ProteoWizard: pwiz::msdata::SpectrumListWrapper Class Reference

ProteoWizard

Inheritable pass-through implementation for wrapping a SpectrumList. More...

#include <SpectrumListWrapper.hpp>

Inheritance diagram for pwiz::msdata::SpectrumListWrapper:

List of all members.

Public Member Functions
	SpectrumListWrapper (const SpectrumListPtr &inner)
virtual size_t	size () const
	returns the number of spectra
virtual bool	empty () const
	returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL)
virtual const SpectrumIdentity &	spectrumIdentity (size_t index) const
	access to a spectrum index
virtual SpectrumPtr	spectrum (size_t index, bool getBinaryData=false) const =0
	retrieve a spectrum by index
virtual SpectrumPtr	spectrum (size_t index, DetailLevel detailLevel) const
	retrieve a spectrum by index
virtual const boost::shared_ptr< const DataProcessing >	dataProcessingPtr () const
	returns the data processing affecting spectra retrieved through this interface
Public Member Functions inherited from pwiz::msdata::SpectrumList
virtual size_t	find (const std::string &id) const
	find id in the spectrum index (returns size() on failure)
virtual IndexList	findNameValue (const std::string &name, const std::string &value) const
	find all spectrum indexes with specified name/value pair
virtual IndexList	findSpotID (const std::string &spotID) const
	find all spectrum indexes with spotID (returns empty vector on failure)
virtual SpectrumPtr	spectrum (const SpectrumPtr &seed, bool getBinaryData) const
	get a copy of the seed spectrum, optionally with its binary data populated this is useful for formats like mzML that can delay loading of binary data
virtual	~SpectrumList ()

Protected Attributes
SpectrumListPtr	inner_
DataProcessingPtr	dp_

Detailed Description

Inheritable pass-through implementation for wrapping a SpectrumList.

Definition at line 37 of file SpectrumListWrapper.hpp.

Constructor & Destructor Documentation

pwiz::msdata::SpectrumListWrapper::SpectrumListWrapper ( const SpectrumListPtr & inner )

inline

Definition at line 41 of file SpectrumListWrapper.hpp.

    :   inner_(inner),
        dp_(inner->dataProcessingPtr().get() ? new DataProcessing(*inner->dataProcessingPtr())
                                             : new DataProcessing("pwiz_Spectrum_Processing"))
    {
        if (!inner.get()) throw std::runtime_error("[SpectrumListWrapper] Null SpectrumListPtr.");
    }

Member Function Documentation

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

inlinevirtual

returns the number of spectra

Implements pwiz::msdata::SpectrumList.

Reimplemented in pwiz::analysis::SpectrumList_Filter, and pwiz::analysis::SpectrumList_Sorter.

Definition at line 49 of file SpectrumListWrapper.hpp.

Referenced by test().

{return inner_->size();}

virtual bool pwiz::msdata::SpectrumListWrapper::empty ( ) const

inlinevirtual

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

Reimplemented from pwiz::msdata::SpectrumList.

Definition at line 50 of file SpectrumListWrapper.hpp.

Referenced by testHasBinaryData().

{return size() == 0;}

virtual const SpectrumIdentity& pwiz::msdata::SpectrumListWrapper::spectrumIdentity ( size_t index ) const

inlinevirtual

access to a spectrum index

Implements pwiz::msdata::SpectrumList.

Reimplemented in pwiz::analysis::SpectrumList_Filter, and pwiz::analysis::SpectrumList_Sorter.

Definition at line 51 of file SpectrumListWrapper.hpp.

{return inner_->spectrumIdentity(index);}

virtual SpectrumPtr pwiz::msdata::SpectrumListWrapper::spectrum	(	size_t	index,
		bool	getBinaryData = `false`
	)		const

pure virtual

retrieve a spectrum by index

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

Implements pwiz::msdata::SpectrumList.

Implemented in pwiz::analysis::SpectrumList_Filter, pwiz::analysis::SpectrumList_Sorter, pwiz::analysis::SpectrumList_TitleMaker, pwiz::analysis::SpectrumList_PrecursorRefine, pwiz::analysis::SpectrumList_ZeroSamplesFilter, pwiz::msdata::SpectrumListCache, pwiz::analysis::SpectrumList_ChargeStateCalculator, pwiz::analysis::SpectrumList_PeakPicker, pwiz::analysis::SpectrumList_Smoother, pwiz::analysis::SpectrumList_PrecursorRecalculator, pwiz::analysis::SpectrumList_PeakFilter, pwiz::analysis::SpectrumList_MetadataFixer, and pwiz::analysis::SpectrumList_MZWindow.

virtual SpectrumPtr pwiz::msdata::SpectrumListWrapper::spectrum	(	size_t	index,
		DetailLevel	detailLevel
	)		const

inlinevirtual

retrieve a spectrum by index

detailLevel determines what fields are guaranteed present on the spectrum after the call
client may assume the underlying Spectrum* is valid

Reimplemented from pwiz::msdata::SpectrumList.

Reimplemented in pwiz::analysis::SpectrumList_Filter.

Definition at line 56 of file SpectrumListWrapper.hpp.

References pwiz::msdata::DetailLevel_FullData, and spectrum().

Referenced by spectrum().

{return spectrum(index, detailLevel == DetailLevel_FullData);}

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

inlinevirtual

returns the data processing affecting spectra retrieved through this interface

may return a null shared pointer

Reimplemented from pwiz::msdata::SpectrumList.

Definition at line 58 of file SpectrumListWrapper.hpp.

{return dp_;}

Member Data Documentation

SpectrumListPtr pwiz::msdata::SpectrumListWrapper::inner_

protected

Definition at line 61 of file SpectrumListWrapper.hpp.

DataProcessingPtr pwiz::msdata::SpectrumListWrapper::dp_

protected

Definition at line 62 of file SpectrumListWrapper.hpp.

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

/Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/msdata/SpectrumListWrapper.hpp