35 #ifndef OPENMS_FORMAT_MASCOTGENERICFILE_H 
   36 #define OPENMS_FORMAT_MASCOTGENERICFILE_H 
   77     void store(
const String& filename, 
const PeakMap& experiment);
 
   80     void store(std::ostream& os, 
const String& filename, 
const PeakMap& experiment);
 
   89     template <
typename MapType>
 
   99       std::ifstream is(filename.c_str());
 
  101       UInt spectrum_number(0);
 
  106         std::vector<std::pair<String, String> > spec;
 
  108         double pre_mz(0), pre_int(0), rt(-1);
 
  112         typename MapType::SpectrumType spectrum;
 
  113         spectrum.setMSLevel(2);
 
  114         spectrum.getPrecursors().resize(1);
 
  116         UInt thread_spectrum_number(-1);
 
  123             has_next = getNextSpectrum_(is, spec, charge, pre_mz, pre_int, rt, title, line_number);
 
  125             thread_spectrum_number = spectrum_number;
 
  127           if (!has_next) 
break;
 
  128           spectrum.resize(spec.size());
 
  130           for (
Size i = 0; i < spec.size(); ++i)
 
  132             p.setPosition(spec[i].first.toDouble()); 
 
  133             p.setIntensity(spec[i].second.toDouble());
 
  136           spectrum.getPrecursors()[0].setMZ(pre_mz);
 
  137           spectrum.getPrecursors()[0].setIntensity(pre_int);
 
  138           spectrum.getPrecursors()[0].setCharge(charge);
 
  142             spectrum.setMetaValue(
"TITLE", title);
 
  146             spectrum.removeMetaValue(
"TITLE");
 
  149           spectrum.setNativeID(
String(
"index=") + (thread_spectrum_number));
 
  154             exp.addSpectrum(spectrum);
 
  160       exp.sortSpectra(
true);
 
  171     std::pair<String, String> getHTTPPeakListEnclosure(
const String& filename) 
const;
 
  176     void writeParameterHeader_(
const String& name, std::ostream& os);
 
  179     void writeHeader_(std::ostream& os);
 
  182     void writeSpectrum_(std::ostream& os, 
const PeakSpectrum& spec, 
const String& filename);
 
  185     void writeMSExperiment_(std::ostream& os, 
const String& filename, 
const PeakMap& experiment);
 
  188     bool getNextSpectrum_(std::istream& is, std::vector<std::pair<String, String> >& spectrum, 
UInt& charge, 
double& precursor_mz, 
double& precursor_int, 
double& rt, 
String& title, 
Size& line_number);
 
  193 #endif // OPENMS_FORMAT_MASCOTGENERICFILE_H 
A more convenient string class. 
Definition: String.h:56
Peak2D PeakType
Definition: MassTrace.h:49
File not found exception. 
Definition: Exception.h:524
Mascot input file adapter. 
Definition: MascotGenericFile.h:64
static bool exists(const String &file)
Method used to test if a file exists. 
size_t Size
Size type e.g. used as variable which can hold result of size() 
Definition: Types.h:144
Base class for all classes that want to report their progess. 
Definition: ProgressLogger.h:56
A base class for all classes handling default parameters. 
Definition: DefaultParamHandler.h:90
void load(const String &filename, MapType &exp)
loads a Mascot Generic File into a PeakMap 
Definition: MascotGenericFile.h:90