void CRemoteBlastDbAdapter::x_FetchData(int oid, int begin, int end)
{
CCachedSeqDataForRemote& cached_seqdata = m_Cache[oid];
_ASSERT( !cached_seqdata.HasSequenceData(begin, end) );
_ASSERT( cached_seqdata.GetLength() != 0 );
_ASSERT( !cached_seqdata.GetIdList().empty() );
_ASSERT( cached_seqdata.IsValid() );
const char seqtype = (GetSequenceType() == CSeqDB::eProtein) ? 'p' : 'n';
CRef<CSeq_interval> seq_int
(new CSeq_interval(*cached_seqdata.GetIdList().front(), begin, end));
CBlastServices::TSeqIntervalVector seqids(1, seq_int);
CBlastServices::TSeqIdVector ids;
CBlastServices::TSeqDataVector seq_data;
string errors, warnings;
const bool kVerbose = (getenv("VERBOSE") ? true : false);
CBlastServices::GetSequenceParts(seqids, m_DbName, seqtype, ids, seq_data,
errors, warnings, kVerbose);
if (seq_data.empty() || !errors.empty() || !warnings.empty() ||
ids.empty() ) {
RemoteBlastDbLoader_ErrorHandler(errors, warnings);
}
_ASSERT(ids.size() == seq_data.size());
cached_seqdata.GetSeqDataChunk(begin, end) = seq_data.front();
_ASSERT(cached_seqdata.HasSequenceData(begin, end));
}
void CRemoteBlastDbAdapter::x_FetchDataByBatch(const vector<int>& oids,
const vector<TSeqRange>& ranges)
{
const char seqtype = (GetSequenceType() == CSeqDB::eProtein) ? 'p' : 'n';
if (oids.empty()) {
return;
}
CBlastServices::TSeqIntervalVector seqids;
seqids.reserve(oids.size());
for (vector<int>::size_type i = 0; i < oids.size(); i++) {
CCachedSeqDataForRemote& cached_seqdata = m_Cache[oids[i]];
_ASSERT( !cached_seqdata.HasSequenceData(ranges[i].GetFrom(),
ranges[i].GetToOpen()) );
_ASSERT( cached_seqdata.GetLength() != 0 );
_ASSERT( !cached_seqdata.GetIdList().empty() );
_ASSERT( cached_seqdata.IsValid() );
CRef<CSeq_interval> seq_int
(new CSeq_interval(*cached_seqdata.GetIdList().front(),
ranges[i].GetFrom(), ranges[i].GetToOpen()));
seqids.push_back(seq_int);
}
CBlastServices::TSeqIdVector ids;
CBlastServices::TSeqDataVector seq_data;
string errors, warnings;
const bool kVerbose = (getenv("VERBOSE") ? true : false);
CBlastServices::GetSequenceParts(seqids, m_DbName, seqtype, ids, seq_data,
errors, warnings, kVerbose);
if (seq_data.empty() || !errors.empty() || !warnings.empty() ||
ids.empty() ) {
RemoteBlastDbLoader_ErrorHandler(errors, warnings);
}
_ASSERT(seqids.size() == ids.size());
_ASSERT(ids.size() == seq_data.size());
for (vector<int>::size_type i = 0; i < oids.size(); i++) {
CCachedSeqDataForRemote& cached_seqdata = m_Cache[oids[i]];
cached_seqdata.GetSeqDataChunk(ranges[i].GetFrom(),
ranges[i].GetToOpen()) = seq_data[i];
_ASSERT(cached_seqdata.HasSequenceData(ranges[i].GetFrom(),
ranges[i].GetToOpen()));
}
}
// very specific "set_diff" for integers
SEXP set_diff(SEXP x, int n) {
SEXP ans, xmatch;
int i, j = 0, *buf;
if (TYPEOF(x) != INTSXP) error("'x' must be an integer");
if (n <= 0) error("'n' must be a positive integer");
xmatch = match(x, seq_int(n, 1), 0); // took a while to realise: matches vec against x - thanks to comment from Matthew in assign.c!
buf = (int *) R_alloc(n, sizeof(int));
for (i=0; i<n; i++) {
if (INTEGER(xmatch)[i] == 0) {
buf[j++] = i+1;
}
}
n = j;
PROTECT(ans = allocVector(INTSXP, n));
memcpy(INTEGER(ans), buf, sizeof(int) * n); // sizeof is of type size_t - no integer overflow issues
UNPROTECT(1);
return(ans);
}
