/usr/include/libpwiz/pwiz/utility/proteome/IPIFASTADatabase.hpp is in libpwiz-dev 3.0.9393-1+b2.
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// $Id: IPIFASTADatabase.hpp 1407 2009-10-10 17:07:39Z paragmallick $
//
//
// Original author: Darren Kessner <darren@proteowizard.org>
//
// Copyright 2006 Louis Warschaw Prostate Cancer Center
// 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 _IPIFASTADATABASE_HPP_
#define _IPIFASTADATABASE_HPP_
#include "pwiz/utility/misc/Export.hpp"
#include <memory>
#include <string>
#include <vector>
#include <iosfwd>
namespace pwiz {
namespace proteome {
/// class for accessing data in ipi.*.fasta files
class PWIZ_API_DECL IPIFASTADatabase
{
public:
/// constructor reads in entire file
IPIFASTADatabase(const std::string& filename);
~IPIFASTADatabase();
/// structure for holding peptide info
struct PWIZ_API_DECL Record
{
int id;
std::string faID;
std::string fullSeqDescription;
std::string sequence;
Record(int _id=0) : id(_id) {}
};
/// access to the data in memory
const std::vector<Record>& records() const;
/// typedef to simplify declaration of Record iterator
typedef std::vector<Record>::const_iterator const_iterator;
// begin() and end()
const_iterator begin();
const_iterator end();
private:
class Impl;
std::auto_ptr<Impl> impl_;
};
PWIZ_API_DECL std::ostream& operator<<(std::ostream& os, const IPIFASTADatabase::Record& record);
} // namespace proteome
} // namespace pwiz
#endif // _IPIFASTADATABASE_HPP_
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