24 #ifndef DATASTRUCTURES_MZ5_HPP_
25 #define DATASTRUCTURES_MZ5_HPP_
27 #include "../../common/cv.hpp"
28 #include "../../common/ParamTypes.hpp"
29 #include "../MSData.hpp"
46 class ReferenceWrite_mz5;
47 class ReferenceRead_mz5;
48 class Configuration_mz5;
111 const std::string&
id,
const std::string&
version);
112 ContVocabMZ5(
const char* uri,
const char* fullname,
const char*
id,
113 const char* version);
117 void init(
const std::string&,
const std::string&,
const std::string&,
121 static void convert(std::vector<ContVocabMZ5>&,
const std::vector<
166 const unsigned long urefid);
188 void init(
const char*
value,
const unsigned long& cvrefid,
189 const unsigned long& urefid);
243 RefListMZ5(
const std::vector<pwiz::data::ParamGroupPtr>&,
245 RefListMZ5(
const std::vector<pwiz::msdata::SourceFilePtr>&,
250 void fill(std::vector<pwiz::msdata::ParamGroupPtr>&,
252 void fill(std::vector<pwiz::msdata::SourceFilePtr>&,
254 static H5::VarLenType
getType();
275 const std::vector<pwiz::msdata::UserParam>& user,
276 const std::vector<pwiz::msdata::ParamGroupPtr>& param,
281 void init(
const unsigned long cvstart,
const unsigned long cvend,
282 const unsigned long usrstart,
const unsigned long usrend,
283 const unsigned long refstart,
const unsigned long refend);
287 std::vector<pwiz::msdata::UserParam>& user, std::vector<
291 static void convert(std::vector<ParamListMZ5>&,
const std::vector<
293 static void convert(std::vector<ParamListMZ5>&,
const std::vector<
295 static void convert(std::vector<ParamListMZ5>&,
const std::vector<
336 static void convert(std::vector<SourceFileMZ5>&,
const std::vector<
338 static void read(
const std::vector<pwiz::msdata::SourceFilePtr>&,
358 static void convert(std::vector<SampleMZ5>&,
const std::vector<
360 static void read(
const std::vector<pwiz::msdata::SamplePtr>&,
380 static void convert(std::vector<SoftwareMZ5>&,
const std::vector<
382 static void read(
const std::vector<pwiz::msdata::SoftwarePtr>&,
412 void fill(std::vector<pwiz::msdata::Product>&,
414 void fill(std::vector<pwiz::msdata::ScanWindow>&,
416 void fill(std::vector<pwiz::msdata::SelectedIon>&,
418 static H5::VarLenType
getType();
441 static void convert(std::vector<ScanSettingMZ5>&,
const std::vector<
443 static void read(
const std::vector<pwiz::msdata::ScanSettingsPtr>&,
484 static H5::VarLenType
getType();
525 const RefMZ5& refScanSetting,
const RefMZ5& refSoftware,
531 const std::vector<pwiz::msdata::InstrumentConfigurationPtr>&,
550 const unsigned long order);
570 void fill(std::vector<pwiz::msdata::ProcessingMethod>&,
572 static H5::VarLenType
getType();
592 static void convert(std::vector<DataProcessingMZ5>&,
const std::vector<
594 static void read(
const std::vector<pwiz::msdata::DataProcessingPtr>&,
638 void fill(std::vector<pwiz::msdata::Precursor>&,
640 static H5::VarLenType
getType();
662 const RefMZ5& refDataProcessing,
const unsigned long index,
686 const RefMZ5& refInstrument,
const RefMZ5& refSourceFile,
702 ScanListMZ5(
const std::vector<pwiz::msdata::Scan>&,
708 static H5::VarLenType
getType();
750 const RefMZ5& refDataProcessing,
const RefMZ5& refSourceFile,
751 const unsigned long index,
const char*
id,
const char*
spotID);
781 const RefMZ5& refChromatogramDP,
782 const RefMZ5& refDefaultInstrument,
const RefMZ5& refSourceFile,
783 const RefMZ5& refSample,
const char*
id,
811 static void convert(std::vector<BinaryDataMZ5>& l,
814 static void convert(std::vector<BinaryDataMZ5>&,