ProteoWizard
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Inheritable pass-through implementation for wrapping a SpectrumList. More...
#include <SpectrumListWrapper.hpp>
Public Member Functions | |
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 SpectrumIdentity & | spectrumIdentity (size_t index) const |
access to a spectrum index More... | |
virtual SpectrumPtr | spectrum (size_t index, bool getBinaryData=false) const =0 |
retrieve a spectrum by index More... | |
virtual SpectrumPtr | spectrum (size_t index, DetailLevel detailLevel) const |
retrieve a spectrum by index More... | |
virtual const boost::shared_ptr< const DataProcessing > | dataProcessingPtr () const |
returns the data processing affecting spectra retrieved through this interface More... | |
SpectrumListPtr | inner () const |
SpectrumListPtr | innermost () const |
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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 () |
Protected Attributes | |
SpectrumListPtr | inner_ |
DataProcessingPtr | dp_ |
Inheritable pass-through implementation for wrapping a SpectrumList.
Definition at line 37 of file SpectrumListWrapper.hpp.
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inline |
Definition at line 41 of file SpectrumListWrapper.hpp.
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inlinevirtual |
returns the number of spectra
Implements pwiz::msdata::SpectrumList.
Reimplemented in pwiz::analysis::SpectrumList_Filter, pwiz::analysis::SpectrumList_Sorter, and pwiz::analysis::SpectrumList_ScanSummer.
Definition at line 49 of file SpectrumListWrapper.hpp.
Referenced by test().
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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().
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inlinevirtual |
access to a spectrum index
Implements pwiz::msdata::SpectrumList.
Reimplemented in pwiz::analysis::SpectrumList_Filter, pwiz::analysis::SpectrumList_Sorter, and pwiz::analysis::SpectrumList_ScanSummer.
Definition at line 51 of file SpectrumListWrapper.hpp.
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pure virtual |
retrieve a spectrum by index
Implements pwiz::msdata::SpectrumList.
Implemented in pwiz::analysis::SpectrumList_ChargeFromIsotope, pwiz::analysis::SpectrumList_Filter, pwiz::analysis::SpectrumList_Sorter, pwiz::analysis::SpectrumList_MZRefiner, pwiz::analysis::SpectrumList_ScanSummer, pwiz::analysis::SpectrumList_TitleMaker, pwiz::analysis::SpectrumList_PrecursorRefine, pwiz::analysis::SpectrumList_ChargeStateCalculator, pwiz::analysis::SpectrumList_PeakPicker, pwiz::analysis::SpectrumList_ZeroSamplesFilter, pwiz::msdata::SpectrumListCache, pwiz::analysis::SpectrumList_Smoother, pwiz::analysis::SpectrumList_PrecursorRecalculator, pwiz::analysis::SpectrumList_3D, pwiz::analysis::SpectrumList_LockmassRefiner, pwiz::analysis::SpectrumList_PeakFilter, pwiz::analysis::SpectrumList_MetadataFixer, pwiz::analysis::SpectrumList_MZWindow, and pwiz::analysis::SpectrumList_IonMobility.
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inlinevirtual |
retrieve a spectrum by index
Reimplemented from pwiz::msdata::SpectrumList.
Reimplemented in pwiz::analysis::SpectrumList_Filter, pwiz::analysis::SpectrumList_ScanSummer, pwiz::analysis::SpectrumList_PeakPicker, pwiz::analysis::SpectrumList_PeakFilter, and pwiz::analysis::SpectrumList_LockmassRefiner.
Definition at line 56 of file SpectrumListWrapper.hpp.
References pwiz::msdata::DetailLevel_FullData, and spectrum().
Referenced by spectrum().
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inlinevirtual |
returns the data processing affecting spectra retrieved through this interface
Reimplemented from pwiz::msdata::SpectrumList.
Definition at line 58 of file SpectrumListWrapper.hpp.
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inline |
Definition at line 60 of file SpectrumListWrapper.hpp.
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inline |
Definition at line 62 of file SpectrumListWrapper.hpp.
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protected |
Definition at line 72 of file SpectrumListWrapper.hpp.
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protected |
Definition at line 73 of file SpectrumListWrapper.hpp.