int edview_search_tag_type(edview *xx, int dir, int strand, char *value) {
contig_iterator *iter;
int start, end;
rangec_t *r;
rangec_t *(*ifunc)(GapIO *io, contig_iterator *ci);
int type = str2type(value);
contig_t *c = cache_search(xx->io, GT_Contig, xx->cnum);
if (dir) {
start = xx->cursor_apos + (dir ? 1 : -1);
end = c->end;
ifunc = contig_iter_next;
} else {
start = c->start;
end = xx->cursor_apos + (dir ? 1 : -1);
ifunc = contig_iter_prev;
}
iter = contig_iter_new_by_type(xx->io, xx->cnum, 1,
dir == 1 ? CITER_FIRST : CITER_LAST,
start, end, GRANGE_FLAG_ISANNO);
if (!iter)
/* Can happen legitimately when we're already at the end of contig */
return -1;
while (r = ifunc(xx->io, iter)) {
if ((dir && r->start < start) ||
(!dir && r->start > end))
continue;
if (r->mqual == type)
break;
}
if (r) {
if (r->flags & GRANGE_FLAG_TAG_SEQ) {
int pos;
sequence_get_position(xx->io, r->pair_rec, NULL, &pos, NULL, NULL);
pos = r->start - pos;
edSetCursorPos(xx, GT_Seq, r->pair_rec, pos, 1);
} else {
edSetCursorPos(xx, GT_Contig, xx->cnum, r->start, 1);
}
contig_iter_del(iter);
return 0;
}
contig_iter_del(iter);
return -1;
}
/*
* Value can be one of several modes:
* 1. By position in contig. eg 30717
* 2. By position in current gel. eg @100
* 3. By position in defined gel. eg @100/xy66a2.s1
* 4. By a relative offset. eg +1000 eg -1000
*/
int edview_search_position(edview *xx, int dir, int strand, char *value) {
int pos;
char *cp;
switch (*value) {
case '\0':
break;
case '+':
case '-':
/* Relative */
pos = atoi(value+1);
edSetCursorPos(xx, GT_Contig, xx->cnum,
xx->cursor_apos + pos, 1);
break;
case '@':
pos = atoi(value+1);
if (NULL != (cp = strchr(value, '/'))) {
tg_rec rec;
int type;
rec = contig_name_to_number(xx->io, cp+1);
if (rec) {
type = GT_Contig;
if (rec != xx->cnum)
return -1;
} else {
rec = get_gel_num(xx->io, cp+1, 0);
type = GT_Seq;
if (rec != xx->cursor_rec)
return -1;
}
edSetCursorPos(xx, type, rec, pos, 1);
} else {
edSetCursorPos(xx, GT_Contig, xx->cursor_rec, pos, 1);
}
break;
default:
pos = atoi(value);
edSetCursorPos(xx, GT_Contig, xx->cnum, pos, 1);
break;
}
return 0;
}
int edview_search_uposition(edview *xx, int dir, int strand, char *value) {
int upos = atoi(value), ppos;
if (0 != consensus_padded_pos(xx->io, xx->cnum, upos, &ppos))
return -1;
edSetCursorPos(xx, GT_Contig, xx->cnum, ppos, 1);
return 0;
}
int edview_search_tag_indel(edview *xx, int dir, int strand, char *value) {
contig_iterator *iter;
int start, end;
rangec_t *r;
rangec_t *(*ifunc)(GapIO *io, contig_iterator *ci);
contig_t *c = cache_search(xx->io, GT_Contig, xx->cnum);
if (dir) {
start = xx->cursor_apos + (dir ? 1 : -1);
end = c->end;
ifunc = contig_iter_next;
} else {
start = c->start;
end = xx->cursor_apos + (dir ? 1 : -1);
ifunc = contig_iter_prev;
}
iter = contig_iter_new_by_type(xx->io, xx->cnum, 1,
dir == 1 ? CITER_FIRST : CITER_LAST,
start, end, GRANGE_FLAG_ISREFPOS);
if (!iter)
return -1;
while (r = ifunc(xx->io, iter)) {
if ((dir && r->start < start) ||
(!dir && r->start > end))
continue;
break;
}
if (r) {
edSetCursorPos(xx, GT_Contig, xx->cnum, r->start, 1);
contig_iter_del(iter);
return 0;
}
contig_iter_del(iter);
return -1;
}
/*
* Attempt to find edits. It's not 100% reliable, but works for most cases.
