virtual void read(const std::string& filename, const std::string& head, MSData& result, int runIndex = 0) const
{
if (runIndex != 0)
throw ReaderFail("[Reader_mzML::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_mzML::read] Unable to open file " + filename).c_str());
switch (type(*is))
{
case Type_mzML:
{
Serializer_mzML::Config config;
config.indexed = false;
Serializer_mzML serializer(config);
serializer.read(is, result);
break;
}
case Type_mzML_Indexed:
{
Serializer_mzML serializer;
serializer.read(is, result);
break;
}
case Type_Unknown:
default:
{
throw runtime_error("[MSDataFile::Reader_mzML] This isn't happening.");
}
}
fillInCommonMetadata(filename, result);
}
void testHasBinaryData(SpectrumListPtr sl)
{
if (os_) *os_ << "testHasBinaryData:\n";
MSData msd;
examples::initializeTiny(msd);
shared_ptr<stringstream> ss(new stringstream);
Serializer_mzML serializer;
serializer.write(*ss, msd);
MSData msd2;
serializer.read(ss, msd2);
sl = msd2.run.spectrumListPtr;
{
SpectrumList_Filter filter(sl, HasBinaryDataPredicate(DetailLevel_FullMetadata));
unit_assert(filter.empty());
}
{
SpectrumList_Filter filter(sl, HasBinaryDataPredicate(DetailLevel_FullData));
if (os_)
{
printSpectrumList(filter, *os_);
*os_ << endl;
}
unit_assert_operator_equal(4, filter.size());
}
}
