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pwiz::msdata::SpectrumListBase Class Reference

common functionality for base SpectrumList implementations More...

#include <SpectrumListBase.hpp>

Inheritance diagram for pwiz::msdata::SpectrumListBase:
pwiz::msdata::SpectrumList MyBase pwiz::msdata::SpectrumListIonMobilityBase pwiz::msdata::SpectrumList_BTDX pwiz::msdata::SpectrumList_MGF pwiz::msdata::SpectrumList_MSn pwiz::msdata::SpectrumList_mzML pwiz::msdata::SpectrumList_mzXML pwiz::msdata::detail::SpectrumList_ABI pwiz::msdata::detail::SpectrumList_ABI_T2D pwiz::msdata::detail::SpectrumList_Shimadzu pwiz::msdata::detail::SpectrumList_UIMF pwiz::msdata::detail::SpectrumList_UNIFI

Public Member Functions

 SpectrumListBase ()
 
virtual const boost::shared_ptr< const DataProcessingdataProcessingPtr () const
 implementation of SpectrumList
 
virtual void setDataProcessingPtr (DataProcessingPtr dp)
 set DataProcessing
 
virtual void warn_once (const char *msg) const
 issues a warning once per SpectrumList instance (based on string hash)
 
- Public Member Functions inherited from pwiz::msdata::SpectrumList
virtual size_t size () const =0
 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 =0
 access to a spectrum index
 
virtual size_t find (const std::string &id) const
 find id in the spectrum index (returns size() on failure)
 
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)
 
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 (size_t index, bool getBinaryData=false) const =0
 retrieve a spectrum by index
 
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 SpectrumPtr spectrum (size_t index, DetailLevel detailLevel) const
 retrieve a spectrum by index
 
virtual ~SpectrumList ()
 

Protected Attributes

DataProcessingPtr dp_
 
const pwiz::util::IntegerSet MSLevelsNone
 

Private Attributes

std::set< size_t > warn_msg_hashes
 

Detailed Description

common functionality for base SpectrumList implementations

Definition at line 40 of file SpectrumListBase.hpp.

Constructor & Destructor Documentation

◆ SpectrumListBase()

pwiz::msdata::SpectrumListBase::SpectrumListBase ( )
inline

Definition at line 43 of file SpectrumListBase.hpp.

43: MSLevelsNone() {};
const pwiz::util::IntegerSet MSLevelsNone

Member Function Documentation

◆ dataProcessingPtr()

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

implementation of SpectrumList

Reimplemented from pwiz::msdata::SpectrumList.

Reimplemented in MyBase.

Definition at line 46 of file SpectrumListBase.hpp.

46{return dp_;}

◆ setDataProcessingPtr()

virtual void pwiz::msdata::SpectrumListBase::setDataProcessingPtr ( DataProcessingPtr  dp)
inlinevirtual

set DataProcessing

Definition at line 49 of file SpectrumListBase.hpp.

49{ dp_ = dp; }

Referenced by hackInMemoryMSData().

◆ warn_once()

virtual void pwiz::msdata::SpectrumListBase::warn_once ( const char *  msg) const
inlinevirtual

issues a warning once per SpectrumList instance (based on string hash)

Reimplemented from pwiz::msdata::SpectrumList.

Definition at line 52 of file SpectrumListBase.hpp.

53 {
54 boost::hash<const char*> H;
55 if (warn_msg_hashes.insert(H(msg)).second) // .second is true iff value is new
56 {
57 std::cerr << msg << std::endl;
58 }
59 }
H
Definition Chemistry.hpp:80

References H.

Member Data Documentation

◆ dp_

DataProcessingPtr pwiz::msdata::SpectrumListBase::dp_
protected

Definition at line 63 of file SpectrumListBase.hpp.

◆ MSLevelsNone

const pwiz::util::IntegerSet pwiz::msdata::SpectrumListBase::MSLevelsNone
protected

Definition at line 66 of file SpectrumListBase.hpp.

◆ warn_msg_hashes

std::set<size_t> pwiz::msdata::SpectrumListBase::warn_msg_hashes
mutableprivate

Definition at line 70 of file SpectrumListBase.hpp.


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