virtual void read(const string& filename, const string& head, MSData& result, int runIndex = 0) const
{
if (runIndex != 0)
throw ReaderFail("[Reader_MGF::read] multiple runs not supported");
shared_ptr<istream> is(new pwiz::util::random_access_compressed_ifstream(filename.c_str()));
if (!is.get() || !*is)
throw runtime_error(("[Reader_MGF::read] Unable to open file " + filename));
Serializer_MGF serializer;
serializer.read(is, result);
fillInCommonMetadata(filename, result);
result.fileDescription.sourceFilePtrs.back()->set(MS_multiple_peak_list_nativeID_format);
result.fileDescription.sourceFilePtrs.back()->set(MS_Mascot_MGF_file);
return;
}
void testModeMetaDataAndBinaryData()
{
// initialize list
MSData msd;
shared_ptr<SpectrumListSimple> sl(new SpectrumListSimple);
sl->spectra.push_back(makeSpectrumPtr(0, "S1"));
sl->spectra.push_back(makeSpectrumPtr(1, "S2"));
sl->spectra.push_back(makeSpectrumPtr(2, "S3"));
sl->spectra.push_back(makeSpectrumPtr(3, "S4"));
msd.run.spectrumListPtr = sl;
// SpectrumListSimple returns the same shared_ptrs regardless of caching;
// serializing to MGF and back will produce different shared_ptrs
boost::shared_ptr<stringstream> ss(new stringstream);
Serializer_MGF serializer;
serializer.write(*ss, msd, 0);
serializer.read(ss, msd);
// access a series of spectra and make sure the cache behaves appropriately:
// in metadata-and-binary-data mode, entries in the cache should:
// - always have metadata
// - always have binary data
SpectrumPtr s;
SpectrumListCache slc(msd.run.spectrumListPtr, MemoryMRUCacheMode_MetaDataAndBinaryData, 2);
SpectrumListCache::CacheType& cache = slc.spectrumCache();
unit_assert(cache.empty());
unit_assert_operator_equal(2, cache.max_size());
// metadata-only access should not affect the cache
s = slc.spectrum(0, false);
if (os_) *os_ << cache << endl;
unit_assert(cache.empty());
unit_assert_operator_equal(0, cache.size());
s = slc.spectrum(1, true);
// pointers should be equal
unit_assert_operator_equal(slc.spectrum(1, true), s);
if (os_) *os_ << cache << endl;
unit_assert_operator_equal(1, cache.size());
unit_assert_operator_equal(1, cache.mru().spectrum->index);
unit_assert(spectrumHasMetadata(*cache.mru().spectrum));
unit_assert(spectrumHasBinaryData(*cache.mru().spectrum));
s = slc.spectrum(2, false);
if (os_) *os_ << cache << endl;
unit_assert_operator_equal(1, cache.size());
unit_assert_operator_equal(1, cache.mru().spectrum->index);
unit_assert(spectrumHasMetadata(*cache.mru().spectrum));
unit_assert(spectrumHasBinaryData(*cache.mru().spectrum));
s = slc.spectrum(3, true);
// pointers should be equal
unit_assert_operator_equal(slc.spectrum(3, true), s);
if (os_) *os_ << cache << endl;
unit_assert_operator_equal(2, cache.size());
unit_assert_operator_equal(3, cache.mru().spectrum->index);
unit_assert(spectrumHasMetadata(*cache.mru().spectrum));
unit_assert(spectrumHasBinaryData(*cache.mru().spectrum));
unit_assert_operator_equal(1, cache.lru().spectrum->index);
unit_assert(spectrumHasMetadata(*cache.lru().spectrum));
unit_assert(spectrumHasBinaryData(*cache.lru().spectrum));
s = slc.spectrum(2, true);
if (os_) *os_ << cache << endl;
unit_assert_operator_equal(2, cache.size());
unit_assert_operator_equal(2, cache.mru().spectrum->index);
unit_assert(spectrumHasMetadata(*cache.mru().spectrum));
unit_assert(spectrumHasBinaryData(*cache.mru().spectrum));
unit_assert_operator_equal(3, cache.lru().spectrum->index);
unit_assert(spectrumHasMetadata(*cache.lru().spectrum));
unit_assert(spectrumHasBinaryData(*cache.lru().spectrum));
}