//------------------------------------------------------------------------------
CSegMasker::TMaskList*
CSegMasker::operator()(const objects::CSeqVector & data)
{
if ( !data.IsProtein() ) {
throw logic_error("SEG can only filter protein sequences");
}
if (data.GetCoding() != CSeq_data::e_Ncbistdaa ) {
throw logic_error("SEG expects protein sequences in ncbistdaa format");
}
string sequence;
BlastSeqLoc* seq_locs = NULL;
data.GetSeqData(data.begin(), data.end(), sequence);
Int2 status = SeqBufferSeg((Uint1*)(sequence.data()),
static_cast<Int4>(sequence.size()), 0,
m_SegParameters, &seq_locs);
sequence.erase();
if (status != 0) {
seq_locs = BlastSeqLocFree(seq_locs);
throw runtime_error("SEG internal error (check that input is protein) " + NStr::IntToString(status));
}
auto_ptr<TMaskList> retval(new TMaskList);
for (BlastSeqLoc* itr = seq_locs; itr; itr = itr->next) {
retval->push_back
(TMaskList::value_type(itr->ssr->left, itr->ssr->right));
}
seq_locs = BlastSeqLocFree(seq_locs);
return retval.release();
}
Int2
BlastSetUp_Filter(EBlastProgramType program_number,
Uint1* sequence,
Int4 length,
Int4 offset,
const SBlastFilterOptions* filter_options,
BlastSeqLoc** seqloc_retval,
Blast_Message* *blast_message)
{
Int2 status=0; /* return value. */
ASSERT(filter_options);
ASSERT(seqloc_retval);
*seqloc_retval = NULL;
status = SBlastFilterOptionsValidate(program_number, filter_options,
blast_message);
if (status)
return status;
if (filter_options->segOptions)
{
SSegOptions* seg_options = filter_options->segOptions;
SegParameters* sparamsp=NULL;
sparamsp = SegParametersNewAa();
sparamsp->overlaps = TRUE;
if (seg_options->window > 0)
sparamsp->window = seg_options->window;
if (seg_options->locut > 0.0)
sparamsp->locut = seg_options->locut;
if (seg_options->hicut > 0.0)
sparamsp->hicut = seg_options->hicut;
status = SeqBufferSeg(sequence, length, offset, sparamsp,
seqloc_retval);
SegParametersFree(sparamsp);
sparamsp = NULL;
}
return status;
}
