/usr/include/pbbam/FastaReader.h is in libpbbam-dev 0.7.4+ds-1.
This file is owned by root:root, with mode 0o644.
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//
// All rights reserved.
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// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
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//
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
//
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// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
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// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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//
// File Description
/// \file FastaReader.h
/// \brief Defines the FastaReader class.
//
// Author: Derek Barnett
#ifndef FASTAREADER_H
#define FASTAREADER_H
#include "pbbam/FastaSequence.h"
#include <memory>
#include <vector>
namespace PacBio {
namespace BAM {
namespace internal { struct FastaReaderPrivate; }
///
/// \brief The FastaReader provides sequential access to FASTA records.
///
class FastaReader
{
public:
///
/// \brief Reads all FASTA sequences from a file
///
/// \param fn FASTA filename
/// \return vector of FastaSequence results
///
static std::vector<FastaSequence> ReadAll(const std::string& fn);
public:
/// \name Constructors & Related Methods
/// \{
explicit FastaReader(const std::string& fn);
FastaReader(FastaReader&& other);
FastaReader& operator=(FastaReader&& other);
~FastaReader(void);
// copy is disabled
FastaReader(const FastaReader&) = delete;
FastaReader& operator=(const FastaReader&) = delete;
/// \}
public:
/// \name Sequence Access
/// \{
///
/// \brief GetNext
///
/// \code{cpp}
///
/// FastaReader reader{ fn };
/// FastaSequence f;
/// while (reader.GetNext(f)) {
/// // do stuff with f
/// }
/// \endcode
///
/// \param[out] record
/// \return success/failure
///
bool GetNext(FastaSequence& record);
/// \}
private:
std::unique_ptr<internal::FastaReaderPrivate> d_;
};
} // namespace BAM
} // namespace PacBio
#endif // FASTAREADER_H
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