* We look for lowercase bases and confidence 100 and 0 (if not N).
* We cannot find deleted bases though.
*/
int edview_search_edit(edview *xx, int dir, int strand, char *value) {
int start, end;
contig_iterator *iter;
rangec_t *(*ifunc)(GapIO *io, contig_iterator *ci);
rangec_t *r;
int best_pos, found = 0;
int fpos;
tg_rec fseq;
if (dir) {
start = xx->cursor_apos + 1;
end = CITER_CEND;
iter = contig_iter_new(xx->io, xx->cnum, 1,
CITER_FIRST | CITER_ISTART,
start, end);
ifunc = contig_iter_next;
best_pos = INT_MAX;
} else {
start = CITER_CSTART;
end = xx->cursor_apos -1;
iter = contig_iter_new(xx->io, xx->cnum, 1,
CITER_LAST | CITER_IEND,
start, end);
ifunc = contig_iter_prev;
best_pos = INT_MIN;
}
if (!iter)
return -1;
while ((r = ifunc(xx->io, iter))) {
seq_t *s, *sorig;
char *seq, *qual;
int seq_len, comp, off = 0, i;
if (found && dir && r->start > best_pos)
break;
if (found && !dir && r->end < best_pos)
break;
if (NULL == (s = sorig = cache_search(xx->io, GT_Seq, r->rec)))
break;
if (r->comp ^ (s->len < 0)) {
s = dup_seq(s);
complement_seq_t(s);
}
seq = s->seq;
qual = s->conf;
seq_len = ABS(s->len);
if (r->start < start) {
off = start - r->start;
seq += off;
qual += off;
seq_len -= off;
}
for (i = 0; i < seq_len; i++) {
if (islower(seq[i]) ||
qual[i] == 100 ||
(qual[i] == 0 && seq[i] != 'N' && seq[i] != '-'
&& seq[i] != '*')) {
int pos = r->start + i + off;
if (dir) {
if (best_pos > pos && pos > xx->cursor_apos) {
found = 1;
best_pos = pos;
fpos = i + off;
fseq = r->rec;
}
break;
} else {
if (best_pos < pos && pos < xx->cursor_apos) {
found = 1;
best_pos = pos;
fpos = i + off;
fseq = r->rec;
}
}
}
}
if (s != sorig)
free(s);
}
if (found) {
edSetCursorPos(xx, fseq == xx->cnum ? GT_Contig : GT_Seq,
fseq, fpos, 1);
}
contig_iter_del(iter);
return found ? 0 : -1;
}
int edview_search_consensus(edview *xx, int dir, int strand, char *value) {
int mismatches = 0; /* exact match */
int where = 2; /* consensus */
char *p;
int start, end;
char cons[WIN_WIDTH+1];
int patlen;
char *uppert, *upperb;
int found = 0, at_end = 0;
tg_rec fseq;
int fpos, i, j;
contig_t *c;
/*
* Parse value search string. It optionally includes two extra params
* separated by #. Ie:
* <string>#<N.mismatches>#<where>.
* <where> is 1 for readings, 2 for consensus, 3 for both.
*/
if (p = strchr(value, '#')) {
mismatches = atoi(p+1);
*p = 0;
if (p = strchr(p+1, '#'))
where = atoi(p+1);
}
/* uppercase search string, remove pads, and store fwd/rev copies */
patlen = strlen(value);
depad_seq(value, &patlen, NULL);
if (NULL == (uppert = (char *)xmalloc(patlen + 1)))
return 0;
if (NULL == (upperb = (char *)xmalloc(patlen + 1)))
return 0;
uppert[patlen] = upperb[patlen] = 0;
for (i = patlen-1; i >= 0; i--) {
upperb[i] = uppert[i] = toupper(value[i]);
}
complement_seq(upperb, patlen);
/* Loop */
if (dir) {
start = xx->cursor_apos + (dir ? 1 : -1);
end = start + (WIN_WIDTH-1);
} else {
end = xx->cursor_apos + (dir ? 1 : -1);
start = end - (WIN_WIDTH-1);
}
fpos = xx->cursor_apos;
c = cache_search(xx->io, GT_Contig, xx->cnum);
cache_incr(xx->io, c);
do {
char *ind, *indt = NULL, *indb = NULL;
calculate_consensus_simple(xx->io, xx->cnum, start, end, cons, NULL);
cons[WIN_WIDTH] = 0;
if (dir) {
if (strand == '+' || strand == '=')
indt = pstrstr_inexact(cons, uppert, mismatches, NULL);
if (strand == '-' || strand == '=')
indb = pstrstr_inexact(cons, upperb, mismatches, NULL);
} else {
if (strand == '+' || strand == '=')
indt = prstrstr_inexact(cons, uppert, mismatches, NULL);
if (strand == '-' || strand == '=')
indb = prstrstr_inexact(cons, upperb, mismatches, NULL);
}
if (indt && indb)
ind = MIN(indt, indb);
else if (indt)
ind = indt;
else if (indb)
ind = indb;
else
ind = NULL;
if (ind != NULL) {
if (dir) {
if (fpos <= start + ind-cons) {
found = 1;
fpos = start + ind-cons;
fseq = xx->cnum;
}
} else {
if (fpos >= start + ind-cons) {
found = 1;
fpos = start + ind-cons;
fseq = xx->cnum;
}
}
break;
}
/* Next search region - overlapping by patlen+pads */
if (dir) {
for (i = WIN_WIDTH-1, j = patlen; j && i; i--) {
if (cons[i] != '*')
j--;
}
if (i == 0)
break;
start += i;
end += i;
if (start > c->end)
at_end = 1;
} else {
for (i = 0, j = patlen; j && i < WIN_WIDTH; i++) {
if (cons[i] != '*')
j--;
}
if (i == WIN_WIDTH)
break;
start -= WIN_WIDTH-i;
end -= WIN_WIDTH-i;
if (end < c->start)
at_end = 1;
}
} while (!at_end);
cache_decr(xx->io, c);
if (found) {
edSetCursorPos(xx, fseq == xx->cnum ? GT_Contig : GT_Seq,
fseq, fpos, 1);
}
free(uppert);
free(upperb);
return found ? 0 : -1;
}
int edview_search_tag_anno(edview *xx, int dir, int strand, char *value) {
contig_iterator *iter;
int start, end;
rangec_t *r;
rangec_t *(*ifunc)(GapIO *io, contig_iterator *ci);
char *r_exp = NULL;
contig_t *c = cache_search(xx->io, GT_Contig, xx->cnum);
if (value) {
if (NULL == (r_exp = REGCMP(xx->interp, value))) {
verror(ERR_WARN, "Search by anno", "invalid regular expression");
return -1;
}
}
if (dir) {
start = xx->cursor_apos + (dir ? 1 : -1);
end = c->end;
ifunc = contig_iter_next;
} else {
start = c->start;
end = xx->cursor_apos + (dir ? 1 : -1);
ifunc = contig_iter_prev;
}
iter = contig_iter_new_by_type(xx->io, xx->cnum, 1,
dir == 1 ? CITER_FIRST : CITER_LAST,
start, end, GRANGE_FLAG_ISANNO);
if (!iter)
return -1;
while (r = ifunc(xx->io, iter)) {
anno_ele_t *ae;
if ((dir && r->start < start) ||
(!dir && r->start > end))
continue;
if (!r_exp)
break; /* blank expr => match all */
ae = cache_search(xx->io, GT_AnnoEle, r->rec);
if (!ae->comment)
continue;
if (REGEX(xx->interp, ae->comment, r_exp))
break;
}
REGFREE(xx->interp, r_exp);
if (r) {
if (r->flags & GRANGE_FLAG_TAG_SEQ) {
int pos;
sequence_get_position(xx->io, r->pair_rec, NULL, &pos, NULL, NULL);
pos = r->start - pos;
edSetCursorPos(xx, GT_Seq, r->pair_rec, pos, 1);
} else {
edSetCursorPos(xx, GT_Contig, xx->cnum, r->start, 1);
}
contig_iter_del(iter);
return 0;
}
contig_iter_del(iter);
return -1;
}
int edview_search_name(edview *xx, int dir, int strand, char *value)
{
tg_rec rec, *rp, cnum = -1, best_rec;
int best_pos, best_off;
int nr, i;
rangec_t *(*ifunc)(GapIO *io, contig_iterator *ci);
int start, end, cstart;
contig_iterator *iter;
contig_t *c;
/* Check for #num where num is a sequence record in this contig */
if (*value == '#') {
char *endp;
int64_t v = strtol64(value+1, &endp, 10);
rec = v;
if (*endp == '\0' && cache_exists(xx->io, GT_Seq, rec)) {
sequence_get_clipped_position(xx->io, rec, &cnum,
&start, NULL, &cstart, NULL, NULL);
if (cnum == xx->cnum) {
edSetCursorPos(xx, GT_Seq, rec, cstart - start, 1);
return 0;
}
}
}
/* Find all hits matching this name */
rp = sequence_index_query_all(xx->io, value, 1, &nr);
/* Also get an position-based iterator */
c = cache_search(xx->io, GT_Contig, xx->cnum);
if (dir) {
start = xx->cursor_apos + 1;
end = c->end;
ifunc = contig_iter_next;
best_pos = end + 1;
best_off = 0;
} else {
start = c->start;
end = xx->cursor_apos - 1;
ifunc = contig_iter_prev;
best_pos = start - 1;
best_off = 0;
}
iter = contig_iter_new_by_type(xx->io, xx->cnum, 1,
dir == 1 ? CITER_FIRST : CITER_LAST,
start-1, end+1, GRANGE_FLAG_ISSEQ);
if (!iter)
return -1;
/*
* The iterator also finds overlapping objects, not just ones beyond this
* point. That's fine if we're on the consensus as we probably want to
* jump to the first seq-name overlapping this point.
*
* However if we're on a sequence already, we want the first one
* after or before that sequence. So we skip along iterator until we're
* at the current record.
