50 <<
"value=\"" << param.
value <<
"\"";
67 "<cvParam cvLabel=\"MS\" accession=\"MS:1000016\" name=\"scan start time\" value=\"5.890500\" " 68 "unitAccession=\"UO:0000031\" unitName=\"minute\"/>\n";
71 "<cvParam cvLabel=\"MS\" accession=\"MS:1000045\" name=\"collision energy\" value=\"35.00\" " 72 "unitAccession=\"UO:0000266\" unitName=\"electronvolt\"/>\n";
77 vector<CVParam> params;
90 copy(params.begin(), params.end(), ostream_iterator<CVParam>(*
os_,
"\n"));
93 *os_ <<
"as mzML <cvParam> elements:\n";
94 for_each(params.begin(), params.end(),
WriteCVParam(*os_));
97 *os_ <<
"value casting:\n";
98 int temp = params[0].valueAs<
int>();
100 float temp2 = params[1].valueAs<
float>();
101 *os_ << temp2 << endl;
102 string temp3 = params[2].valueAs<
string>();
103 *os_ << temp3 <<
"\n\n";
108 unit_assert(2000.012345 == params[1].valueAs<double>());
110 unit_assert(5.890500 == params[3].valueAs<double>());
121 ostringstream ossScanTime;
125 <<
"ossScanTime: " << ossScanTime.str() << endl;
130 ostringstream ossCollisionEnergy;
133 <<
"ossCollisionEnergy: " << ossCollisionEnergy.str() << endl;
140 vector<CVParam> params;
145 vector<CVParam>::const_iterator it =
157 vector<CVParam> params;
164 vector<CVParam>::const_iterator itDiss =
167 vector<CVParam>::const_iterator itUnit =
172 *
os_ <<
"find dissociation method: " 173 << (itDiss!=params.end() ?
cvTermInfo(itDiss->cvid).
name :
"not found")
176 *
os_ <<
"find unit: " 177 << (itUnit!=params.end() ?
cvTermInfo(itUnit->cvid).
name :
"not found")
217 string result =
"goober";
260 int main(
int argc,
char* argv[])
266 if (argc>1 && !strcmp(argv[1],
"-v"))
os_ = &cout;
MS_deisotoping
deisotoping: The removal of isotope peaks to represent the fragment ion as one data point and is comm...
MS_MSn_spectrum
MSn spectrum: MSn refers to multi-stage MS2 experiments designed to record product ion spectra where ...
PWIZ_API_DECL const CVTermInfo & cvTermInfo(CVID cvid)
returns CV term info for the specified CVID
MS_PQD
PQD (pulsed q dissociation): A process that involves precursor ion activation at high Q...
CVParam cvParam(CVID cvid) const
finds cvid in the container:
MS_plasma_desorption
plasma desorption: The ionization of material in a solid sample by bombarding it with ionic or neutra...
boost::shared_ptr< ParamGroup > ParamGroupPtr
MS_highest_observed_m_z
highest observed m/z: Highest m/z value observed in the m/z array.
void testParamContainer()
MS_scan_start_time
scan start time: The time that an analyzer started a scan, relative to the start of the MS run...
#define unit_assert_equal(x, y, epsilon)
std::vector< CVParam > cvParamChildren(CVID cvid) const
finds all children of cvid in the container:
MS_CID
CID (collision-induced dissociation): The dissociation of an ion after collisional excitation...
MS_collision_induced_dissociation
collision-induced dissociation: The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended.
functor for finding children of a specified CVID in a collection of CVParams:
MS_ms_level
ms level: Stages of ms achieved in a multi stage mass spectrometry experiment.
UO_second
second: A time unit which is equal to the duration of 9 192 631 770 periods of the radiation correspo...
MS_selected_ion_m_z
selected ion m/z: Mass-to-charge ratio of an selected ion.
UserParam userParam(const std::string &) const
finds UserParam with specified name
bool empty() const
returns true iff name, value, type, and units are all empty
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.
bool hasCVParam(CVID cvid) const
returns true iff cvParams contains exact cvid (recursive)
MS_collision_energy
collision energy: Energy for an ion experiencing collision with a stationary gas particle resulting i...
std::vector< UserParam > userParams
a collection of uncontrolled user terms
const char * mzmlScanTime
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
UO_mass_unit
mass unit: A unit which is a standard measure of the amount of matter/energy of a physical object...
MS_ionization_type
ionization type: The method by which gas phase ions are generated from the sample.
double timeInSeconds() const
convenience function to return time in seconds (throws if units not a time unit)
The base class for elements that may contain cvParams, userParams, or paramGroup references.
MS_ETD
ETD (electron transfer dissociation): A process to fragment ions in a mass spectrometer by inducing f...
std::vector< CVParam > cvParams
a collection of controlled vocabulary terms
void operator()(const CVParam ¶m)
std::vector< ParamGroupPtr > paramGroupPtrs
a collection of references to ParamGroups
UO_dalton
dalton: An independently to the base SI units defined mass unit which is equal to one twelfth of the ...
MS_reflectron_on
reflectron on: Reflectron is on.
UO_unit
unit: A unit of measurement is a standardized quantity of a physical quality.
const char * mzmlCollisionEnergy
WriteCVParam(ostream &os)
MS_spectrum_type
spectrum type: Spectrum type.
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.
value_type valueAs() const
Templated value access with type conversion.
bool hasCVParamChild(CVID cvid) const
returns true iff cvParams contains a child (is_a) of cvid (recursive)
void set(CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
set/add a CVParam (not recursive)
#define TEST_PROLOG(argc, argv)
UO_electronvolt
electronvolt: A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electro...
MS_dissociation_method
dissociation method: Fragmentation method used for dissociation or fragmentation. ...
PWIZ_API_DECL std::string value(const std::string &id, const std::string &name)
convenience function to extract a named value from an id string
MS_reflectron_off
reflectron off: Reflectron is off.
CVParam cvParamChild(CVID cvid) const
finds child of cvid in the container:
MS_lowest_observed_m_z
lowest observed m/z: Lowest m/z value observed in the m/z array.
value_type valueAs() const
templated value access with type conversion
functor for finding CVParam with specified exact CVID in a collection of CVParams: ...
int main(int argc, char *argv[])
MS_peak_picking
peak picking: Spectral peak processing conducted on the acquired data to convert profile data to cent...
represents a tag-value pair, where the tag comes from the controlled vocabulary