/*
* Compute the visible end position of a contig. This isn't just the extents
* of start_used / end_used in the bins as this can included invisible
* data such as cached consensus sequences.
*/
int contig_visible_end(GapIO *io, tg_rec crec) {
rangec_t *r;
contig_iterator *ci;
ci = contig_iter_new_by_type(io, crec, 1, CITER_LAST | CITER_IEND,
CITER_CSTART, CITER_CEND,
GRANGE_FLAG_ISANY);
if (!ci) {
contig_t *c = cache_search(io, GT_Contig, crec);
return c->end;
}
while (r = contig_iter_prev(io, ci)) {
int v;
if ((r->flags & GRANGE_FLAG_ISMASK) == GRANGE_FLAG_ISCONS)
continue;
v = r->end;
contig_iter_del(ci);
return v;
}
contig_iter_del(ci);
return 0;
}
static void tag_shift_for_delete(GapIO *io, tg_rec crec, tg_rec srec,
int start, int end, int pos, tg_rec brec) {
contig_iterator *ci;
rangec_t *r;
contig_t *c = cache_search(io, GT_Contig, crec);;
//printf("< tag in seq %"PRIrec" at %d\n", srec, pos);
cache_incr(io, c);
ci = contig_iter_new_by_type(io, crec, 0, CITER_FIRST | CITER_ISTART,
start+pos, end, GRANGE_FLAG_ISANNO);
if (!ci) {
cache_decr(io, c);
return;
}
while ((r = contig_iter_next(io, ci))) {
range_t r2, *r_out;
anno_ele_t *a;
bin_index_t *bin;
if (r->pair_rec != srec)
continue;
bin_remove_item(io, &c, GT_AnnoEle, r->rec);
r2.start = (r->start > start+pos) ? r->start-1 : r->start;
r2.end = r->end-1;
r2.mqual = r->mqual;
r2.rec = r->rec;
r2.pair_rec = r->pair_rec;
r2.flags = r->flags;
if (r2.end < r2.start) {
/* Tag entirely removed now, it must have been on a pad */
a = cache_search(io, GT_AnnoEle, r->rec);
a = cache_rw(io, a);
cache_deallocate(io, a);
continue;
}
bin = bin_add_to_range(io, &c, brec, &r2, &r_out, NULL, 0);
a = cache_search(io, GT_AnnoEle, r->rec);
if (a->bin != bin->rec /*||
a->idx != r_out - ArrayBase(range_t, bin->rng)*/) {
/* Annotation moved bins */
a = cache_rw(io, a);
a->bin = bin->rec;
//a->bin_idx = r_out - ArrayBase(range_t, bin->rng);
}
}
cache_decr(io, c);
contig_iter_del(ci);
}
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;
}
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;
}
/*
* Removes all tags of specific types (hashed in h, or all if h == NULL)
* from a specified contig.
*
* Returns 0 on success
* -1 on failure
*/
static int delete_tag_single_contig(GapIO *io, tg_rec crec,
HashTable *h, int verbose) {
contig_iterator *ci;
rangec_t *r;
contig_t *c;
int ret = -1;
ci = contig_iter_new_by_type(io, crec, 1, CITER_FIRST,
CITER_CSTART, CITER_CEND,
GRANGE_FLAG_ISANNO);
if (!ci)
return -1;
if (!(c = cache_search(io, GT_Contig, crec))) {
contig_iter_del(ci);
return -1;
}
cache_incr(io, c);
while (NULL != (r = contig_iter_next(io, ci))) {
char t[5];
(void)type2str(r->mqual, t);
if (!h || HashTableSearch(h, t, 4)) {
anno_ele_t *e;
if (verbose)
vmessage("Removing anno %s #%"PRIrec"\tContig %s\t%d..%d\n",
t, r->rec, c->name, r->start, r->end);
if (bin_remove_item(io, &c, GT_AnnoEle, r->rec)) goto fail;
/* FIXME: Need to reclaim the GT_AnnoEle record itself */
}
}
ret = 0;
fail:
contig_iter_del(ci);
cache_decr(io, c);
return ret;
}
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;
}