*/
if (xx->cursor_type == GT_Seq) {
rangec_t *r;
while ((r = ifunc(xx->io, iter))) {
if (r->rec == xx->cursor_rec)
break;
}
}
/* Alternate between the by-name and by-position scan */
best_rec = -1;
for (i = 0; i < nr; i++) {
int start, end;
rangec_t *r;
/* From name index */
rec = rp[i++];
sequence_get_clipped_position(xx->io, rec, &cnum, &start, &end,
&cstart, NULL, NULL);
if (cnum == xx->cnum) {
if ((dir && best_pos > cstart && cstart > xx->cursor_apos) ||
(!dir && best_pos < cstart && cstart < xx->cursor_apos)) {
best_pos = cstart;
best_off = cstart - start;
best_rec = rec;
}
}
/* From iterator */
if ((r = ifunc(xx->io, iter))) {
seq_t *s;
if (NULL == (s = cache_search(xx->io, GT_Seq, r->rec))) {
/* No match */
best_rec = -1;
break;
}
if (strncmp(s->name, value, strlen(value)) == 0) {
/* prefix match */
puts("Found by pos iterator");
best_rec = r->rec;
break;
}
} else {
/* End of contig - bail out early */
best_rec = -1;
break;
}
}
contig_iter_del(iter);
if (rp)
free(rp);
if (best_rec != -1) {
edSetCursorPos(xx, GT_Seq, best_rec, best_off, 1);
return 0;
}
return -1;
}
int edview_search_cons_discrep(edview *xx, int dir, int strand, char *value) {
int start, end;
int found = 0, at_end = 0;
int fpos, i;
double qval = atof(value);
consensus_t cons[WIN_WIDTH+1];
contig_t *c;
/* Set initial start positions */
if (dir) {
start = xx->cursor_apos + (dir ? 1 : -1);
end = start + (WIN_WIDTH-1);
} else {
end = xx->cursor_apos + (dir ? 1 : -1);
start = end - (WIN_WIDTH-1);
}
fpos = xx->cursor_apos;
/* Loop WIN_WIDTH block at a time */
c = cache_search(xx->io, GT_Contig, xx->cnum);
cache_incr(xx->io, c);
do {
calculate_consensus(xx->io, xx->cnum, start, end, cons);
if (dir) {
for (i = 0; i < WIN_WIDTH; i++) {
if (cons[i].discrep >= qval) {
found = 1;
break;
}
}
} else {
for (i = WIN_WIDTH-1; i; i--) {
if (cons[i].discrep >= qval) {
found = 1;
break;
}
}
}
if (found) {
fpos = start + i;
break;
}
/* Next search region - overlapping by patlen+pads */
if (dir) {
start += WIN_WIDTH;
end += WIN_WIDTH;
if (start > c->end)
at_end = 1;
} else {
start -= WIN_WIDTH;
end -= WIN_WIDTH;
if (end < c->start)
at_end = 1;
}
} while (!at_end);
cache_decr(xx->io, c);
if (found) {
edSetCursorPos(xx, GT_Contig, xx->cnum, fpos, 1);
return 0;
}
return -1;
}
int edview_search_sequence(edview *xx, int dir, int strand, char *value) {
int mismatches = 0; /* exact match */
int where = 2; /* consensus */
char *p;
int start, end;
int patlen;
char *uppert, *upperb;
int found = 0, at_end = 0;
tg_rec fseq;
int fpos, i, j;
contig_t *c;
contig_iterator *iter;
rangec_t *(*ifunc)(GapIO *io, contig_iterator *ci);
rangec_t *r;
int best_pos;
if (dir) {
start = xx->cursor_apos + 1;
end = CITER_CEND;
iter = contig_iter_new(xx->io, xx->cnum, 1,
CITER_FIRST | CITER_ISTART,
start, end);
ifunc = contig_iter_next;
best_pos = INT_MAX;
} else {
start = CITER_CSTART;
end = xx->cursor_apos -1;
iter = contig_iter_new(xx->io, xx->cnum, 1,
CITER_LAST | CITER_IEND,
start, end);
ifunc = contig_iter_prev;
best_pos = INT_MIN;
}
if (!iter)
return -1;
/*
* Parse value search string. It optionally includes two extra params
* separated by #. Ie:
* <string>#<N.mismatches>#<where>.
* <where> is 1 for readings, 2 for consensus, 3 for both.
