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;
}
virtual void read(const string& filename, const string& head, MSData& result, int runIndex = 0) const
{
if (runIndex != 0)
throw ReaderFail("[Reader_MSn::read] multiple runs not supported");
MSn_Type filetype = MSn_Type_UNKNOWN;
if( (bal::to_lower_copy(bfs::extension(filename)) == ".ms2" )){
filetype = MSn_Type_MS2;
}else if( (bal::to_lower_copy(bfs::extension(filename)) == ".cms2" )){
filetype = MSn_Type_CMS2;
}else if( (bal::to_lower_copy(bfs::extension(filename)) == ".bms2" )){
filetype = MSn_Type_BMS2;
}
shared_ptr<istream> is(new pwiz::util::random_access_compressed_ifstream(filename.c_str()));
if (!is.get() || !*is)
throw runtime_error(("[Reader_MSn::read] Unable to open file " + filename));
Serializer_MSn serializer(filetype);
serializer.read(is, result);
fillInCommonMetadata(filename, result);
result.fileDescription.sourceFilePtrs.back()->set(MS_scan_number_only_nativeID_format);
result.fileDescription.sourceFilePtrs.back()->set(MS_MS2_file);
return;
}
virtual void read(const std::string& filename, const std::string& head, MSData& result, int runsIndex = 0) const
{
if (runsIndex != 0)
throw ReaderFail("[Reader_mzXML::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_mzXML::read] Unable to open file " + filename).c_str());
try
{
// assume there is a scan index
Serializer_mzXML serializer;
serializer.read(is, result);
fillInCommonMetadata(filename, result);
result.fileDescription.sourceFilePtrs.back()->set(MS_scan_number_only_nativeID_format);
result.fileDescription.sourceFilePtrs.back()->set(MS_ISB_mzXML_file);
return;
}
catch (SpectrumList_mzXML::index_not_found&)
{}
// error looking for index -- try again, but generate index
is->seekg(0);
Serializer_mzXML::Config config;
config.indexed = false;
Serializer_mzXML serializer(config);
serializer.read(is, result);
fillInCommonMetadata(filename, result);
result.fileDescription.sourceFilePtrs.back()->set(MS_scan_number_only_nativeID_format);
result.fileDescription.sourceFilePtrs.back()->set(MS_ISB_mzXML_file);
return;
}
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);
}
virtual void read(const std::string& filename, const std::string& head, TraData& result, int documentIndex = 0) const
{
if (documentIndex != 0)
throw ReaderFail("[Reader_traML::read] multiple documents not supported");
shared_ptr<istream> is(new pwiz::util::random_access_compressed_ifstream(filename.c_str()));
if (!is.get() || !*is)
throw runtime_error(("[Reader_traML::read] Unable to open file " + filename).c_str());
switch (type(*is))
{
case Type_traML:
{
Serializer_traML serializer;
serializer.read(is, result);
break;
}
case Type_Unknown:
default:
{
throw runtime_error("[Reader_traML::read] This isn't happening.");
}
}
fillInCommonMetadata(filename, result);
}
PWIZ_API_DECL void Reader_Agilent::read(const string& filename, const string& head, MSData& result, int sampleIndex /* = 0 */, const Config& config) const
{
throw ReaderFail("[Reader_Agilent::read()] Agilent MassHunter reader not implemented: "
#ifdef _MSC_VER // should be possible, apparently somebody decided to skip it
"support was explicitly disabled when program was built"
#elif defined(WIN32) // wrong compiler
"program was built without COM support and cannot access Agilent DLLs - try building with MSVC instead of GCC"
#else // wrong platform
"Agilent DLLs only work on Windows"
#endif
);
}
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;
}
PWIZ_API_DECL
void Reader_ABI_T2D::read(const string& filename,
const string& head,
MSData& result,
int runIndex,
const Config& config) const
{
if (runIndex != 0)
throw ReaderFail("[Reader_ABI_T2D::read] multiple runs not supported");
DataPtr t2d_data = Data::create(filename);
fillInSources(filename, result, t2d_data);
SpectrumList_ABI_T2D* sl = new SpectrumList_ABI_T2D(result, t2d_data);
result.run.spectrumListPtr = SpectrumListPtr(sl);
fillInMetadata(filename, result, t2d_data);
}
