = ++cp;
}
else if (argn & 1)
{
val = ++cp;
}
else
{
do_opt (opt, val, &ap);
opt = ++cp;
}
}
if (!pf)
{
nak (EBADOP);
exit (0);
}
if (ap != (ackbuf + 2))
{
if (tp->th_opcode == WRQ)
(*pf->f_recv) (pf, (struct tftphdr *) ackbuf, ap - ackbuf);
else
(*pf->f_send) (pf, (struct tftphdr *) ackbuf, ap - ackbuf);
}
else
{
if (tp->th_opcode == WRQ)
(*pf->f_recv) (pf, NULL, 0);
else
(*pf->f_send) (pf, NULL, 0);
}
exit (0); /* Request completed */
}
int
last_calc(
unsigned char **aa0, unsigned char *aa1save, int maxn,
struct beststr **bptr, int nbest,
const struct mngmsg *m_msg, struct pstruct *ppst
, void **f_str
, void *rstat_str)
{
unsigned char *aa1;
int nopt, ib;
struct beststr *bbp;
long loffset, l_off;
int n0, n1;
struct rstruct rst;
struct lmf_str *m_fptr;
char bline[60];
int tat_samp, tat_inc, loop_cnt, i;
double min_escore, ess;
n0 = m_msg->n0;
sortbestz(bptr,nbest);
tat_inc = 500;
/*
if (zs_to_E(bptr[0]->zscore,bptr[0]->n1,0,ppst->zdb_size,m_msg->db)/
zs_to_E(bptr[nbest-1]->zscore,bptr[nbest-1]->n1,0,ppst->zdb_size,m_msg->db)
< 1e-20) { tat_inc /= 4 ;}
*/
/* || (zs_to_E(bptr[0]->zscore,bptr[0]->n1,0,ppst->zdb_size,m_msg->db)< 1e-5); */
ib = tat_samp = 0;
for (loop_cnt = 0; loop_cnt < 5; loop_cnt++) {
tat_samp += tat_inc;
nopt = min(nbest,tat_samp);
min_escore = 1000000.0;
for ( ; ib<nopt; ib++) {
bbp = bptr[ib];
if (bbp->rst.score[0] < 0) break;
if (bbp->seq->aa1b == NULL) {
if ((m_fptr=re_openlib(bbp->mseq->m_file_p,!m_msg->quiet))==NULL) {
fprintf(stderr,"*** cannot re-open %s\n",bbp->mseq->m_file_p->lb_name);
exit(1);
}
RANLIB(bline,sizeof(bline),bbp->mseq->lseek,bbp->mseq->libstr,m_fptr);
n1 = re_getlib(aa1save,NULL,maxn,m_msg->ldb_info.maxt3,
m_msg->ldb_info.l_overlap,bbp->mseq->cont,
m_msg->ldb_info.term_code,
&loffset,&l_off,bbp->mseq->m_file_p);
aa1 = aa1save;
}
else {
n1 = bbp->seq->n1;
aa1 = bbp->seq->aa1b;
loffset = bbp->seq->l_offset;
l_off = bbp->seq->l_off;
}
do_opt(aa0[bbp->frame],m_msg->n0,aa1,n1,bbp->frame,ppst,
f_str[bbp->frame],&rst);
memcpy(&(bbp->rst),&rst,sizeof(struct rstruct));
if ((ess=scale_one_score(ib, bbp->rst.escore, m_msg->db, rstat_str)) <
min_escore) { min_escore = ess;}
/*
fprintf(stderr,"%d: %4d %2d %3d %.4g %.4g\n",
ib, bbp->rst.score[0], bbp->segnum,bbp->seglen,bbp->escore, ess);
*/
}
if (min_escore > m_msg->e_cut) goto done;
}
done:
return ib;
}
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");
}
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");
}