*/
if (p = strchr(value, '#')) {
mismatches = atoi(p+1);
*p = 0;
if (p = strchr(p+1, '#'))
where = atoi(p+1);
}
/* uppercase search string, remove pads, and store fwd/rev copies */
patlen = strlen(value);
depad_seq(value, &patlen, NULL);
if (NULL == (uppert = (char *)xmalloc(patlen + 1)))
return 0;
if (NULL == (upperb = (char *)xmalloc(patlen + 1)))
return 0;
uppert[patlen] = upperb[patlen] = 0;
for (i = patlen-1; i >= 0; i--) {
upperb[i] = uppert[i] = toupper(value[i]);
}
complement_seq(upperb, patlen);
while ((r = ifunc(xx->io, iter))) {
seq_t *s, *sorig;
char *ind, *indt = NULL, *indb = NULL, *seq;
int seq_len, comp, off = 0;
if (found && dir && r->start > best_pos)
break;
if (found && !dir && r->end < best_pos)
break;
if (NULL == (s = sorig = cache_search(xx->io, GT_Seq, r->rec)))
break;
if (r->comp ^ (s->len < 0)) {
s = dup_seq(s);
complement_seq_t(s);
}
seq = s->seq;
seq_len = ABS(s->len);
if (r->start < start) {
off = start - r->start;
seq += off;
seq_len -= off;
}
if (r->end - (patlen-1) > end)
seq_len -= r->end - (patlen-1) - end;
if (dir) {
if (strand == '+' || strand == '=')
indt = pstrnstr_inexact(seq, seq_len, uppert, patlen,
mismatches, NULL);
if (strand == '-' || strand == '=')
indb = pstrnstr_inexact(seq, seq_len, upperb, patlen,
mismatches, NULL);
} else {
if (strand == '+' || strand == '=')
indt = prstrnstr_inexact(seq, seq_len, uppert, patlen,
mismatches, NULL);
if (strand == '-' || strand == '=')
indb = prstrnstr_inexact(seq, seq_len, upperb, patlen,
mismatches, NULL);
}
if (indt && indb)
ind = MIN(indt, indb);
else if (indt)
ind = indt;
else if (indb)
ind = indb;
else
ind = NULL;
if (ind) {
int pos = r->start + ind - seq + off;
if (dir) {
if (best_pos > pos) {
found = 1;
best_pos = pos;
fpos = ind - s->seq;
fseq = r->rec;
}
} else {
if (best_pos < pos) {
found = 1;
best_pos = pos;
fpos = ind - s->seq;
fseq = r->rec;
}
}
//printf("Matches #%"PRIrec": at abs pos %d\n", r->rec, pos);
}
if (s != sorig)
free(s);
}
if (found) {
edSetCursorPos(xx, fseq == xx->cnum ? GT_Contig : GT_Seq,
fseq, fpos, 1);
}
free(uppert);
free(upperb);
contig_iter_del(iter);
return found ? 0 : -1;
}
int edview_search_consquality(edview *xx, int dir, int strand, char *value) {
int start, end;
float qual[WIN_WIDTH+1];
int found = 0, at_end = 0;
int fpos, i, qval = atoi(value);
/* Set initial start positions */
if (dir) {
start = xx->cursor_apos + (dir ? 1 : -1);
end = start + (WIN_WIDTH-1);
} else {
end = xx->cursor_apos + (dir ? 1 : -1);
start = end - (WIN_WIDTH-1);
}
fpos = xx->cursor_apos;
/* Loop WIN_WIDTH block at a time */
do {
calculate_consensus_simple(xx->io, xx->cnum, start, end, NULL, qual);
if (dir) {
for (i = 0; i < WIN_WIDTH; i++) {
if (qual[i] < qval) {
found = 1;
break;
}
}
} else {
for (i = WIN_WIDTH-1; i; i--) {
if (qual[i] < qval) {
found = 1;
break;
}
}
}
if (found) {
fpos = start + i;
break;
}
/* Next search region - overlapping by patlen+pads */
if (dir) {
start += WIN_WIDTH;
end += WIN_WIDTH;
if (start > xx->contig->end)
at_end = 1;
} else {
start -= WIN_WIDTH;
end -= WIN_WIDTH;
if (end < xx->contig->start)
at_end = 1;
}
} while (!at_end);
if (found) {
edSetCursorPos(xx, GT_Contig, xx->contig->rec, fpos, 1);
return 0;
}
return -1;
}
