35 using boost::iostreams::stream_offset;
41 template <
typename object_type>
44 if (
os_) *
os_ <<
"testObject(): " <<
typeid(a).name() << endl;
51 if (
os_) *
os_ << oss.str() << endl;
56 istringstream iss(oss.str());
62 if (diff &&
os_) *
os_ <<
"diff:\n" << diff << endl;
67 template <
typename object_type>
70 if (
os_) *
os_ <<
"testObject(): " <<
typeid(a).name() << endl;
77 if (
os_) *
os_ << oss.str() << endl;
82 istringstream iss(oss.str());
88 if (diff &&
os_) *
os_ <<
"diff:\n" << diff << endl;
95 if (
os_) *
os_ <<
"testObject_SpectrumList(): " << endl;
103 if (
os_) *
os_ << oss.str() << endl;
108 istringstream iss(oss.str());
114 if (diff &&
os_) *
os_ <<
"diff:\n" << diff << endl;
123 if (
os_) *
os_ <<
"testObject_ChromatogramList(): " << endl;
130 if (
os_) *
os_ << oss.str() << endl;
135 istringstream iss(oss.str());
141 if (diff &&
os_) *
os_ <<
"diff:\n" << diff << endl;
191 template <
typename object_type>
195 a.userParams.push_back(
UserParam(
"goober",
"goo",
"peanuts"));
205 SourceFile a(
"id123",
"name456",
"location789");
234 Sample a(
"id123",
"name456");
304 a.
id =
"msdata processing";
404 a.
scans.push_back(a1);
405 a.
scans.push_back(a2);
414 if (
os_) *
os_ <<
"testBinaryDataArray():\n";
417 for (
int i=0; i<10; i++) a.
data.push_back(i);
425 if (
os_) *
os_ << oss.str() << endl;
430 istringstream iss(oss.str());
436 if (diff &&
os_) *
os_ <<
"diff:\n" << diff << endl;
445 config.
precision = BinaryDataEncoder::Precision_32;
446 config.
byteOrder = BinaryDataEncoder::ByteOrder_LittleEndian;
449 config.
precision = BinaryDataEncoder::Precision_64;
450 config.
byteOrder = BinaryDataEncoder::ByteOrder_LittleEndian;
460 <binaryDataArray encodedLength=\"160\" arrayLength=\"15\"> \ 461 <referenceableParamGroupRef ref=\"mz_params\"/> \ 462 <binary>AAAAAAAAAAAAAAAAAADwPwAAAAAAAABAAAAAAAAACEAAAAAAAAAQQAAAAAAAABRAAAAAAAAAGEAAAAAAAAAcQAAAAAAAACBAAAAAAAAAIkAAAAAAAAAkQAAAAAAAACZAAAAAAAAAKEAAAAAAAAAqQAAAAAAAACxA</binary> \ 472 pg->id =
"mz_params";
486 for (
size_t i=0; i<15; i++)
493 if (
os_) *
os_ <<
"testSpectrum():\n";
540 if (
os_) *
os_ << oss.str() << endl;
545 istringstream iss(oss.str());
552 if (diff &&
os_) *
os_ <<
"diff:\n" << diff << endl;
571 if (
os_) *
os_ <<
"testChromatogram():\n";
594 if (
os_) *
os_ << oss.str() << endl;
599 istringstream iss(oss.str());
606 if (diff &&
os_) *
os_ <<
"diff:\n" << diff << endl;
628 spectrum1->id =
"goober";
629 spectrum1->index = 0;
630 spectrum1->defaultArrayLength = 666;
631 spectrum1->userParams.push_back(
UserParam(
"description1"));
634 spectrum2->id =
"raisinet";
635 spectrum2->index = 1;
636 spectrum2->defaultArrayLength = 667;
637 spectrum2->userParams.push_back(
UserParam(
"description2"));
639 a.
spectra.push_back(spectrum1);
640 a.
spectra.push_back(spectrum2);
649 if (
os_) *
os_ <<
"testSpectrumListWithPositions()\n ";
654 spectrum1->id =
"goober";
655 spectrum1->index = 0;
656 spectrum1->defaultArrayLength = 666;
657 spectrum1->userParams.push_back(
UserParam(
"description1"));
660 spectrum2->id =
"raisinet";
661 spectrum2->index = 1;
662 spectrum2->defaultArrayLength = 667;
663 spectrum2->userParams.push_back(
UserParam(
"description2"));
665 a.
