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//
// $Id$
//
//
// Original author: Darren Kessner <darren@proteowizard.org>
//
// Copyright 2007 Spielberg Family Center for Applied Proteomics
// Cedars Sinai Medical Center, Los Angeles, California 90048
//
// 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 _ISOTOPEENVELOPEESTIMATOR_HPP_
#define _ISOTOPEENVELOPEESTIMATOR_HPP_
#include "pwiz/utility/misc/Export.hpp"
#include "Chemistry.hpp"
#include "IsotopeCalculator.hpp"
namespace pwiz {
namespace chemistry {
/// Class used for calculating a theoretical isotope envelope for a given mass,
/// based on an estimate of the elemental composition for that mass. For peptides,
/// the elemental composition estimate is based on the average elemental composition
/// of amino acid residues. Mass distributions are calculated on construction of the
/// object and cached for quick access.
class PWIZ_API_DECL IsotopeEnvelopeEstimator
{
public:
struct PWIZ_API_DECL Config
{
enum Type {Peptide};
Type type;
unsigned int cacheSize;
double cacheMaxMass;
int normalization;
const IsotopeCalculator* isotopeCalculator; // must be valid during construction only
Config()
: type(Peptide),
cacheSize(10000),
cacheMaxMass(100000),
normalization(IsotopeCalculator::NormalizeMass | // monoisotopic == 0
IsotopeCalculator::NormalizeAbundance), // norm_2 == 1
isotopeCalculator(0)
{}
};
IsotopeEnvelopeEstimator(const Config& config);
~IsotopeEnvelopeEstimator();
MassDistribution isotopeEnvelope(double mass) const;
private:
class Impl;
std::auto_ptr<Impl> impl_;
// no copying
IsotopeEnvelopeEstimator(const IsotopeEnvelopeEstimator&);
IsotopeEnvelopeEstimator& operator=(const IsotopeEnvelopeEstimator&);
};
} // namespace chemistry
} // namespace pwiz
#endif // _ISOTOPEENVELOPEESTIMATOR_HPP_
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