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first pass at block reads

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This commit is contained in:
Greg Landrum
2016-01-19 01:24:32 -05:00
parent 6e6c200bd3
commit 55c96db67e
1 changed files with 20 additions and 13 deletions
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33
Code/DataStructs/FPBReader.cpp
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@@ -161,13 +161,14 @@ void extractArena(FPBReader_impl *dp_impl, boost::uint64_t sz,
// enough to hold the result!), otherwise
// we update it to a pointer to the memory dp_impl owns.
void extractBytes(const FPBReader_impl *dp_impl, unsigned int which,
boost::uint8_t *&fpData) {
boost::uint8_t *&fpData, unsigned int nToRead = 1) {
PRECONDITION(dp_impl, "bad reader pointer");
PRECONDITION((dp_impl->df_lazy || dp_impl->dp_fpData), "bad fpdata pointer");
PRECONDITION(!dp_impl->df_lazy || dp_impl->istrm, "no stream in lazy mode");
PRECONDITION(!dp_impl->df_lazy || fpData, "no fpData in lazy mode");
PRECONDITION(nToRead > 0, "bad nToRead");
if (which >= dp_impl->len) {
if (which + nToRead > dp_impl->len) {
throw ValueErrorException("bad index");
}
boost::uint64_t offset = which * dp_impl->numBytesStoredPerFingerprint;
@@ -177,7 +178,7 @@ void extractBytes(const FPBReader_impl *dp_impl, unsigned int which,
dp_impl->istrm->seekg(dp_impl->fpDataOffset +
static_cast<std::streampos>(offset));
dp_impl->istrm->read(reinterpret_cast<char *>(fpData),
dp_impl->numBytesStoredPerFingerprint);
nToRead * dp_impl->numBytesStoredPerFingerprint);
}
};
@@ -416,10 +417,11 @@ std::string extractId(const FPBReader_impl *dp_impl, unsigned int which) {
void tanimotoNeighbors(const FPBReader_impl *dp_impl, const boost::uint8_t *bv,
double threshold,
std::vector<std::pair<double, unsigned int> > &res,
bool usePopcountScreen) {
bool usePopcountScreen, unsigned int readCache = 1000) {
PRECONDITION(dp_impl, "bad reader pointer");
PRECONDITION(bv, "bad bv");
RANGE_CHECK(-1e-6, threshold, 1.0 + 1e-6);
PRECONDITION(readCache > 0, "bad cache size");
res.clear();
boost::uint64_t probeCount =
CalcBitmapPopcount(bv, dp_impl->numBytesStoredPerFingerprint);
@@ -446,16 +448,21 @@ void tanimotoNeighbors(const FPBReader_impl *dp_impl, const boost::uint8_t *bv,
}
boost::uint8_t *dbv;
if (dp_impl->df_lazy) {
dbv = new boost::uint8_t[dp_impl->numBytesStoredPerFingerprint];
dbv = new boost::uint8_t[dp_impl->numBytesStoredPerFingerprint * readCache];
}
for (boost::uint64_t i = startScan; i < endScan; ++i) {
extractBytes(dp_impl, i, dbv);
double tani =
CalcBitmapTanimoto(dbv, bv, dp_impl->numBytesStoredPerFingerprint);
// std::cerr << " i:" << i << " " << tani << " ? " << threshold <<
// std::endl;
if (tani >= threshold) {
res.push_back(std::make_pair(tani, i));
for (boost::uint64_t i = startScan; i < endScan; i += readCache) {
unsigned int toRead = readCache;
if (i + toRead >= endScan) {
toRead = endScan - i;
}
extractBytes(dp_impl, i, dbv, toRead);
for (unsigned int j = 0; j < toRead; ++j) {
double tani =
CalcBitmapTanimoto(dbv + j * dp_impl->numBytesStoredPerFingerprint,
bv, dp_impl->numBytesStoredPerFingerprint);
if (tani >= threshold) {
res.push_back(std::make_pair(tani, i + j));
}
}
}
if (dp_impl->df_lazy) delete[] dbv;