spectra.push_back(spectrum1);
666 a.
spectra.push_back(spectrum2);
670 vector<stream_offset> positions;
676 copy(positions.begin(), positions.end(), ostream_iterator<stream_offset>(*
os_,
" "));
677 *os_ << endl << oss.str() << endl;
697 const vector<size_t>&
indices()
const {
return indices_;}
715 const vector<size_t>&
indices()
const {
return indices_;}
724 if (
os_) *
os_ <<
"testSpectrumListWriteProgress()\n ";
728 for (
size_t i=0; i<11; i++)
733 spectrum->defaultArrayLength = 666;
750 *
os_ <<
"callback indices: ";
752 ostream_iterator<size_t>(*
os_,
" "));
776 *
os_ <<
"callback indices: ";
777 copy(cancelListener.
indices().begin(), cancelListener.
indices().end(),
778 ostream_iterator<size_t>(*
os_,
" "));
793 chromatogram1->id =
"goober";
794 chromatogram1->index = 0;
795 chromatogram1->defaultArrayLength = 666;
798 chromatogram2->id =
"raisinet";
799 chromatogram2->index = 1;
800 chromatogram2->defaultArrayLength = 667;
812 if (
os_) *
os_ <<
"testChromatogramListWithPositions()\n ";
817 chromatogram1->id =
"goober";
818 chromatogram1->index = 0;
819 chromatogram1->defaultArrayLength = 666;
822 chromatogram2->id =
"raisinet";
823 chromatogram2->index = 1;
824 chromatogram2->defaultArrayLength = 667;
831 vector<stream_offset> positions;
836 copy(positions.begin(), positions.end(), ostream_iterator<stream_offset>(*
os_,
" "));
837 *os_ << endl << oss.str() << endl;
849 if (
os_) *
os_ <<
"testRun():\n";
864 spectrum1->id =
"goober";
865 spectrum1->index = 0;
866 spectrum1->defaultArrayLength = 666;
867 spectrum1->userParams.push_back(
UserParam(
"description1"));
870 spectrum2->id =
"raisinet";
871 spectrum2->index = 1;
872 spectrum2->defaultArrayLength = 667;
873 spectrum2->userParams.push_back(
UserParam(
"description2"));
875 spectrumListSimple->spectra.push_back(spectrum1);
876 spectrumListSimple->spectra.push_back(spectrum2);
885 chromatogram1->id =
"goober";
886 chromatogram1->index = 0;
887 chromatogram1->defaultArrayLength = 666;
890 chromatogram2->id =
"raisinet";
891 chromatogram2->index = 1;
892 chromatogram2->defaultArrayLength = 667;
894 chromatogramListSimple->chromatograms.push_back(chromatogram1);
895 chromatogramListSimple->chromatograms.push_back(chromatogram2);
906 if (
os_) *
os_ << oss.str() << endl;
911 istringstream iss(oss.str());
917 if (diff &&
os_) *
os_ <<
"diff:\n" << diff << endl;
927 IO::read(iss, c, IO::ReadSpectrumList);
932 if (diff &&
os_) *
os_ <<
"diff:\n" << diff << endl;
953 cv.
URI =
"http://psidev.sourceforge.net/ms/xml/mzdata/psi-ms.2.0.2.obo";
955 cv.
fullName =
"Proteomics Standards Initiative Mass Spectrometry Ontology";
966 sfp->name =
"tiny1.RAW";
967 sfp->location =
"file://F:/data/Exp01";
969 sfp->cvParams.push_back(
CVParam(
MS_SHA_1,
"71be39fb2700ab2f3c8b2234b91274968b6899b1"));
979 "Higglesworth University, 12 Higglesworth Avenue, 12045, HI, USA"));
986 pg1->id =
"CommonMS1SpectrumParams";
991 pg2->id =
"CommonMS2SpectrumParams";
999 samplePtr->name =
"Sample1";
1005 instrumentConfigurationPtr->id =
"LCQ Deca";
1006 instrumentConfigurationPtr->cvParams.push_back(
MS_LCQ_Deca);
1013 softwareXcalibur->id =
"Xcalibur";
1015 softwareXcalibur->version =
"2.0.5";
1016 instrumentConfigurationPtr->softwarePtr = softwareXcalibur;
1023 softwareBioworks->id =
"Bioworks";
1025 softwareBioworks->version =
"3.3.1 sp1";
1028 software_pwiz->id =
"pwiz";
1030 software_pwiz->version =
"1.0";
1039 dpXcalibur->id =
"Xcalibur Processing";
1048 dpXcalibur->processingMethods.push_back(procXcal);
1051 dp_msconvert->id =
"pwiz conversion";
1054 proc_msconvert.
