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.
11// You may obtain a copy of the License at
12//
13// http://www.apache.org/licenses/LICENSE-2.0
14//
15// Unless required by applicable law or agreed to in writing, software
16// distributed under the License is distributed on an "AS IS" BASIS,
17// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
18// See the License for the specific language governing permissions and
19// limitations under the License.
20//
21
22
23#ifndef _SPECTRUMLIST_PEAKPICKER_HPP_
24#define _SPECTRUMLIST_PEAKPICKER_HPP_
25
26
32
33
34namespace pwiz {
35namespace 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
62class 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_
#define PWIZ_API_DECL
Definition Export.hpp:32
SpectrumList implementation to replace peak profiles with picked peaks.
virtual msdata::SpectrumPtr spectrum(size_t index, msdata::DetailLevel detailLevel) const
retrieve a spectrum by index
SpectrumList_PeakPicker(const msdata::SpectrumListPtr &inner, PeakDetectorPtr algorithm, bool preferVendorPeakPicking, const util::IntegerSet &msLevelsToPeakPick)
static bool accept(const msdata::SpectrumListPtr &inner)
virtual msdata::SpectrumPtr spectrum(size_t index, bool getBinaryData=false) const
retrieve a spectrum by index
Inheritable pass-through implementation for wrapping a SpectrumList.
a virtual container of integers, accessible via an iterator interface, stored as union of intervals
boost::shared_ptr< PeakDetector > PeakDetectorPtr
boost::shared_ptr< SpectrumList > SpectrumListPtr
Definition MSData.hpp:711
boost::shared_ptr< Spectrum > SpectrumPtr
Definition MSData.hpp:573
STL namespace.