/usr/include/libpwiz/pwiz/analysis/peptideid/PeptideID_pepXML.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: PeptideID_pepXML.hpp 3095 2011-11-01 21:12:23Z broter $
//
//
// Original author: Robert Burke <robert.burke@cshs.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 _PEPTIDEID_PEPXML_HPP_
#define _PEPTIDEID_PEPXML_HPP_
#include "pwiz/utility/misc/Export.hpp"
#include <map>
#include <boost/shared_ptr.hpp>
#include "PeptideID.hpp"
namespace pwiz {
namespace peptideid {
/// This class allows access to identified proteins in PeptideProphet files.
/// A PeptideID_pepXML object is contructed with either the path to a
/// PeptideProphet format file (*.pep.xml), or an std::istream open to
/// the beginning of a pep.xml file.
class PWIZ_API_DECL PeptideID_pepXml : public PeptideID
{
public:
/// Constructor taking path to input file in std::string.
PeptideID_pepXml(const std::string& filename);
/// Constructor taking path to input file from const char*.
PeptideID_pepXml(const char* filename);
/// Constructor taking std::istream as input.
PeptideID_pepXml(std::istream* in);
/// Destructor.
virtual ~PeptideID_pepXml() {}
/// Returns the Record object associated with the given nativeID.
/// A range_error is thrown if the nativeID isn't associated with
/// a Record.
virtual Record record(const Location& location) const;
virtual std::multimap<double, boost::shared_ptr<PeptideID::Record> >::const_iterator
record(double retention_time_sec) const;
virtual Iterator begin() const;
virtual Iterator end() const;
private:
class Impl;
boost::shared_ptr<Impl> pimpl;
};
} // namespace peptideid
} // namespace pwiz
#endif // _PEPTIDEID_PEPXML_HPP_
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