Int2 SBlastOptionsSetWindowSize(SBlastOptions* options, Int4 window_size)
{
if (!options || !options->score_options || !options->word_options)
return -1;
if (window_size < 0)
return -2;
if (Blast_QueryIsNucleotide(options->program) == TRUE && Blast_QueryIsTranslated(options->program) == FALSE)
return 0;
if (window_size == 0)
{
Int2 status=0;
if ((status=BLAST_GetSuggestedWindowSize(options->program, options->score_options->matrix, &window_size)) != 0)
return status;
}
options->word_options->window_size = window_size;
return 0;
}
Int2 SBlastOptionsSetThreshold(SBlastOptions* options, double threshold)
{
if (!options || !options->lookup_options || !options->score_options)
return -1;
if (threshold < 0)
return -2;
if (Blast_QueryIsNucleotide(options->program) == TRUE && Blast_QueryIsTranslated(options->program) == FALSE)
return 0;
if (threshold == 0)
{
Int2 status=0;
if ((status=BLAST_GetSuggestedThreshold(options->program, options->score_options->matrix, &threshold)) != 0)
return status;
}
options->lookup_options->threshold = threshold;
return 0;
}
void
CQuerySplitter::x_ComputeQueryContextsForChunks()
{
const EBlastProgramType kProgram = m_Options->GetProgramType();
const unsigned int kNumContexts = GetNumberOfContexts(kProgram);
const ENa_strand kStrandOption = m_Options->GetStrandOption();
auto_ptr<CQueryDataPerChunk> qdpc;
if (Blast_QueryIsTranslated(kProgram)) {
qdpc.reset(new CQueryDataPerChunk(*m_SplitBlk, kProgram,
m_LocalQueryData));
}
for (size_t chunk_num = 0; chunk_num < m_NumChunks; chunk_num++) {
vector<size_t> queries = m_SplitBlk->GetQueryIndices(chunk_num);
for (size_t i = 0; i < queries.size(); i++) {
CConstRef<CSeq_loc> sl = m_LocalQueryData->GetSeq_loc(queries[i]);
const ENa_strand kStrand =
BlastSetup_GetStrand(*sl, kProgram, kStrandOption);
if (Blast_QueryIsTranslated(kProgram)) {
size_t qlength = qdpc->GetQueryLength(queries[i]);
int last_query_chunk = qdpc->GetLastChunk(queries[i]);
_ASSERT(last_query_chunk != -1);
int shift = s_GetShiftForTranslatedNegStrand(qlength);
for (unsigned int ctx = 0; ctx < kNumContexts; ctx++) {
// handle the plus strand...
if (ctx % NUM_FRAMES < CODON_LENGTH) {
if (kStrand == eNa_strand_minus) {
m_SplitBlk->AddContextToChunk(chunk_num,
kInvalidContext);
} else {
m_SplitBlk->AddContextToChunk(chunk_num,
kNumContexts*queries[i]+ctx);
}
} else { // handle the negative strand
if (kStrand == eNa_strand_plus) {
m_SplitBlk->AddContextToChunk(chunk_num,
kInvalidContext);
} else {
if (chunk_num == (size_t)last_query_chunk) {
// last chunk doesn't have shift
m_SplitBlk->AddContextToChunk(chunk_num,
kNumContexts*queries[i]+ctx);
} else {
m_SplitBlk->AddContextToChunk(chunk_num,
kNumContexts*queries[i]+
s_AddShift(ctx, shift));
}
}
}
}
} else if (Blast_QueryIsNucleotide(kProgram)) {
for (unsigned int ctx = 0; ctx < kNumContexts; ctx++) {
// handle the plus strand...
if (ctx % NUM_STRANDS == 0) {
if (kStrand == eNa_strand_minus) {
m_SplitBlk->AddContextToChunk(chunk_num,
kInvalidContext);
} else {
m_SplitBlk->AddContextToChunk(chunk_num,
kNumContexts*queries[i]+ctx);
}
} else { // handle the negative strand
if (kStrand == eNa_strand_plus) {
m_SplitBlk->AddContextToChunk(chunk_num,
kInvalidContext);
} else {
m_SplitBlk->AddContextToChunk(chunk_num,
kNumContexts*queries[i]+ctx);
}
}
}
} else if (Blast_QueryIsProtein(kProgram)) {
m_SplitBlk->AddContextToChunk(chunk_num,
kNumContexts*queries[i]);
} else {
abort();
}
}
}
}