order = 2;
1058 dp_msconvert->processingMethods.push_back(proc_msconvert);
1064 as1->sourceFilePtrs.push_back(sfp_parameters);
1069 as1->targets.push_back(t1);
1070 as1->targets.push_back(t2);
1075 msd.
run.
id =
"Exp01";
1087 Spectrum& s19 = *spectrumList->spectra[0];
1111 s19_mz->dataProcessingPtr = dpXcalibur;
1113 s19_mz->data.resize(10);
1114 for (
int i=0; i<10; i++)
1115 s19_mz->data[i] = i;
1118 s19_intensity->dataProcessingPtr = dpXcalibur;
1120 s19_intensity->data.resize(10);
1121 for (
int i=0; i<10; i++)
1122 s19_intensity->data[i] = 10-i;
1127 Spectrum& s20 = *spectrumList->spectra[1];
1163 s20_mz->dataProcessingPtr = dpXcalibur;
1165 s20_mz->data.resize(10);
1166 for (
int i=0; i<10; i++)
1167 s20_mz->data[i] = i;
1170 s20_intensity->dataProcessingPtr = dpXcalibur;
1172 s20_intensity->data.resize(10);
1173 for (
int i=0; i<10; i++)
1174 s20_intensity->data[i] = 10-i;
1186 Chromatogram& tic = *chromatogramList->chromatograms[0];
1193 tic_time->dataProcessingPtr = dp_msconvert;
1195 tic_time->data.resize(10);
1196 for (
int i=0; i<10; i++)
1197 tic_time->data[i] = i;
1200 tic_intensity->dataProcessingPtr = dp_msconvert;
1202 tic_intensity->data.resize(10);
1203 for (
int i=0; i<10; i++)
1204 tic_intensity->data[i] = 10-i;
1213 if (
os_) *
os_ <<
"testMSData():\n";
1223 if (
os_) *
os_ << oss.str() << endl;
1228 istringstream iss(oss.str());
1234 if (diff &&
os_) *
os_ <<
"diff:\n" << diff << endl;
1244 IO::read(iss, c, IO::ReadSpectrumList);
1249 if (diff &&
os_) *
os_ <<
"diff:\n" << diff << endl;
1267 testNamedParamContainer<FileContent>();
1269 testNamedParamContainer<Contact>();
1278 testNamedParamContainer<Target>();
1280 testNamedParamContainer<IsolationWindow>();
1281 testNamedParamContainer<SelectedIon>();
1282 testNamedParamContainer<Activation>();
1285 testNamedParamContainer<ScanWindow>();
1308 if (argc>1 && !strcmp(argv[1],
"-v"))
os_ = &cout;
1312 catch (exception& e)
MS_contact_address
contact address: Postal address of the contact person or organization.
std::string id
the short label to be used as a reference tag with which to refer to this particular Controlled Vocab...
void testObject(const object_type &a)
IsolationWindow isolationWindow
this element captures the isolation (or 'selection') window configured to isolate one or more precurs...
MS_deisotoping
deisotoping: The removal of isotope peaks to represent the fragment ion as one data point and is comm...
MS_Bioworks
Bioworks: Thermo Finnigan software for data analysis of peptides and proteins.
MS_charge_state
charge state: The charge state of the ion, single or multiple and positive or negatively charged...
std::vector< Product > products
list and descriptions of product ion information
This summarizes the different types of spectra that can be expected in the file. This is expected to ...
void testProcessingMethod()
MS_MSn_spectrum
MSn spectrum: MSn refers to multi-stage MS2 experiments designed to record product ion spectra where ...
Interface for accessing chromatograms, which may be stored in memory or backed by a data file (RAW...
std::string id
a unique identifier for this chromatogram. It should be expected that external files may use this ide...
PWIZ_API_DECL const CV & cv(const std::string &prefix)
returns a CV object for the specified namespace (prefix); currently supported namespaces are: MS UO ...
The XMLWriter class provides simple, tag-level XML syntax writing.
std::vector< SourceFilePtr > sourceFilePtrs
list and descriptions of the source files this mzML document was generated or derived from...
MS_total_ion_current_chromatogram
total ion current chromatogram: Chromatogram obtained by plotting the total ion current detected in e...
const vector< size_t > & indices() const
Description of the way in which a particular software was used.
ComponentList componentList
list with the different components used in the mass spectrometer. At least one source, one mass analyzer and one detector need to be specified.
ScanList scanList
list of scans
MS_isolation_window_lower_offset
isolation window lower offset: The extent of the isolation window in m/z below the isolation window t...
boost::shared_ptr< Software > SoftwarePtr
MS_base_peak_intensity
base peak intensity: The intensity of the greatest peak in the mass spectrum.
boost::shared_ptr< ParamGroup > ParamGroupPtr
Description of the source file, including location and type.
void addListener(const IterationListenerPtr &listener, size_t iterationPeriod)
Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile...
std::vector< InstrumentConfigurationPtr > instrumentConfigurationPtrs
list and descriptions of instrument configurations.
The method of precursor ion selection and activation.
ChromatogramListPtr chromatogramListPtr
all chromatograms for this run.
std::vector< BinaryDataArrayPtr > binaryDataArrayPtrs
list of binary data arrays.
MS_highest_observed_m_z
highest observed m/z: Highest m/z value observed in the m/z array.
A component of an instrument corresponding to a source (i.e. ion source), an analyzer (i...
SoftwarePtr softwarePtr
reference to a previously defined software element.
std::vector< ChromatogramPtr > chromatograms
boost::shared_ptr< Spectrum > SpectrumPtr
MS_total_ion_current
total ion current: The sum of all the separate ion currents carried by the ions of different m/z cont...
MS_contact_URL
contact URL: Uniform Resource Locator related to the contact person or organization.
void testChromatogramListWithPositions()
boost::shared_ptr< ScanSettings > ScanSettingsPtr
std::string value
the value for the parameter, where appropriate.
void testChromatogramList()
void testSpectrumListWithPositions()
MS_scan_start_time
scan start time: The time that an analyzer started a scan, relative to the start of the MS run...
Calculate diffs of objects in a ProteoWizard data model hierarchy.
std::vector< ProcessingMethod > processingMethods
description of the default peak processing method(s). This element describes the base method used in ...
std::vector< Precursor > precursors
list and descriptions of precursors to the spectrum currently being described.
vector< size_t > indices_
MS_positive_scan
positive scan: Polarity of the scan is positive.
IsolationWindow isolationWindow
this element captures the isolation (or 'selection') window configured to isolate one or more precurs...
MS_nanoelectrospray
nanoelectrospray: Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is sy...
boost::shared_ptr< DataProcessing > DataProcessingPtr
SoftwarePtr softwarePtr
this attribute MUST reference the 'id' of the appropriate SoftwareType.
MS_Thermo_RAW_format
Thermo RAW format: Thermo Scientific RAW file format.
MS_electron_multiplier
electron multiplier: A device to amplify the current of a beam or packet of charged particles or phot...
MS_scan_window_upper_limit
scan window upper limit: The lower m/z bound of a mass spectrometer scan window.
Information about an ontology or CV source and a short 'lookup' tag to refer to.
MS_collision_induced_dissociation
collision-induced dissociation: The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended.
size_t defaultArrayLength
default length of binary data arrays contained in this element.
void testBinaryDataArray(const BinaryDataEncoder::Config &config)
void initializeTestData(MSData &msd)
void testFileDescription()
size_t index
the zero-based, consecutive index of the chromatogram in the ChromatogramList.
FileDescription fileDescription
information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is sto...
FileContent fileContent
this summarizes the different types of spectra that can be expected in the file. This is expected to ...
MS_LCQ_Deca
LCQ Deca: ThermoFinnigan LCQ Deca.
std::vector< ScanSettingsPtr > scanSettingsPtrs
list with the descriptions of the acquisition settings applied prior to the start of data acquisition...
MS_ms_level
ms level: Stages of ms achieved in a multi stage mass spectrometry experiment.
float lexical_cast(const std::string &str)
MS_64_bit_float
64-bit float: 64-bit precision little-endian floating point conforming to IEEE-754.
Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW...
MS_contact_email
contact email: Email address of the contact person or organization.
vector< size_t > indices_
UO_second
second: A time unit which is equal to the duration of 9 192 631 770 periods of the radiation correspo...
std::string id
an optional id for the mzML document. It is recommended to use LSIDs when possible.
void testNamedParamContainer()
MS_selected_ion_m_z
selected ion m/z: Mass-to-charge ratio of an selected ion.
std::string id
a unique identifier for this run.
