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pwiz::analysis::SpectrumList_PrecursorRefine Class Reference

SpectrumList wrapper that recalculates precursor info on spectrum() requests. More...

#include <SpectrumList_PrecursorRefine.hpp>

Inheritance diagram for pwiz::analysis::SpectrumList_PrecursorRefine:
pwiz::msdata::SpectrumListWrapper pwiz::msdata::SpectrumList

Classes

struct  PrecursorInfo
 

Public Member Functions

 SpectrumList_PrecursorRefine (const msdata::MSData &msd)
 constructor needs the full MSData object for instrument info; SpectrumList_PrecursorRefine holds a reference to the original SpectrumListPtr More...
 
 ~SpectrumList_PrecursorRefine ()
 
SpectrumList interface
virtual msdata::SpectrumPtr spectrum (size_t index, bool getBinaryData=false) const
 retrieve a spectrum by index More...
 
- Public Member Functions inherited from pwiz::msdata::SpectrumListWrapper
 SpectrumListWrapper (const SpectrumListPtr &inner)
 
virtual size_t size () const
 returns the number of spectra More...
 
virtual bool empty () const
 returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL) More...
 
virtual const SpectrumIdentityspectrumIdentity (size_t index) const
 access to a spectrum index More...
 
virtual SpectrumPtr spectrum (size_t index, DetailLevel detailLevel) const
 retrieve a spectrum by index More...
 
virtual const boost::shared_ptr< const DataProcessingdataProcessingPtr () const
 returns the data processing affecting spectra retrieved through this interface More...
 
SpectrumListPtr inner () const
 
SpectrumListPtr innermost () const
 
- 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) More...
 
virtual size_t findAbbreviated (const std::string &abbreviatedId, char delimiter='.') const
 find an abbreviated id (e.g. "1.1.123.2" for "sample=1 period=1 cycle=123 experiment=2") in the spectrum index (returns size() on failure) More...
 
virtual IndexList findNameValue (const std::string &name, const std::string &value) const
 find all spectrum indexes with specified name/value pair More...
 
virtual IndexList findSpotID (const std::string &spotID) const
 find all spectrum indexes with spotID (returns empty vector on failure) More...
 
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 More...
 
virtual void warn_once (const char *msg) const
 issues a warning once per SpectrumList instance (based on string hash) More...
 
virtual ~SpectrumList ()
 

Private Member Functions

double RefineMassVal (double initialEstimate, size_t index) const
 
 SpectrumList_PrecursorRefine (SpectrumList_PrecursorRefine &)
 
SpectrumList_PrecursorRefineoperator= (SpectrumList_PrecursorRefine &)
 

Private Attributes

boost::shared_ptr< Impl > impl_
 
int numRefined
 
int numTotal
 

Additional Inherited Members

- Protected Attributes inherited from pwiz::msdata::SpectrumListWrapper
SpectrumListPtr inner_
 
DataProcessingPtr dp_
 

Detailed Description

SpectrumList wrapper that recalculates precursor info on spectrum() requests.

Definition at line 37 of file SpectrumList_PrecursorRefine.hpp.

Constructor & Destructor Documentation

§ SpectrumList_PrecursorRefine() [1/2]

pwiz::analysis::SpectrumList_PrecursorRefine::SpectrumList_PrecursorRefine ( const msdata::MSData msd)

constructor needs the full MSData object for instrument info; SpectrumList_PrecursorRefine holds a reference to the original SpectrumListPtr

§ ~SpectrumList_PrecursorRefine()

pwiz::analysis::SpectrumList_PrecursorRefine::~SpectrumList_PrecursorRefine ( )

§ SpectrumList_PrecursorRefine() [2/2]

pwiz::analysis::SpectrumList_PrecursorRefine::SpectrumList_PrecursorRefine ( SpectrumList_PrecursorRefine )
private

Member Function Documentation

§ spectrum()

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

§ RefineMassVal()

double pwiz::analysis::SpectrumList_PrecursorRefine::RefineMassVal ( double  initialEstimate,
size_t  index 
) const
private

§ operator=()

SpectrumList_PrecursorRefine& pwiz::analysis::SpectrumList_PrecursorRefine::operator= ( SpectrumList_PrecursorRefine )
private

Member Data Documentation

§ impl_

boost::shared_ptr<Impl> pwiz::analysis::SpectrumList_PrecursorRefine::impl_
private

Definition at line 63 of file SpectrumList_PrecursorRefine.hpp.

§ numRefined

int pwiz::analysis::SpectrumList_PrecursorRefine::numRefined
mutableprivate

Definition at line 68 of file SpectrumList_PrecursorRefine.hpp.

§ numTotal

int pwiz::analysis::SpectrumList_PrecursorRefine::numTotal
mutableprivate

Definition at line 69 of file SpectrumList_PrecursorRefine.hpp.


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