virtual void read(const string& filename, const string& head, MSData& result, int runIndex = 0) const
{
if (runIndex != 0)
throw ReaderFail("[Reader_BTDX::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_BTDX::read] Unable to open file " + filename));
result.fileDescription.fileContent.set(MS_MSn_spectrum);
result.fileDescription.fileContent.set(MS_centroid_spectrum);
SourceFilePtr sourceFile(new SourceFile);
sourceFile->id = "BTDX1";
bfs::path p(filename);
sourceFile->name = p.leaf();
string location = bfs::complete(p.branch_path()).string();
if (location.empty()) location = ".";
sourceFile->location = string("file:///") + location;
result.fileDescription.sourceFilePtrs.push_back(sourceFile);
result.id = result.run.id = bfs::basename(filename);
result.run.spectrumListPtr = SpectrumListPtr(SpectrumList_BTDX::create(is, result));
result.run.chromatogramListPtr = ChromatogramListPtr(new ChromatogramListSimple);
return;
}
PWIZ_API_DECL
void Reader_ABI::read(const string& filename,
const string& head,
MSData& result,
int runIndex,
const Config& config) const
{
try
{
runIndex++; // one-based index
WiffFilePtr wifffile = WiffFile::create(filename);
// Loading the experiments is an expensive operation, so cache them.
ExperimentsMap experimentsMap;
cacheExperiments(wifffile, experimentsMap, runIndex);
SpectrumList_ABI* sl = new SpectrumList_ABI(result, wifffile, experimentsMap, runIndex, config);
ChromatogramList_ABI* cl = new ChromatogramList_ABI(result, wifffile, experimentsMap, runIndex);
result.run.spectrumListPtr = SpectrumListPtr(sl);
result.run.chromatogramListPtr = ChromatogramListPtr(cl);
fillInMetadata(filename, result, wifffile, experimentsMap, runIndex);
}
catch (std::exception& e)
{
throw std::runtime_error(e.what());
}
catch (...)
{
throw runtime_error("[Reader_ABI::read()] unhandled exception");
}
}
PWIZ_API_DECL
ChromatogramListPtr ChromatogramList_mz5::create(boost::shared_ptr<ReferenceRead_mz5> readPtr,
boost::shared_ptr<Connection_mz5> connectionPtr,
const MSData& msd)
{
return ChromatogramListPtr(new ChromatogramList_mz5Impl(readPtr, connectionPtr, msd));
}
PWIZ_API_DECL
void Reader_ABI::read(const string& filename,
const string& head,
vector<MSDataPtr>& results,
const Config& config) const
{
try
{
WiffFilePtr wifffile = WiffFile::create(filename);
int sampleCount = wifffile->getSampleCount();
for (int i=1; i <= sampleCount; ++i)
{
try
{
MSDataPtr msDataPtr = MSDataPtr(new MSData);
MSData& result = *msDataPtr;
// Loading the experiments is an expensive operation, so cache them.
ExperimentsMap experimentsMap;
cacheExperiments(wifffile, experimentsMap, i);
SpectrumList_ABI* sl = new SpectrumList_ABI(result, wifffile, experimentsMap, i, config);
ChromatogramList_ABI* cl = new ChromatogramList_ABI(result, wifffile, experimentsMap, i);
result.run.spectrumListPtr = SpectrumListPtr(sl);
result.run.chromatogramListPtr = ChromatogramListPtr(cl);
fillInMetadata(filename, result, wifffile, experimentsMap, i);
results.push_back(msDataPtr);
}
catch (exception& e)
{
// TODO: make this a critical logged warning
cerr << "[Reader_ABI::read] Error opening run " << i << " in " << bfs::path(filename).leaf() << ":\n" << e.what() << endl;
}
}
}
catch (std::exception& e)
{
throw std::runtime_error(e.what());
}
catch (...)
{
throw runtime_error("[Reader_ABI::read()] unhandled exception");
}
}