MS_filter_string
filter string: A string unique to Thermo instrument describing instrument settings for the scan...
MS_no_compression
no compression: No Compression.
DataProcessingPtr dataProcessingPtr
this optional attribute may reference the 'id' attribute of the appropriate dataProcessing.
MS_intensity_array
intensity array: A data array of intensity values.
boost::shared_ptr< IterationListener > IterationListenerPtr
void diff(const string &filename1, const string &filename2)
MS_instrument_serial_number
instrument serial number: Serial Number of the instrument.
void testObject_ChromatogramList(const ChromatogramList &a)
std::string fullName
the usual name for the resource (e.g. The PSI-MS Controlled Vocabulary).
MS_SHA_1
SHA-1: SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Secu...
SourceFilePtr defaultSourceFilePtr
default source file reference
MS_m_z_array
m/z array: A data array of m/z values.
Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead.
std::string id
a unique identifier for this spectrum. It should be expected that external files may use this identif...
const char * bdaWithExternalMetadata
MS_collision_energy
collision energy: Energy for an ion experiencing collision with a stationary gas particle resulting i...
size_t defaultArrayLength
default length of binary data arrays contained in this element.
boost::iostreams::stream_offset sourceFilePosition
for file-based MSData implementations, this attribute may refer to the spectrum's position in the fil...
Description of the default peak processing method. This element describes the base method used in the...
std::vector< UserParam > userParams
a collection of uncontrolled user terms
Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is sto...
std::string spectrumID
reference to the id attribute of the spectrum from which the precursor was selected.
int order
this attributes allows a series of consecutive steps to be placed in the correct order.
A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument...
MS_time_array
time array: A data array of relative time offset values from a reference time.
std::string type
the datatype of the parameter, where appropriate (e.g.: xsd:float).
Simple writeable in-memory implementation of ChromatogramList.
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
MS_base_peak_m_z
base peak m/z: M/z value of the signal of highest intensity in the mass spectrum. ...
Run run
a run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument...
std::string accession
an optional accession number for the mzML document.
std::vector< Target > targets
target list (or 'inclusion list') configured prior to the run.
MS_ionization_type
ionization type: The method by which gas phase ions are generated from the sample.
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)
std::string id
a unique identifier for this data processing that is unique across all DataProcessingTypes.
Activation activation
the type and energy level used for activation.
std::string id
a unique identifier for this acquisition setting.
std::string URI
the URI for the resource.
std::vector< ScanWindow > scanWindows
container for a list of select windows.
virtual Status update(const UpdateMessage &updateMessage)
MS_scan_window_lower_limit
scan window lower limit: The upper m/z bound of a mass spectrometer scan window.
std::string version
the software version.
std::vector< CVParam > cvParams
a collection of controlled vocabulary terms
std::vector< Contact > contacts
structure allowing the use of a controlled (cvParam) or uncontrolled vocabulary (userParam), or a reference to a predefined set of these in this mzML file (paramGroupRef)
const vector< size_t > & indices() const
size_t index
the zero-based, consecutive index of the spectrum in the SpectrumList.
MS_isolation_window_target_m_z
isolation window target m/z: The primary or reference m/z about which the isolation window is defined...
void testObject_SpectrumList(const SpectrumList &a)
std::vector< CV > cvs
container for one or more controlled vocabulary definitions.
void testBinaryDataArrayExternalMetadata()
std::vector< ParamGroupPtr > paramGroupPtrs
a collection of references to ParamGroups
boost::iostreams::stream_offset sourceFilePosition
for file-based MSData implementations, this attribute may refer to the chromatogram's position in the...
void testInstrumentConfiguration()
std::string startTimeStamp
the optional start timestamp of the run, in UT.
std::string name
the name for the parameter.
MS_reflectron_on
reflectron on: Reflectron is on.
InstrumentConfigurationPtr instrumentConfigurationPtr
this attribute MUST reference the 'id' attribute of the appropriate instrument configuration.
MS_sum_of_spectra
sum of spectra: Spectra Sum.
List with the different components used in the mass spectrometer. At least one source, one mass analyzer and one detector need to be specified.
interface to be implemented by clients who want progress callbacks
std::vector< SourceFilePtr > sourceFilePtrs
container for a list of source file references.
