/usr/include/libpwiz/pwiz/analysis/spectrum_processing/SpectrumList_ScanSummer.hpp is in libpwiz-dev 3.0.9393-1+b2.
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// $Id: SpectrumList_ScanSummer.hpp 6567 2014-08-01 20:14:32Z pcbrefugee $
//
//
// Original author: William French <william.r.french .@. vanderbilt.edu>
//
// Copyright 2008 Spielberg Family Center for Applied Proteomics
// Cedars-Sinai Medical Center, Los Angeles, California 90048
// 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_SCANSUMMER_HPP_
#define _SPECTRUMLIST_SCANSUMMER_HPP_
#include "pwiz/utility/misc/Export.hpp"
#include "pwiz/data/msdata/SpectrumListWrapper.hpp"
typedef struct {
double mz;
double intensity;
} parentIon;
typedef struct {
double precursorMZ;
double rTimeStart;
std::vector <int> indexList;
} precursorGroup;
namespace pwiz {
namespace analysis {
/// Provides a custom-sorted spectrum list
class PWIZ_API_DECL SpectrumList_ScanSummer : public msdata::SpectrumListWrapper
{
public:
SpectrumList_ScanSummer(const msdata::SpectrumListPtr& inner, double precursorTol, double rTimeTol);
void pushSpectrum(const msdata::SpectrumIdentity&);
double getPrecursorMz(const msdata::Spectrum&) const;
//void sumSubScansResample( std::vector<double> &, std::vector<double> &, size_t, msdata::DetailLevel) const;
void sumSubScansNaive( std::vector<double> &, std::vector<double> &, size_t, msdata::DetailLevel) const;
virtual size_t size() const;
virtual const msdata::SpectrumIdentity& spectrumIdentity(size_t index) const;
virtual msdata::SpectrumPtr spectrum(size_t index, bool getBinaryData = false) const;
virtual msdata::SpectrumPtr spectrum(size_t index, msdata::DetailLevel) const;
private:
double lowerMZlimit;
double upperMZlimit;
double TotalDaltons;
double precursorTol_;
double rTimeTol_;
mutable int ms2cnt;
std::vector<msdata::SpectrumIdentity> spectrumIdentities; // local cache, with fixed up index fields
std::vector<size_t> indexMap; // maps index -> original index
std::vector< precursorGroup > precursorList;
std::vector< precursorGroup > ms2RetentionTimes;
SpectrumList_ScanSummer(SpectrumList_ScanSummer&); //copy constructor
SpectrumList_ScanSummer& operator=(SpectrumList_ScanSummer&); //assignment operator
};
} // namespace analysis
} // namespace pwiz
#endif // _SPECTRUMLIST_SCANSUMMER_HPP_
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