A single chromatogram. More...
#include <MSData.hpp>
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< CVParam > | cvParamChildren (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< BinaryDataArrayPtr > | binaryDataArrayPtrs |
| 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< ParamGroupPtr > | paramGroupPtrs |
| a collection of references to ParamGroups | |
| std::vector< CVParam > | cvParams |
| a collection of controlled vocabulary terms | |
| std::vector< UserParam > | userParams |
| a collection of uncontrolled user terms | |
Detailed Description
A single chromatogram.
Definition at line 568 of file MSData.hpp.
Constructor & Destructor Documentation
|
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:
- /Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/msdata/MSData.hpp
