pwiz::msdata::ChromatogramList Class Reference

Interface for accessing chromatograms, which may be stored in memory or backed by a data file (RAW, mzXML, mzML). More...

#include <MSData.hpp>

Inheritance diagram for pwiz::msdata::ChromatogramList:

List of all members.

Public Member Functions
virtual size_t	size () const =0
	returns the number of chromatograms
bool	empty () const
	returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL)
virtual const ChromatogramIdentity &	chromatogramIdentity (size_t index) const =0
	access to a chromatogram index
virtual size_t	find (const std::string &id) const
	find id in the chromatogram index (returns size() on failure)
virtual ChromatogramPtr	chromatogram (size_t index, bool getBinaryData=false) const =0
	retrieve a chromatogram by index
virtual const boost::shared_ptr< const DataProcessing >	dataProcessingPtr () const
	returns the data processing affecting spectra retrieved through this interface
virtual	~ChromatogramList ()

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Detailed Description

Interface for accessing chromatograms, which may be stored in memory or backed by a data file (RAW, mzXML, mzML).

Implementation notes:

• Implementations are expected to keep a chromatogram index in the form of vector<ChromatogramIdentity> or equivalent. The default find*() functions search the index linearly. Implementations may provide constant time indexing.

• The semantics of chromatogram() may vary slightly with implementation. In particular, a ChromatogramList implementation that is backed by a file may choose either to cache or discard the ChromatogramPtrs for future access, with the caveat that the client may write to the underlying data.

• It is the implementation's responsibility to return a valid ChromatogramPtr from chromatogram(). If this cannot be done, an exception must be thrown.

• The 'getBinaryData' flag is a hint if false : implementations may provide valid BinaryDataArrayPtrs on chromatogram(index, false); implementations must provide valid BinaryDataArrayPtrs on chromatogram(index, true).

Definition at line 750 of file MSData.hpp.

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Constructor & Destructor Documentation

virtual pwiz::msdata::ChromatogramList::~ChromatogramList ( )

inlinevirtual

Definition at line 775 of file MSData.hpp.

{} 

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Member Function Documentation

virtual size_t pwiz::msdata::ChromatogramList::size ( ) const

pure virtual

returns the number of chromatograms

Implemented in pwiz::msdata::ChromatogramListSimple, pwiz::msdata::detail::ChromatogramList_Thermo, pwiz::analysis::ChromatogramListWrapper, pwiz::msdata::detail::ChromatogramList_Agilent, pwiz::msdata::detail::ChromatogramList_Bruker, pwiz::msdata::detail::ChromatogramList_ABI, pwiz::msdata::detail::ChromatogramList_Waters, MyBase, and MyBase.

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

bool pwiz::msdata::ChromatogramList::empty

(

)

const

returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL)

Reimplemented in pwiz::msdata::ChromatogramListSimple, and pwiz::analysis::ChromatogramListWrapper.

virtual const ChromatogramIdentity& pwiz::msdata::ChromatogramList::chromatogramIdentity ( size_t  index ) const

pure virtual

access to a chromatogram index

Implemented in pwiz::msdata::ChromatogramListSimple, pwiz::msdata::detail::ChromatogramList_Thermo, pwiz::analysis::ChromatogramListWrapper, pwiz::msdata::detail::ChromatogramList_Agilent, pwiz::msdata::detail::ChromatogramList_Bruker, pwiz::msdata::detail::ChromatogramList_ABI, pwiz::msdata::detail::ChromatogramList_Waters, and MyBase.

virtual size_t pwiz::msdata::ChromatogramList::find ( const std::string &  id ) const

virtual

find id in the chromatogram index (returns size() on failure)

Reimplemented in pwiz::msdata::detail::ChromatogramList_Thermo, pwiz::analysis::ChromatogramListWrapper, pwiz::msdata::detail::ChromatogramList_Agilent, pwiz::msdata::detail::ChromatogramList_Bruker, pwiz::msdata::detail::ChromatogramList_ABI, and pwiz::msdata::detail::ChromatogramList_Waters.

virtual ChromatogramPtr pwiz::msdata::ChromatogramList::chromatogram ( size_t  index, bool  getBinaryData = false  ) const

pure virtual

retrieve a chromatogram by index

• binary data arrays will be provided if (getBinaryData == true);
• client may assume the underlying Chromatogram* is valid

Implemented in pwiz::msdata::ChromatogramListSimple, pwiz::msdata::detail::ChromatogramList_Thermo, pwiz::analysis::ChromatogramListWrapper, pwiz::msdata::detail::ChromatogramList_Agilent, pwiz::msdata::detail::ChromatogramList_Bruker, pwiz::analysis::ChromatogramList_SavitzkyGolaySmoother, pwiz::msdata::detail::ChromatogramList_ABI, pwiz::msdata::detail::ChromatogramList_Waters, and MyBase.

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

virtual const boost::shared_ptr<const DataProcessing> pwiz::msdata::ChromatogramList::dataProcessingPtr ( ) const

virtual

returns the data processing affecting spectra retrieved through this interface

• may return a null shared pointer

Reimplemented in pwiz::msdata::ChromatogramListSimple, pwiz::msdata::ChromatogramListBase, and MyBase.

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

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

• /Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/msdata/MSData.hpp