40 if (
os_) *
os_ <<
"testParamContainer()\n";
66 if (
os_) *
os_ <<
"testFileDescription()\n";
97 fd.
sourceFilePtrs[0]->paramGroupPtrs[0]->userParams[0].name ==
"user2");
100 fd.
sourceFilePtrs[1]->paramGroupPtrs[0]->userParams[0].name ==
"user3");
103 fd.
contacts[0].paramGroupPtrs[0]->userParams[0].name ==
"user4");
106 fd.
contacts[1].paramGroupPtrs[0]->userParams[0].name ==
"user5");
112 if (
os_) *
os_ <<
"testComponentList()\n";
136 if (
os_) *
os_ <<
"testInstrumentConfiguration()\n";
164 if (
os_) *
os_ <<
"testDataProcessing()\n";
190 if (
os_) *
os_ <<
"testScanSettings()\n";
221 if (
os_) *
os_ <<
"testPrecursor()\n";
250 if (
os_) *
os_ <<
"testProduct()\n";
269 if (
os_) *
os_ <<
"testScan()\n";
297 if (
os_) *
os_ <<
"testScanList()\n";
322 if (
os_) *
os_ <<
"testBinaryDataArray()\n";
348 if (
os_) *
os_ <<
"testSpectrum()\n";
381 unit_assert(spectrum.
products.back().isolationWindow.paramGroupPtrs.back()->userParams.empty());
393 unit_assert(!spectrum.
products.back().isolationWindow.paramGroupPtrs.back()->userParams.empty());
400 if (
os_) *
os_ <<
"testChromatogram()\n";
430 if (
os_) *
os_ <<
"testRun()\n";
466 if (
os_) *
os_ <<
"testMSData()\n";
524 int main(
int argc,
char* argv[])
530 if (argc>1 && !strcmp(argv[1],
"-v"))
os_ = &cout;
IsolationWindow isolationWindow
this element captures the isolation (or 'selection') window configured to isolate one or more precurs...
std::vector< Product > products
list and descriptions of product ion information
std::vector< SourceFilePtr > sourceFilePtrs
list and descriptions of the source files this mzML document was generated or derived from...
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
void testDataProcessing()
boost::shared_ptr< Software > SoftwarePtr
boost::shared_ptr< ParamGroup > ParamGroupPtr
Description of the source file, including location and type.
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.
std::vector< BinaryDataArrayPtr > binaryDataArrayPtrs
list of binary data arrays.
void testInstrumentConfiguration()
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< 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.
int main(int argc, char *argv[])
void testBinaryDataArray()
IsolationWindow isolationWindow
this element captures the isolation (or 'selection') window configured to isolate one or more precurs...
boost::shared_ptr< DataProcessing > DataProcessingPtr
void testFileDescription()
void testParamContainer()
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 ...
Component & source(size_t index)
returns the source component with ordinal <index+1>
DataProcessingPtr dataProcessingPtr
this optional attribute may reference the 'id' attribute of the appropriate dataProcessing.
SourceFilePtr defaultSourceFilePtr
default source file reference
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.
Description of the default peak processing method. This element describes the base method used in the...
Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is sto...
A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument...
Run run
a run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument...
std::vector< Target > targets
target list (or 'inclusion list') configured prior to the run.
The base class for elements that may contain cvParams, userParams, or paramGroup references.
Activation activation
the type and energy level used for activation.
std::vector< ScanWindow > scanWindows
container for a list of select windows.
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)
std::vector< ParamGroupPtr > paramGroupPtrs
a collection of references to ParamGroups
MS_reflectron_on
reflectron on: Reflectron is on.
InstrumentConfigurationPtr instrumentConfigurationPtr
this attribute MUST reference the 'id' attribute of the appropriate instrument configuration.
List with the different components used in the mass spectrometer. At least one source, one mass analyzer and one detector need to be specified.
std::vector< SourceFilePtr > sourceFilePtrs
container for a list of source file references.
Component & analyzer(size_t index)
returns the analyzer component with ordinal <index+1>
A collection of CVParam and UserParam elements that can be referenced from elsewhere in this mzML doc...
std::vector< SamplePtr > samplePtrs
list and descriptions of samples.
Description of a particular hardware configuration of a mass spectrometer. Each configuration MUST ha...
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...
PWIZ_API_DECL void resolve(ContactRole &cr, IdentData &mzid)
std::vector< SelectedIon > selectedIons
this list of precursor ions that were selected.
#define TEST_PROLOG_EX(argc, argv, suffix)
DataProcessingPtr dataProcessingPtr
this attribute can optionally reference the 'id' of the appropriate dataProcessing.
std::vector< ParamGroupPtr > paramGroupPtrs
container for a list of referenceableParamGroups
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...
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.
Expansible description of the sample used to generate the dataset, named in sampleName.
SourceFilePtr sourceFilePtr
this attribute can optionally reference the 'id' of the appropriate sourceFile.
Component & detector(size_t index)
returns the detector component with ordinal <index+1>
boost::shared_ptr< Sample > SamplePtr
MS_reflectron_off
reflectron off: Reflectron is off.
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) ...
SamplePtr samplePtr
this attribute MUST reference the 'id' of the appropriate sample.
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
boost::shared_ptr< BinaryDataArray > BinaryDataArrayPtr
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...