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Public Member Functions | Public Attributes
pwiz::msdata::Chromatogram Struct Reference

A single chromatogram. More...

#include <MSData.hpp>

Inheritance diagram for pwiz::msdata::Chromatogram:
pwiz::msdata::ChromatogramIdentity pwiz::data::ParamContainer

List of all members.

Public Member Functions

 Chromatogram ()
bool empty () const
 returns true iff the element contains no params and all members are empty or null
void getTimeIntensityPairs (std::vector< TimeIntensityPair > &output) const
 copy binary data arrays into time-intensity pair array
void getTimeIntensityPairs (TimeIntensityPair *output, size_t expectedSize) const
 copy binary data arrays into time-intensity pair array note: this overload is to allow client to allocate own buffer; the client must determine the correct size beforehand, or an exception will be thrown
BinaryDataArrayPtr getTimeArray () const
 get time array (may be null)
BinaryDataArrayPtr getIntensityArray () const
 get intensity array (may be null)
void setTimeIntensityPairs (const std::vector< TimeIntensityPair > &input, CVID timeUnits, CVID intensityUnits)
 set binary data arrays
void setTimeIntensityPairs (const TimeIntensityPair *input, size_t size, CVID timeUnits, CVID intensityUnits)
 set binary data arrays
void setTimeIntensityArrays (const std::vector< double > &timeArray, const std::vector< double > &intensityArray, CVID timeUnits, CVID intensityUnits)
 set time and intensity arrays separately (they must be the same size)
- Public Member Functions inherited from pwiz::msdata::ChromatogramIdentity
 ChromatogramIdentity ()
- Public Member Functions inherited from pwiz::data::ParamContainer
CVParam cvParam (CVID cvid) const
 finds cvid in the container:
CVParam cvParamChild (CVID cvid) const
 finds child of cvid in the container:
std::vector< CVParamcvParamChildren (CVID cvid) const
 finds all children of cvid in the container:
bool hasCVParam (CVID cvid) const
 returns true iff cvParams contains exact cvid (recursive)
bool hasCVParamChild (CVID cvid) const
 returns true iff cvParams contains a child (is_a) of cvid (recursive)
UserParam userParam (const std::string &) const
 finds UserParam with specified name
void set (CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
 set/add a CVParam (not recursive)
void set (CVID cvid, double value, CVID units=CVID_Unknown)
 set/add a CVParam (not recursive)
void set (CVID cvid, int value, CVID units=CVID_Unknown)
 set/add a CVParam (not recursive)
template<typename value_type >
void set (CVID cvid, value_type value, CVID units=CVID_Unknown)
 set/add a CVParam (not recursive)
void clear ()
 clears the collections
bool operator== (const ParamContainer &that) const
 returns true iff this and that have the exact same cvParams and userParams
bool operator!= (const ParamContainer &that) const
 returns !(this==that)
template<>
void set (CVID cvid, bool value, CVID units)
 special case for bool (outside the class for gcc 3.4, and inline for msvc)

Public Attributes

size_t defaultArrayLength
 default length of binary data arrays contained in this element.
DataProcessingPtr dataProcessingPtr
 this attribute can optionally reference the 'id' of the appropriate dataProcessing.
Precursor precursor
 description of precursor ion information (i.e. Q1 settings)
Product product
 description of product ion information (i.e. Q3 settings)
std::vector< BinaryDataArrayPtrbinaryDataArrayPtrs
 list of binary data arrays.
- Public Attributes inherited from pwiz::msdata::ChromatogramIdentity
size_t index
 the zero-based, consecutive index of the chromatogram in the ChromatogramList.
std::string id
 a unique identifier for this chromatogram. It should be expected that external files may use this identifier together with the mzML filename or accession to reference a particular chromatogram.
boost::iostreams::stream_offset sourceFilePosition
 for file-based MSData implementations, this attribute may refer to the chromatogram's position in the file
- Public Attributes inherited from pwiz::data::ParamContainer
std::vector< ParamGroupPtrparamGroupPtrs
 a collection of references to ParamGroups
std::vector< CVParamcvParams
 a collection of controlled vocabulary terms
std::vector< UserParamuserParams
 a collection of uncontrolled user terms

Detailed Description

A single chromatogram.

Definition at line 568 of file MSData.hpp.


Constructor & Destructor Documentation

pwiz::msdata::Chromatogram::Chromatogram ( )
inline

Definition at line 585 of file MSData.hpp.


Member Function Documentation

bool pwiz::msdata::Chromatogram::empty ( ) const

returns true iff the element contains no params and all members are empty or null

Reimplemented from pwiz::data::ParamContainer.

void pwiz::msdata::Chromatogram::getTimeIntensityPairs ( std::vector< TimeIntensityPair > &  output) const

copy binary data arrays into time-intensity pair array

void pwiz::msdata::Chromatogram::getTimeIntensityPairs ( TimeIntensityPair output,
size_t  expectedSize 
) const

copy binary data arrays into time-intensity pair array note: this overload is to allow client to allocate own buffer; the client must determine the correct size beforehand, or an exception will be thrown

BinaryDataArrayPtr pwiz::msdata::Chromatogram::getTimeArray ( ) const

get time array (may be null)

BinaryDataArrayPtr pwiz::msdata::Chromatogram::getIntensityArray ( ) const

get intensity array (may be null)

void pwiz::msdata::Chromatogram::setTimeIntensityPairs ( const std::vector< TimeIntensityPair > &  input,
CVID  timeUnits,
CVID  intensityUnits 
)

set binary data arrays

void pwiz::msdata::Chromatogram::setTimeIntensityPairs ( const TimeIntensityPair input,
size_t  size,
CVID  timeUnits,
CVID  intensityUnits 
)

set binary data arrays

void pwiz::msdata::Chromatogram::setTimeIntensityArrays ( const std::vector< double > &  timeArray,
const std::vector< double > &  intensityArray,
CVID  timeUnits,
CVID  intensityUnits 
)

set time and intensity arrays separately (they must be the same size)


Member Data Documentation

size_t pwiz::msdata::Chromatogram::defaultArrayLength

default length of binary data arrays contained in this element.

Definition at line 571 of file MSData.hpp.

Referenced by initializeTestData(), pwiz::msdata::TextWriter::operator()(), and testChromatogram().

DataProcessingPtr pwiz::msdata::Chromatogram::dataProcessingPtr

this attribute can optionally reference the 'id' of the appropriate dataProcessing.

Definition at line 574 of file MSData.hpp.

Referenced by pwiz::msdata::TextWriter::operator()(), and testChromatogram().

Precursor pwiz::msdata::Chromatogram::precursor

description of precursor ion information (i.e. Q1 settings)

Definition at line 577 of file MSData.hpp.

Product pwiz::msdata::Chromatogram::product

description of product ion information (i.e. Q3 settings)

Definition at line 580 of file MSData.hpp.

std::vector<BinaryDataArrayPtr> pwiz::msdata::Chromatogram::binaryDataArrayPtrs

list of binary data arrays.

Definition at line 583 of file MSData.hpp.

Referenced by initializeTestData(), pwiz::msdata::TextWriter::operator()(), and testChromatogram().


The documentation for this struct was generated from the following file: