static GtUword condenseq_unique_extract_encoded(const GtCondenseq *cs,
GtUword id,
GtUchar *buffer,
GtUword frompos,
GtUword topos)
{
GtCondenseqUnique unique = cs->uniques[id];
GtUword startoffset,
startpos,
uniquelength,
targetlength,
endpos;
gt_assert(unique.orig_startpos <= frompos);
startoffset = frompos - unique.orig_startpos;
gt_assert(startoffset < unique.len);
startpos = gt_encseq_seqstartpos(cs->unique_es, id) + startoffset;
uniquelength = unique.len - startoffset;
targetlength = topos - frompos + 1;
if (uniquelength < targetlength)
endpos = startpos + uniquelength - 1;
else
endpos = startpos + targetlength - 1;
gt_encseq_extract_encoded(cs->unique_es, buffer, startpos, endpos);
return endpos - startpos + 1;
}
void gt_bioseq_get_encoded_sequence_range(const GtBioseq *bs, GtUchar *out,
GtUword idx,
GtUword start,
GtUword end)
{
GtUword startpos;
gt_assert(bs);
gt_assert(idx < gt_encseq_num_of_sequences(bs->encseq) && end >= start);
startpos = gt_encseq_seqstartpos(bs->encseq, idx);
gt_encseq_extract_encoded(bs->encseq, out, startpos + start, startpos + end);
}
void gt_bioseq_get_encoded_sequence(const GtBioseq *bs, GtUchar *out,
GtUword idx)
{
GtUword startpos;
gt_assert(bs);
gt_assert(idx < gt_encseq_num_of_sequences(bs->encseq));
startpos = gt_encseq_seqstartpos(bs->encseq, idx);
gt_encseq_extract_encoded(bs->encseq, out, startpos,
startpos
+ gt_encseq_seqlength(bs->encseq, idx) - 1);
}
static int encseq_lua_extract_encoded(lua_State *L)
{
GtEncseq **encseq;
GtUword from, to;
unsigned char *string;
encseq = check_encseq(L, 1);
from = luaL_checknumber(L, 2);
to = luaL_checknumber(L, 3);
luaL_argcheck(L, from <= to, 2, "must be <= range endposition");
luaL_argcheck(L, to < gt_encseq_total_length(*encseq), 3,
"cannot exceed total length of encoded sequence");
string = gt_malloc((to - from + 1) * sizeof (unsigned char));
gt_encseq_extract_encoded(*encseq, string, from, to);
encseq_lua_push_buffer(L, string, (to - from + 1));
return 1;
}
static GtUword samplesubstring(GtUchar *seqspace,
const GtEncseq *encseq,
GtUword substringlength)
{
GtUword start, totallength;
totallength = gt_encseq_total_length(encseq);
start = (GtUword) (random() % totallength);
if (start + substringlength > totallength)
{
substringlength = totallength - start;
}
gt_assert(substringlength > 0);
gt_encseq_extract_encoded(encseq,seqspace,start,
start+substringlength-1);
return substringlength;
}
static void gt_show_seed_extend_plain(GtSequencepairbuffer *seqpairbuf,
GtLinspaceManagement
*linspace_spacemanager,
GtScoreHandler *linspace_scorehandler,
GtAlignment *alignment,
GtUchar *alignment_show_buffer,
GtUword alignmentwidth,
bool showeoplist,
const GtUchar *characters,
GtUchar wildcardshow,
const GtEncseq *aencseq,
const GtEncseq *bencseq,
const GtQuerymatch *querymatchptr)
{
GtUword edist;
GtReadmode query_readmode = gt_querymatch_query_readmode(querymatchptr);
const GtUword distance = gt_querymatch_distance(querymatchptr),
dblen = gt_querymatch_dblen(querymatchptr),
queryseqnum = gt_querymatch_queryseqnum(querymatchptr),
querystart_fwdstrand
= gt_querymatch_querystart_fwdstrand(querymatchptr),
querylen = gt_querymatch_querylen(querymatchptr);
const GtUword apos_ab = gt_querymatch_dbstart(querymatchptr);
const GtUword bpos_ab = gt_encseq_seqstartpos(bencseq, queryseqnum) +
querystart_fwdstrand;
gt_querymatch_coordinates_out(querymatchptr);
if (dblen >= seqpairbuf->a_allocated)
{
seqpairbuf->a_sequence = gt_realloc(seqpairbuf->a_sequence,
sizeof *seqpairbuf->a_sequence * dblen);
seqpairbuf->a_allocated = dblen;
}
if (querylen >= seqpairbuf->b_allocated)
{
seqpairbuf->b_sequence = gt_realloc(seqpairbuf->b_sequence,
sizeof *seqpairbuf->b_sequence *
querylen);
seqpairbuf->b_allocated = querylen;
}
gt_encseq_extract_encoded(aencseq, seqpairbuf->a_sequence, apos_ab,
apos_ab + dblen - 1);
gt_encseq_extract_encoded(bencseq, seqpairbuf->b_sequence, bpos_ab,
bpos_ab + querylen - 1);
if (query_readmode != GT_READMODE_FORWARD)
{
gt_assert(query_readmode == GT_READMODE_REVCOMPL);
gt_inplace_reverse_complement(seqpairbuf->b_sequence,querylen);
}
edist = gt_computelinearspace_generic(linspace_spacemanager,
linspace_scorehandler,
alignment,
seqpairbuf->a_sequence,
0,
dblen,
seqpairbuf->b_sequence,
0,
querylen);
if (edist < distance)
{
printf("# edist=" GT_WU " (smaller by " GT_WU ")\n",edist,distance - edist);
}
gt_assert(edist <= distance);
if (alignmentwidth > 0)
{
gt_alignment_show_generic(alignment_show_buffer,
false,
alignment,
stdout,
alignmentwidth,
characters,
wildcardshow);
}
if (showeoplist && distance > 0)
{
gt_alignment_show_multieop_list(alignment, stdout);
}
if (alignmentwidth > 0 || showeoplist)
{
gt_alignment_reset(alignment);
}
}
