27#include "boost/iostreams/positioning.hpp"
54 Spectrum& s20 = *spectrumList->spectra[0];
76 for (
int i=0; i<10; i++)
79 for (
int i=0; i<10; i++)
101 Spectrum& s20 = *spectrumList->spectra[0];
130 for (
int i=0; 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;
151 shared_ptr<istream> iss(
new istringstream(oss.str()));
152 serializer.
read(iss, msd2);
167 serializer.
write(oss, msd);
169 if (
os_) *
os_ <<
"oss:\n" << oss.str() << endl;
172 shared_ptr<istream> iss(
new istringstream(oss.str()));
173 serializer.
read(iss, msd2);
188 serializer.
write(oss, msd);
190 if (
os_) *
os_ <<
"oss:\n" << oss.str() << endl;
193 shared_ptr<istream> iss(
new istringstream(oss.str()));
194 serializer.
read(iss, msd2);
209 serializer.
write(oss, msd);
211 if (
os_) *
os_ <<
"oss:\n" << oss.str() << endl;
214 shared_ptr<istream> iss(
new istringstream(oss.str()));
215 serializer.
read(iss, msd2);
229 serializer.
write(oss, msd);
231 if (
os_) *
os_ <<
"oss:\n" << oss.str() << endl;
234 shared_ptr<istream> iss(
new istringstream(oss.str()));
235 serializer.
read(iss, msd2);
250 serializer.
write(oss, msd);
252 if (
os_) *
os_ <<
"oss:\n" << oss.str() << endl;
255 shared_ptr<istream> iss(
new istringstream(oss.str()));
256 serializer.
read(iss, msd2);
282int main(
int argc,
char* argv[])
288 if (argc>1 && !strcmp(argv[1],
"-v"))
os_ = &cout;
void diff(const string &filename1, const string &filename2)
void testWriteReadMS1(const MSData &msd)
void initializeTinyMS2(MSData &msd)
int main(int argc, char *argv[])
void testWriteReadMS2(const MSData &msd)
void testWriteReadBMS1(const MSData &msd)
void initializeTinyMS1(MSData &msd)
void testWriteReadCMS2(const MSData &msd)
void testWriteReadCMS1(const MSData &msd)
void testWriteReadBMS2(const MSData &msd)
MSData <-> MSn stream serialization.
void write(std::ostream &os, const MSData &msd, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry=0) const
write MSData object to ostream as MSn; iterationListenerRegistry may be used to receive progress upda...
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,...
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_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_scan_number_only_nativeID_format
scan number only nativeID format: Native format defined by scan=xsd:nonNegativeInteger.
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_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
MS_isolation_window_target_m_z
isolation window target m/z: The primary or reference m/z about which the isolation window is defined...
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_MS2_format
MS2 format: MS2 file format for MS2 spectral data.
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.
UO_second
second: A time unit which is equal to the duration of 9 192 631 770 periods of the radiation correspo...
boost::shared_ptr< Spectrum > SpectrumPtr
boost::shared_ptr< SourceFile > SourceFilePtr
Description of the source file, including location and type.
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 ignoreMetadata
ignore all file level metadata, and most scan level metadata, i.e.
bool ignoreDataProcessing
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 ...
std::vector< SourceFilePtr > sourceFilePtrs
list and descriptions of the source files this mzML document was generated or derived from.
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.
IsolationWindow isolationWindow
this element captures the isolation (or 'selection') window configured to isolate one or more precurs...
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
Description of the source file, including location and type.
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)