CCmdLineBlastXMLReportData::CCmdLineBlastXMLReportData
(CRef<blast::CBlastQueryVector> queries,
const blast::CSearchResultSet& results,
const blast::CBlastOptions& opts,
const string& dbname, bool db_is_aa,
int qgencode, int dbgencode,
bool is_remote,
int dbfilt_algorithm /* = -1 */)
: m_Queries(queries), m_Options(opts),
m_DbName(dbname),
m_QueryGeneticCode(qgencode),
m_DbGeneticCode(dbgencode),
m_NoHitsFound(false),
m_NumSequences(0),
m_NumBases(0)
{
_ASSERT( !m_Queries->Empty() );
x_FillScoreMatrix(m_Options.GetMatrixName());
vector<CBlastFormatUtil::SDbInfo> dbinformation;
if ( !m_DbName.empty() ){
CBlastFormatUtil::GetBlastDbInfo(dbinformation, m_DbName, db_is_aa,
dbfilt_algorithm, is_remote);
ITERATE(vector<CBlastFormatUtil::SDbInfo>, i, dbinformation) {
m_NumSequences += i->number_seqs;
}
ITERATE(vector<CBlastFormatUtil::SDbInfo>, i, dbinformation) {
m_NumBases += i->total_length;
}
}
void
CCmdLineBlastXML2ReportData::x_InitCommon(
const CSearchResults & results,
CConstRef<CBlastOptions> opts)
{
if(opts.Empty()) {
NCBI_THROW(CException, eUnknown, "blastxml2: Empty blast options");
}
if(m_Scope.Empty()) {
NCBI_THROW(CException, eUnknown, "blastxml2: Empty scope");
}
x_FillScoreMatrix(m_Options->GetMatrixName());
string resolved = SeqDB_ResolveDbPath("taxdb.bti");
if(!resolved.empty()) {
m_TaxDBFound = true;
}
m_isIterative = opts->IsIterativeSearch();
}
