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pwiz::analysis::SpectrumList_TitleMaker Class Reference

SpectrumList implementation to add (or replace) a spectrum title to each spectrum according to a user-specified format. More...

#include <SpectrumList_TitleMaker.hpp>

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

Public Member Functions

 SpectrumList_TitleMaker (const msdata::MSData &msd, const std::string &format)
 The format string recognizes some keywords to replace with the appropriate field: <RunId> - Run::id <Index> - SpectrumIdentity::index <Id> - SpectrumIdentity::id (nativeID) <ScanNumber> - if the nativeID can be represented as a single number, that number, else index <ActivationType> - for the first precursor, Activation::cvParamChild("dissociation method") <IsolationMz> - for the first precursor, IsolationWindow::cvParam("isolation target m/z") <SelectedIonMz> - for the first selected ion of the first precursor, SelectedIon::cvParam("selected ion m/z") <ChargeState> - for the first selected ion of the first precursor, SelectedIon::cvParam("charge state") <SpectrumType> - Spectrum::cvParamChild("spectrum type") <ScanStartTimeInSeconds> - for the first scan, Scan::cvParam("scan start time") converted to seconds <ScanStartTimeInMinutes> - for the first scan, Scan::cvParam("scan start time") converted to minutes <BasePeakMz> - Spectrum::cvParam("base peak m/z") <BasePeakIntensity> - Spectrum::cvParam("base peak intensity") <TotalIonCurrent> - Spectrum::cvParam("total ion current") More...
 
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 ()
 

Static Public Member Functions

static bool accept (const msdata::SpectrumListPtr &inner)
 

Private Attributes

const msdata::MSDatamsd_
 
const std::string format_
 
cv::CVID nativeIdFormat_
 

Additional Inherited Members

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

Detailed Description

SpectrumList implementation to add (or replace) a spectrum title to each spectrum according to a user-specified format.

Definition at line 37 of file SpectrumList_TitleMaker.hpp.

Constructor & Destructor Documentation

§ SpectrumList_TitleMaker()

pwiz::analysis::SpectrumList_TitleMaker::SpectrumList_TitleMaker ( const msdata::MSData msd,
const std::string &  format 
)

The format string recognizes some keywords to replace with the appropriate field: <RunId> - Run::id <Index> - SpectrumIdentity::index <Id> - SpectrumIdentity::id (nativeID) <ScanNumber> - if the nativeID can be represented as a single number, that number, else index <ActivationType> - for the first precursor, Activation::cvParamChild("dissociation method") <IsolationMz> - for the first precursor, IsolationWindow::cvParam("isolation target m/z") <SelectedIonMz> - for the first selected ion of the first precursor, SelectedIon::cvParam("selected ion m/z") <ChargeState> - for the first selected ion of the first precursor, SelectedIon::cvParam("charge state") <SpectrumType> - Spectrum::cvParamChild("spectrum type") <ScanStartTimeInSeconds> - for the first scan, Scan::cvParam("scan start time") converted to seconds <ScanStartTimeInMinutes> - for the first scan, Scan::cvParam("scan start time") converted to minutes <BasePeakMz> - Spectrum::cvParam("base peak m/z") <BasePeakIntensity> - Spectrum::cvParam("base peak intensity") <TotalIonCurrent> - Spectrum::cvParam("total ion current")

Member Function Documentation

§ accept()

static bool pwiz::analysis::SpectrumList_TitleMaker::accept ( const msdata::SpectrumListPtr inner)
inlinestatic

Definition at line 58 of file SpectrumList_TitleMaker.hpp.

58 {return true;}

§ spectrum()

virtual msdata::SpectrumPtr pwiz::analysis::SpectrumList_TitleMaker::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.

Member Data Documentation

§ msd_

const msdata::MSData& pwiz::analysis::SpectrumList_TitleMaker::msd_
private

Definition at line 63 of file SpectrumList_TitleMaker.hpp.

§ format_

const std::string pwiz::analysis::SpectrumList_TitleMaker::format_
private

Definition at line 64 of file SpectrumList_TitleMaker.hpp.

§ nativeIdFormat_

cv::CVID pwiz::analysis::SpectrumList_TitleMaker::nativeIdFormat_
private

Definition at line 65 of file SpectrumList_TitleMaker.hpp.


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