CRef< CStructWrapper<BlastHSPStream> >
x_GetSampleHspStream(CRef<CBlastOptions> opts, CSeqDB & db)
{
CSeq_id sid("gi|158292535");
vector<int> OIDS;
db.SeqidToOids(sid, OIDS);
BOOST_REQUIRE(OIDS.size());
const int k_num_hsps_start = 12;
//const int k_num_hsps_end = 10;
// Taken from traceback unit test.
BlastHSPList* hsp_list =
(BlastHSPList*) calloc(1, sizeof(BlastHSPList));
hsp_list->oid = OIDS[0];
hsp_list->hspcnt = k_num_hsps_start;
hsp_list->allocated = k_num_hsps_start;
hsp_list->hsp_max = k_num_hsps_start;
hsp_list->do_not_reallocate = FALSE;
hsp_list->hsp_array = (BlastHSP**)
malloc(hsp_list->allocated*sizeof(BlastHSP*));
BlastHSPWriterInfo * writer_info = BlastHSPCollectorInfoNew(
BlastHSPCollectorParamsNew(
opts->GetHitSaveOpts(),
opts->GetExtnOpts()->compositionBasedStats,
opts->GetScoringOpts()->gapped_calculation));
BlastHSPWriter* writer = BlastHSPWriterNew(&writer_info, NULL);
BOOST_REQUIRE(writer_info == NULL);
BlastHSPStream* hsp_stream = BlastHSPStreamNew(
opts->GetProgramType(),
opts->GetExtnOpts(),
FALSE, 1, writer);
const int query_offset[k_num_hsps_start] =
{ 0, 3864, 3254, 1828, 2189, 795,
607, 1780, 1363, 2751, 3599, 242 };
const int query_end[k_num_hsps_start] =
{ 307, 4287, 3556, 2058, 2269, 914,
741, 1821, 1451, 2810, 3631, 285 };
const int subject_offset[k_num_hsps_start] =
{ 1, 2723, 2267, 1028, 1292, 634,
501, 925, 1195, 1795, 477, 1233 };
const int subject_end[k_num_hsps_start] =
{ 321, 3171, 2537, 1243, 1371, 749,
618, 966, 1286, 1869, 509, 1276 };
const int score[k_num_hsps_start] =
{ 370, 319, 139, 120, 89, 84,
75, 70, 69, 60, 47, 43 };
const int query_gapped_start[k_num_hsps_start] =
{ 47, 4181, 3286, 2034, 2228, 871,
632, 1798, 1383, 2759, 3606, 259 };
const int subject_gapped_start[k_num_hsps_start] =
{ 48, 3073, 2299, 1219, 1330, 709,
526, 943, 1215, 1803, 484, 1250 };
for (int index=0; index<k_num_hsps_start; index++) {
BlastHSP * h1
= hsp_list->hsp_array[index]
= (BlastHSP*) calloc(1, sizeof(BlastHSP));
h1->query.offset = query_offset[index];
h1->query.end = query_end[index];
h1->subject.offset = subject_offset[index];
h1->subject.end = subject_end[index];
h1->score = score[index];
h1->query.gapped_start = query_gapped_start[index];
h1->subject.gapped_start = subject_gapped_start[index];
}
// needed after tie-breaking algorithm for scores was changed
// in ScoreCompareHSP (blast_hits.c, revision 1.139)
Blast_HSPListSortByScore(hsp_list);
BlastHSPStreamWrite(hsp_stream, &hsp_list);
CRef< CStructWrapper<BlastHSPStream> >
hsps(WrapStruct(hsp_stream, BlastHSPStreamFree));
return hsps;
}
CRef< CStructWrapper<BlastHSPStream> >
x_GetSelfHitHspStream(CRef<CBlastOptions> opts, CSeqDB & db, CSeq_id& sid)
{
vector<int> OIDS;
db.SeqidToOids(sid, OIDS);
BOOST_REQUIRE(OIDS.size());
const int k_num_hsps_start = 1;
const int k_seq_length = db.GetSeqLength(OIDS.front());
BlastHSPList* hsp_list =
(BlastHSPList*) calloc(1, sizeof(BlastHSPList));
hsp_list->oid = OIDS.front();
hsp_list->hspcnt = k_num_hsps_start;
hsp_list->allocated = k_num_hsps_start;
hsp_list->hsp_max = k_num_hsps_start;
hsp_list->do_not_reallocate = FALSE;
hsp_list->hsp_array = (BlastHSP**)
malloc(hsp_list->allocated*sizeof(BlastHSP*));
BlastHSPWriterInfo * writer_info = BlastHSPCollectorInfoNew(
BlastHSPCollectorParamsNew(
opts->GetHitSaveOpts(),
opts->GetExtnOpts()->compositionBasedStats,
opts->GetScoringOpts()->gapped_calculation));
BlastHSPWriter* writer = BlastHSPWriterNew(&writer_info, NULL);
BOOST_REQUIRE(writer_info == NULL);
BlastHSPStream* hsp_stream = BlastHSPStreamNew(
opts->GetProgramType(),
opts->GetExtnOpts(),
FALSE, 1, writer);
const int query_offset[k_num_hsps_start] = { 0 };
const int query_end[k_num_hsps_start] = { k_seq_length - 1 };
const int subject_offset[k_num_hsps_start] = { 0 };
const int subject_end[k_num_hsps_start] = { k_seq_length - 1 };
const int score[k_num_hsps_start] = { 0 };
const int query_gapped_start[k_num_hsps_start] = { 0 };
const int subject_gapped_start[k_num_hsps_start] = { 0 };
for (int index=0; index<k_num_hsps_start; index++) {
BlastHSP * h1
= hsp_list->hsp_array[index]
= (BlastHSP*) calloc(1, sizeof(BlastHSP));
h1->query.offset = query_offset[index];
h1->query.end = query_end[index];
h1->subject.offset = subject_offset[index];
h1->subject.end = subject_end[index];
h1->score = score[index];
h1->query.gapped_start = query_gapped_start[index];
h1->subject.gapped_start = subject_gapped_start[index];
}
// needed after tie-breaking algorithm for scores was changed
// in ScoreCompareHSP (blast_hits.c, revision 1.139)
Blast_HSPListSortByScore(hsp_list);
BlastHSPStreamWrite(hsp_stream, &hsp_list);
CRef< CStructWrapper<BlastHSPStream> >
hsps(WrapStruct(hsp_stream, BlastHSPStreamFree));
return hsps;
}