56 Spectrum& s20 = *spectrumList->spectra[0];
88 for (
int i=0; i<10; i++)
91 for (
int i=0; i<10; i++)
97 Spectrum& s21 = *spectrumList->spectra[1];
130 for (
int i=1; i<=10; i++)
133 for (
int i=0; i<10; i++)
146 serializer.
write(oss, msd);
148 if (
os_) *
os_ <<
"oss:\n" << oss.str() << endl;
150 shared_ptr<istringstream> iss(
new istringstream(oss.str()));
152 serializer.
read(iss, msd2);
187int main(
int argc,
char* argv[])
193 if (argc>1 && !strcmp(argv[1],
"-v"))
os_ = &cout;
void diff(const string &filename1, const string &filename2)
int main(int argc, char *argv[])
void initializeTinyMGF(MSData &msd)
MSData <-> MGF stream serialization.
void read(boost::shared_ptr< std::istream > is, MSData &msd) const
read in MSData object from an MGF istream note: istream may be managed by MSData's SpectrumList,...
void write(std::ostream &os, const MSData &msd, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry=0) const
write MSData object to ostream as MGF; iterationListenerRegistry may be used to receive progress upda...
MSData <-> mzML stream serialization.
void write(std::ostream &os, const MSData &msd, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry=0) const
write MSData object to ostream as mzML; iterationListenerRegistry may be used to receive progress upd...
A custom vector class that can store its contents in either a std::vector or a cli::array (when compi...
void push_back(const T &value)
MS_no_combination
no combination: Use this term if only one scan was recorded or there is no information about scans av...
MS_highest_observed_m_z
highest observed m/z: Highest m/z value observed in the m/z array.
MS_possible_charge_state
possible charge state: A possible charge state of the ion in a situation where the charge of an ion i...
MS_lowest_observed_m_z
lowest observed m/z: Lowest m/z value observed in the m/z array.
MS_ms_level
ms level: Stages of ms achieved in a multi stage mass spectrometry experiment.
MS_centroid_spectrum
centroid spectrum: Processing of profile data to produce spectra that contains discrete peaks of zero...
MS_MSn_spectrum
MSn spectrum: MSn refers to multi-stage MS2 experiments designed to record product ion spectra where ...
MS_negative_scan
negative scan: Polarity of the scan is negative.
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_charge_state
charge state: The charge state of the ion, single or multiple and positive or negatively charged.
MS_spectrum_title
spectrum title: A free-form text title describing a spectrum.
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_selected_ion_m_z
selected ion m/z: Mass-to-charge ratio of an selected ion.
MS_scan_start_time
scan start time: The time that an analyzer started a scan, relative to the start of the MS run.
MS_number_of_detector_counts
number of detector counts: The number of counted events observed in one or a group of elements of a d...
MS_base_peak_intensity
base peak intensity: The intensity of the greatest peak in the mass spectrum.
MS_base_peak_m_z
base peak m/z: M/z value of the signal of highest intensity in the mass spectrum.
MS_positive_scan
positive scan: Polarity of the scan is positive.
UO_second
second: A time unit which is equal to the duration of 9 192 631 770 periods of the radiation correspo...
MS_peak_intensity
peak intensity: Intensity of ions as measured by the height or area of a peak in a mass spectrum.
boost::shared_ptr< Spectrum > SpectrumPtr
represents a tag-value pair, where the tag comes from the controlled vocabulary
Calculate diffs of objects in a ProteoWizard data model hierarchy.
void set(CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
set/add a CVParam (not recursive)
configuration struct for diffing MSData types
bool ignoreIdentity
ignore members of SpectrumIdentity and ChromatogramIdentity
This summarizes the different types of spectra that can be expected in the file. This is expected to ...
FileContent fileContent
this summarizes the different types of spectra that can be expected in the file. This is expected to ...
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
Run run
a run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument.
FileDescription fileDescription
information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is sto...
The method of precursor ion selection and activation.
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....
Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile.
std::vector< Scan > scans
The structure that captures the generation of a peak list (including the underlying acquisitions)
void setMZIntensityArrays(const std::vector< double > &mzArray, const std::vector< double > &intensityArray, CVID intensityUnits)
set m/z and intensity arrays separately (they must be the same size)
BinaryDataArrayPtr getIntensityArray() const
get intensity array (may be null)
size_t defaultArrayLength
default length of binary data arrays contained in this element.
BinaryDataArrayPtr getMZArray() const
get m/z array (may be null)
ScanList scanList
list of scans
std::vector< Precursor > precursors
list and descriptions of precursors to the spectrum currently being described.
std::string id
a unique identifier for this spectrum. It should be expected that external files may use this identif...
size_t index
the zero-based, consecutive index of the spectrum in the SpectrumList.
Simple writeable in-memory implementation of SpectrumList.
#define TEST_PROLOG(argc, argv)