/usr/include/libpwiz/pwiz/analysis/peakdetect/PeakelPicker.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: PeakelPicker.hpp 1191 2009-08-14 19:33:05Z chambm $
//
//
// 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 _PEAKELPICKER_HPP_
#define _PEAKELPICKER_HPP_
#include "PeakelPicker.hpp"
#include "MZRTField.hpp"
#include "pwiz/utility/misc/Export.hpp"
namespace pwiz {
namespace analysis {
///
/// interface for picking Peakels and arranging into Features;
/// note: Peakels are actually removed from the PeakelField
///
class PWIZ_API_DECL PeakelPicker
{
public:
virtual void pick(PeakelField& peakels, FeatureField& features) const = 0;
virtual ~PeakelPicker(){}
};
///
/// basic implementation
///
class PWIZ_API_DECL PeakelPicker_Basic : public PeakelPicker
{
public:
struct Config
{
std::ostream* log;
size_t minCharge;
size_t maxCharge;
size_t minMonoisotopicPeakelSize;
MZTolerance mzTolerance;
double rtTolerance;
size_t minPeakelCount;
//double intensityThreshold; // ? // some kind of tolerance to match isotope envelope
//double relativeIntensityTolerance;
Config()
: log(0),
minCharge(2),
maxCharge(5),
minMonoisotopicPeakelSize(3),
mzTolerance(10, MZTolerance::PPM),
rtTolerance(5), // seconds
minPeakelCount(3)
{}
};
PeakelPicker_Basic(const Config& config = Config()) : config_(config) {}
virtual void pick(PeakelField& peakels, FeatureField& features) const;
private:
Config config_;
};
} // namespace analysis
} // namespace pwiz
#endif // _PEAKELPICKER_HPP_
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