43 if (
os_) *
os_ <<
"test(): indexed=\"" << boolalpha << indexed <<
"\"\n";
53 serializer.write(oss, tiny);
55 if (
os_) *
os_ <<
"oss:\n" << oss.str() << endl;
57 shared_ptr<istream> is(
new istringstream(oss.str()));
94 IndexList indexList = sl->findNameValue(
"scan",
"19");
95 unit_assert(indexList.size()==1 && indexList[0]==0);
97 indexList = sl->findNameValue(
"scan",
"20");
98 unit_assert(indexList.size()==1 && indexList[0]==1);
100 indexList = sl->findNameValue(
"scan",
"21");
101 unit_assert(indexList.size()==1 && indexList[0]==2);
106 unit_assert(sl->spectrumIdentity(0).id ==
"scan=19");
107 unit_assert(sl->spectrumIdentity(0).sourceFilePosition != -1);
118 Scan& scan = s->scanList.scans[0];
126 unit_assert(s->binaryDataArrayPtrs[0]->data.empty() && s->binaryDataArrayPtrs[1]->data.empty());
128 s = sl->spectrum(0,
true);
131 unit_assert(!s->binaryDataArrayPtrs[0]->data.empty() && !s->binaryDataArrayPtrs[1]->data.empty());
133 vector<MZIntensityPair> pairs;
134 s->getMZIntensityPairs(pairs);
138 *
os_ <<
"scan 19:\n";
139 copy(pairs.begin(), pairs.end(), ostream_iterator<MZIntensityPair>(*
os_,
"\n"));
144 for (
int i=0; i<15; i++)
147 Scan& scan19 = s->scanList.scans[0];
150 unit_assert(!instrumentConfiguration.cvParams.empty());
151 unit_assert(instrumentConfiguration.userParams.size() == 1 &&
152 instrumentConfiguration.userParams[0].name ==
"doobie");
157 unit_assert(sl->spectrumIdentity(1).id ==
"scan=20");
159 s = sl->spectrum(1,
true);
181 s->getMZIntensityPairs(pairs);
185 *
os_ <<
"scan 20:\n";
186 copy(pairs.begin(), pairs.end(), ostream_iterator<MZIntensityPair>(*
os_,
"\n"));
191 for (
int i=0; i<10; i++)
192 unit_assert(pairs[i].
mz==2*i && pairs[i].intensity==(10-i)*2);
198 unit_assert(sl->spectrumIdentity(2).id ==
"scan=21");
200 s = sl->spectrum(2,
false);
203 UserParam exampleUserParam = s->userParam(
"example");
212 unit_assert(sl->spectrumIdentity(3).id ==
"scan=22");
214 s = sl->spectrum(3,
false);
218 Precursor& precursor22 = s->precursors[0];
MS_charge_state
charge state: The charge state of the ion, single or multiple and positive or negatively charged...
std::vector< SourceFilePtr > sourceFilePtrs
list and descriptions of the source files this mzML document was generated or derived from...
MS_Bruker_Agilent_YEP_nativeID_format
Bruker/Agilent YEP nativeID format: Native format defined by scan=xsd:nonNegativeInteger.
Description of the way in which a particular software was used.
boost::shared_ptr< Software > SoftwarePtr
MS_base_peak_intensity
base peak intensity: The intensity of the greatest peak in the mass spectrum.
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.
boost::shared_ptr< Spectrum > SpectrumPtr
std::string value
the value for the parameter, where appropriate.
MS_ProteoWizard_software
ProteoWizard software: ProteoWizard software for data processing and analysis. Primarily developed by...
MS_scan_start_time
scan start time: The time that an analyzer started a scan, relative to the start of the MS run...
MS_positive_scan
positive scan: Polarity of the scan is positive.
boost::shared_ptr< DataProcessing > DataProcessingPtr
MS_CID
CID (collision-induced dissociation): The dissociation of an ion after collisional excitation...
FileDescription fileDescription
information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is sto...
MS_LCQ_Deca
LCQ Deca: ThermoFinnigan LCQ Deca.
MS_ms_level
ms level: Stages of ms achieved in a multi stage mass spectrometry experiment.
MS_selected_ion_m_z
selected ion m/z: Mass-to-charge ratio of an selected ion.
MS_Bruker_Agilent_YEP_format
Bruker/Agilent YEP format: Bruker/Agilent YEP file format.
bool empty() const
returns true iff name, value, type, and units are all empty
MS_peak_intensity
peak intensity: Intensity of ions as measured by the height or area of a peak in a mass spectrum...
MS_intensity_array
intensity array: A data array of intensity values.
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.
MS_collision_energy
collision energy: Energy for an ion experiencing collision with a stationary gas particle resulting i...
Description of the default peak processing method. This element describes the base method used in the...
std::string type
the datatype of the parameter, where appropriate (e.g.: xsd:float).
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)
MS_ETD
ETD (electron transfer dissociation): A process to fragment ions in a mass spectrometer by inducing f...
boost::shared_ptr< SpectrumList > SpectrumListPtr
double mz(double neutralMass, int protonDelta, int electronDelta=0, int neutronDelta=0)
std::string name
the name for the parameter.
InstrumentConfigurationPtr instrumentConfigurationPtr
this attribute MUST reference the 'id' attribute of the appropriate instrument configuration.
Description of a particular hardware configuration of a mass spectrometer. Each configuration MUST ha...
boost::shared_ptr< InstrumentConfiguration > InstrumentConfigurationPtr
PWIZ_API_DECL void initializeTiny(IdentData &mzid)
std::vector< SoftwarePtr > softwarePtrs
list and descriptions of software used to acquire and/or process the data in this mzML file...
std::vector< DataProcessingPtr > dataProcessingPtrs
list and descriptions of data processing applied to this data.
MSData <-> mzXML stream serialization.
Serializer_mzXML configuration.
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
MS_Conversion_to_mzML
Conversion to mzML: Conversion of a file format to Proteomics Standards Initiative mzML file format...
bool indexed
(indexed==true): read/write with <index>
boost::shared_ptr< SourceFile > SourceFilePtr
Description of the source file, including location and type.