/usr/include/libpwiz/pwiz/analysis/spectrum_processing/SpectrumList_PeakPicker.hpp is in libpwiz-dev 3.0.9393-1+b2.
This file is owned by root:root, with mode 0o644.
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// $Id: SpectrumList_PeakPicker.hpp 9035 2015-10-24 18:58:07Z pcbrefugee $
//
//
// Original author: Matt Chambers <matt.chambers <a.t> vanderbilt.edu>
//
// Copyright 2008 Vanderbilt University - Nashville, TN 37232
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
#ifndef _SPECTRUMLIST_PEAKPICKER_HPP_
#define _SPECTRUMLIST_PEAKPICKER_HPP_
#include "pwiz/utility/misc/Export.hpp"
#include "pwiz/utility/misc/IntegerSet.hpp"
#include "pwiz/data/msdata/SpectrumListWrapper.hpp"
#include "pwiz/analysis/common/LocalMaximumPeakDetector.hpp"
#include "pwiz/analysis/common/CwtPeakDetector.hpp"
namespace pwiz {
namespace analysis {
/// SpectrumList implementation to replace peak profiles with picked peaks
class PWIZ_API_DECL SpectrumList_PeakPicker : public msdata::SpectrumListWrapper
{
public:
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, msdata::DetailLevel detailLevel) const;
virtual msdata::SpectrumPtr spectrum(size_t index, bool getBinaryData = false) const;
private:
PeakDetectorPtr algorithm_;
const util::IntegerSet msLevelsToPeakPick_;
int mode_;
};
class PWIZ_API_DECL NoVendorPeakPickingException : public std::runtime_error
{
public:
NoVendorPeakPickingException() : std::runtime_error("[PeakDetector::NoVendorPeakPickingException]") {}
};
} // namespace analysis
} // namespace pwiz
#endif // _SPECTRUMLIST_PEAKPICKER_HPP_
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