ProteoWizard
SpectrumList_PeakPicker.hpp
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1 //
2 // $Id$
3 //
4 //
5 // Original author: Matt Chambers <matt.chambers <a.t> vanderbilt.edu>
6 //
7 // Copyright 2008 Vanderbilt University - Nashville, TN 37232
8 //
9 // Licensed under the Apache License, Version 2.0 (the "License");
10 // you may not use this file except in compliance with the License.
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13 // http://www.apache.org/licenses/LICENSE-2.0
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21 
22 
23 #ifndef _SPECTRUMLIST_PEAKPICKER_HPP_
24 #define _SPECTRUMLIST_PEAKPICKER_HPP_
25 
26 
32 
33 
34 namespace pwiz {
35 namespace analysis {
36 
37 
38 /// SpectrumList implementation to replace peak profiles with picked peaks
40 {
41  public:
42 
44  PeakDetectorPtr algorithm,
45  bool preferVendorPeakPicking,
46  const util::IntegerSet& msLevelsToPeakPick);
47 
48 
49  static bool accept(const msdata::SpectrumListPtr& inner);
50 
51  virtual msdata::SpectrumPtr spectrum(size_t index, msdata::DetailLevel detailLevel) const;
52  virtual msdata::SpectrumPtr spectrum(size_t index, bool getBinaryData = false) const;
53 
54  const util::IntegerSet& msLevels() const { return msLevelsToPeakPick_; }
55 
56  private:
59  int mode_;
60 };
61 
62 class PWIZ_API_DECL NoVendorPeakPickingException : public std::runtime_error
63 {
64  public:
65  NoVendorPeakPickingException() : std::runtime_error("[PeakDetector::NoVendorPeakPickingException]") {}
66 };
67 
68 
69 
70 } // namespace analysis
71 } // namespace pwiz
72 
73 
74 #endif // _SPECTRUMLIST_PEAKPICKER_HPP_
pwiz::analysis::SpectrumList_PeakPicker
SpectrumList implementation to replace peak profiles with picked peaks.
Definition: SpectrumList_PeakPicker.hpp:40
pwiz::msdata::SpectrumListPtr
boost::shared_ptr< SpectrumList > SpectrumListPtr
Definition: MSData.hpp:711
pwiz::analysis::SpectrumList_PeakPicker::msLevelsToPeakPick_
const util::IntegerSet msLevelsToPeakPick_
Definition: SpectrumList_PeakPicker.hpp:58
pwiz::analysis::NoVendorPeakPickingException::NoVendorPeakPickingException
NoVendorPeakPickingException()
Definition: SpectrumList_PeakPicker.hpp:65
pwiz
Definition: ChromatogramList_Filter.hpp:36
pwiz::msdata::SpectrumListWrapper
Inheritable pass-through implementation for wrapping a SpectrumList.
Definition: SpectrumListWrapper.hpp:38
PWIZ_API_DECL
#define PWIZ_API_DECL
Definition: Export.hpp:32
pwiz::analysis::SpectrumList_PeakPicker::accept
static bool accept(const msdata::SpectrumListPtr &inner)
pwiz::analysis::SpectrumList_PeakPicker::spectrum
virtual msdata::SpectrumPtr spectrum(size_t index, bool getBinaryData=false) const
retrieve a spectrum by index
Export.hpp
pwiz::analysis::SpectrumList_PeakPicker::spectrum
virtual msdata::SpectrumPtr spectrum(size_t index, msdata::DetailLevel detailLevel) const
retrieve a spectrum by index
pwiz::analysis::SpectrumList_PeakPicker::msLevels
const util::IntegerSet & msLevels() const
Definition: SpectrumList_PeakPicker.hpp:54
pwiz::msdata::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: MSData.hpp:573
pwiz::analysis::SpectrumList_PeakPicker::algorithm_
PeakDetectorPtr algorithm_
Definition: SpectrumList_PeakPicker.hpp:57
LocalMaximumPeakDetector.hpp
pwiz::analysis::SpectrumList_PeakPicker::mode_
int mode_
Definition: SpectrumList_PeakPicker.hpp:59
CwtPeakDetector.hpp
pwiz::msdata::DetailLevel
DetailLevel
Definition: MSData.hpp:631
IntegerSet.hpp
pwiz::analysis::NoVendorPeakPickingException
Definition: SpectrumList_PeakPicker.hpp:63
pwiz::util::IntegerSet
a virtual container of integers, accessible via an iterator interface, stored as union of intervals
Definition: IntegerSet.hpp:38
SpectrumListWrapper.hpp
pwiz::analysis::SpectrumList_PeakPicker::SpectrumList_PeakPicker
SpectrumList_PeakPicker(const msdata::SpectrumListPtr &inner, PeakDetectorPtr algorithm, bool preferVendorPeakPicking, const util::IntegerSet &msLevelsToPeakPick)
pwiz::analysis::PeakDetectorPtr
boost::shared_ptr< PeakDetector > PeakDetectorPtr
Definition: PeakDetector.hpp:57