A collection of CVParam and UserParam elements that can be referenced from elsewhere in this mzML doc...
UO_minute
minute: A time unit which is equal to 60 seconds.
std::vector< SamplePtr > samplePtrs
list and descriptions of samples.
std::vector< double > data
the binary data.
Description of a particular hardware configuration of a mass spectrometer. Each configuration MUST ha...
CVID units
an optional CV parameter for the unit term associated with the value, if any (e.g. MS_electron_volt).
boost::shared_ptr< InstrumentConfiguration > InstrumentConfigurationPtr
std::vector< Scan > scans
The structure into which encoded binary data goes. Byte ordering is always little endian (Intel style...
std::vector< SelectedIon > selectedIons
this list of precursor ions that were selected.
SpectrumListPtr spectrumListPtr
all mass spectra and the acquisitions underlying them are described and attached here. Subsidiary data arrays are also both described and attached here.
#define TEST_PROLOG_EX(argc, argv, suffix)
PWIZ_API_DECL void read(std::istream &is, CV &cv)
DataProcessingPtr dataProcessingPtr
this attribute can optionally reference the 'id' of the appropriate dataProcessing.
std::vector< ParamGroupPtr > paramGroupPtrs
container for a list of referenceableParamGroups
encoding/decoding configuration
std::vector< SpectrumPtr > spectra
handles registration of IterationListeners and broadcast of update messages
void testDataProcessing()
std::vector< SoftwarePtr > softwarePtrs
list and descriptions of software used to acquire and/or process the data in this mzML file...
Description of the acquisition settings of the instrument prior to the start of the run...
MS_centroid_spectrum
centroid spectrum: Processing of profile data to produce spectra that contains discrete peaks of zero...
std::vector< DataProcessingPtr > dataProcessingPtrs
list and descriptions of data processing applied to this data.
std::vector< BinaryDataArrayPtr > binaryDataArrayPtrs
list of binary data arrays.
List and descriptions of scans.
void testObjectWithMSData(const object_type &a, const MSData &msd)
virtual Status update(const UpdateMessage &updateMessage)
MS_pwiz
pwiz (ProteoWizard software): ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb.
void set(CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
set/add a CVParam (not recursive)
MS_quadrupole_ion_trap
quadrupole ion trap: Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion t...
Expansible description of the sample used to generate the dataset, named in sampleName.
UO_electronvolt
electronvolt: A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electro...
MS_Xcalibur
Xcalibur: Thermo Finnigan software for data acquisition and analysis.
int main(int argc, char *argv[])
SourceFilePtr sourceFilePtr
this attribute can optionally reference the 'id' of the appropriate sourceFile.
boost::shared_ptr< Sample > SamplePtr
MS_reflectron_off
reflectron off: Reflectron is off.
MS_charge_deconvolution
charge deconvolution: The determination of the mass of an ion based on the mass spectral peaks that r...
MS_contact_name
contact name: Name of the contact person or organization.
DataProcessingPtr dataProcessingPtr
this attribute can optionally reference the 'id' of the appropriate dataProcessing.
The structure that captures the generation of a peak list (including the underlying acquisitions) ...
std::string version
the version of the CV from which the referred-to terms are drawn.
SamplePtr samplePtr
this attribute MUST reference the 'id' of the appropriate sample.
MS_isolation_window_upper_offset
isolation window upper offset: The extent of the isolation window in m/z above the isolation window t...
MS_lowest_observed_m_z
lowest observed m/z: Lowest m/z value observed in the m/z array.
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
std::string id
an identifier for this instrument configuration.
Simple writeable in-memory implementation of SpectrumList.
MS_Conversion_to_mzML
Conversion to mzML: Conversion of a file format to Proteomics Standards Initiative mzML file format...
void testSpectrumListWriteProgress()
MS_peak_picking
peak picking: Spectral peak processing conducted on the acquired data to convert profile data to cent...
boost::shared_ptr< Chromatogram > ChromatogramPtr
boost::shared_ptr< BinaryDataArray > BinaryDataArrayPtr
represents a tag-value pair, where the tag comes from the controlled vocabulary
std::string id
an identifier for this software that is unique across all SoftwareTypes.
boost::shared_ptr< SourceFile > SourceFilePtr
Description of the source file, including location and type.
InstrumentConfigurationPtr defaultInstrumentConfigurationPtr
this attribute MUST reference the 'id' of the default instrument configuration. If a scan does not re...