/usr/include/libpwiz/pwiz/analysis/peakdetect/PeakFinder.hpp is in libpwiz-dev 3.0.9393-1+b2.
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// $Id: PeakFinder.hpp 1318 2009-09-15 17:48:07Z dkessner $
//
//
// Original author: Darren Kessner <darren@proteowizard.org>
//
// Copyright 2009 Center for Applied Molecular Medicine
// University of Southern California, Los Angeles, CA
//
// 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 _PEAKFINDER_HPP_
#define _PEAKFINDER_HPP_
#include "pwiz/utility/misc/Export.hpp"
#include "pwiz/analysis/peakdetect/Noise.hpp"
#include "boost/shared_ptr.hpp"
namespace pwiz {
namespace analysis {
///
/// interface for finding peaks in an array of ordered pairs
///
class PWIZ_API_DECL PeakFinder
{
public:
virtual void findPeaks(const math::OrderedPairContainerRef& pairs,
std::vector<size_t>& resultIndices) const = 0;
virtual ~PeakFinder(){}
};
///
/// PeakFinder implementation based on signal-to-noise ratio
///
class PWIZ_API_DECL PeakFinder_SNR : public PeakFinder
{
public:
struct Config
{
size_t windowRadius;
double zValueThreshold;
bool preprocessWithLogarithm;
std::ostream* log;
Config(size_t _windowRadius = 2,
double _zValueThreshold = 3,
bool _preprocessWithLogarithm = true,
std::ostream* _log = 0)
: windowRadius(_windowRadius),
zValueThreshold(_zValueThreshold),
preprocessWithLogarithm(_preprocessWithLogarithm),
log(_log)
{}
};
PeakFinder_SNR(boost::shared_ptr<NoiseCalculator> noiseCalculator,
const Config& config = Config());
virtual void findPeaks(const math::OrderedPairContainerRef& pairs,
std::vector<size_t>& resultIndices) const;
private:
boost::shared_ptr<NoiseCalculator> noiseCalculator_;
Config config_;
};
} // namespace analysis
} // namespace pwiz
#endif // _PEAKFINDER_HPP_
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