/usr/include/libpwiz/pwiz/analysis/peptideid/PeptideID.hpp is in libpwiz-dev 3.0.9393-1+b2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// $Id: PeptideID.hpp 3095 2011-11-01 21:12:23Z broter $
//
//
// Original author: Darren Kessner <darren@proteowizard.org>
// Modifying author: Robert Burke <Robert.Burke@cshs.org>
//
// Copyright 2008 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 _PEPTIDEID_HPP_
#define _PEPTIDEID_HPP_
#include "pwiz/utility/misc/Export.hpp"
#include <boost/shared_ptr.hpp>
#include <boost/iterator/iterator_facade.hpp>
#include <string>
#include <vector>
#include <iterator>
namespace pwiz {
namespace peptideid {
/// This is an interface for classes that allow access to data sources
/// of identified peptides.
class PWIZ_API_DECL PeptideID
{
public:
struct PWIZ_API_DECL Location
{
std::string nativeID;
double mz;
double retentionTimeSec;
Location(){}
Location(std::string nativeID, double retentionTimeSec, double mz)
: nativeID(nativeID), mz(mz), retentionTimeSec(retentionTimeSec)
{}
};
struct PWIZ_API_DECL Record
{
std::string nativeID;
std::string sequence;
std::string protein_descr;
double mz;
double retentionTimeSec;
double normalizedScore; // in [0,1]
Record() : normalizedScore(0) {}
Record(const Record& record)
: nativeID(record.nativeID),
sequence(record.sequence),
protein_descr(record.protein_descr),
mz(record.mz),
retentionTimeSec(record.retentionTimeSec),
normalizedScore(record.normalizedScore)
{
}
};
/**
* Interface for
*/
struct IteratorInternal {
virtual void increment() = 0;
virtual bool equal(const boost::shared_ptr<IteratorInternal>& li) const = 0;
virtual const PeptideID::Record& dereference() const = 0;
};
/**
* Iterator for
*/
class Iterator : public boost::iterator_facade<Iterator,
const PeptideID::Record,
boost::forward_traversal_tag>
{
public:
Iterator() {}
Iterator(const Iterator& it) : pimpl(it.pimpl) {}
Iterator(boost::shared_ptr<PeptideID::IteratorInternal> pimpl)
: pimpl(pimpl)
{}
protected:
friend class boost::iterator_core_access;
void increment() { pimpl->increment(); }
bool equal(const PeptideID::Iterator& li) const
{
return pimpl->equal(li.pimpl);
}
const PeptideID::Record& dereference() const
{
return pimpl->dereference();
}
boost::shared_ptr<PeptideID::IteratorInternal> pimpl;
};
virtual Record record(const Location& location) const = 0;
virtual ~PeptideID() {}
virtual Iterator begin() const = 0;
virtual Iterator end() const = 0;
};
struct nativeID_less
{
bool operator()(const PeptideID::Record& a, const PeptideID::Record& b) const
{
return atof(a.nativeID.c_str()) < atof(b.nativeID.c_str());
}
};
class location_less
{
public:
bool operator()(const PeptideID::Location& a, const PeptideID::Location& b) const
{
return a.nativeID.compare(b.nativeID) < 0 && a.mz < b.mz && a.retentionTimeSec < b.retentionTimeSec;
}
};
} // namespace peptideid
} // namespace pwiz
#endif // _PEPTIDEID_HPP_
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