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Public Member Functions | Protected Attributes
pwiz::msdata::SpectrumListWrapper Class Reference

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

#include <SpectrumListWrapper.hpp>

Inheritance diagram for pwiz::msdata::SpectrumListWrapper:
pwiz::msdata::SpectrumList pwiz::analysis::SpectrumList_ChargeStateCalculator pwiz::analysis::SpectrumList_Filter pwiz::analysis::SpectrumList_MetadataFixer pwiz::analysis::SpectrumList_MZWindow pwiz::analysis::SpectrumList_PeakFilter pwiz::analysis::SpectrumList_PeakPicker pwiz::analysis::SpectrumList_PrecursorRecalculator pwiz::analysis::SpectrumList_PrecursorRefine pwiz::analysis::SpectrumList_Smoother pwiz::analysis::SpectrumList_Sorter pwiz::analysis::SpectrumList_TitleMaker pwiz::analysis::SpectrumList_ZeroSamplesFilter pwiz::msdata::SpectrumListCache

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 SpectrumIdentityspectrumIdentity (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
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: