/usr/include/ngs/adapter/ReferenceSequenceItf.hpp is in libngs-sdk-dev 1.3.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
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* ===========================================================================
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*/
#ifndef _hpp_ngs_adapt_referencesequenceitf_
#define _hpp_ngs_adapt_referencesequenceitf_
#ifndef _hpp_ngs_adapt_refcount_
#include <ngs/adapter/Refcount.hpp>
#endif
#ifndef _h_ngs_itf_referenceitf_
#include <ngs/itf/ReferenceSequenceItf.h>
#endif
namespace ngs_adapt
{
/*----------------------------------------------------------------------
* forwards
*/
class StringItf;
/*----------------------------------------------------------------------
* ReferenceSequence
*/
class ReferenceSequenceItf : public Refcount < ReferenceSequenceItf, NGS_ReferenceSequence_v1 >
{
public:
virtual StringItf * getCanonicalName () const = 0;
virtual bool getIsCircular () const = 0;
virtual uint64_t getLength () const = 0;
virtual StringItf * getReferenceBases ( uint64_t offset, uint64_t length ) const = 0;
virtual StringItf * getReferenceChunk ( uint64_t offset, uint64_t length ) const = 0;
protected:
ReferenceSequenceItf ();
static NGS_ReferenceSequence_v1_vt ivt;
private:
static NGS_String_v1 * CC get_canon_name ( const NGS_ReferenceSequence_v1 * self, NGS_ErrBlock_v1 * err );
static bool CC is_circular ( const NGS_ReferenceSequence_v1 * self, NGS_ErrBlock_v1 * err );
static uint64_t CC get_length ( const NGS_ReferenceSequence_v1 * self, NGS_ErrBlock_v1 * err );
static NGS_String_v1 * CC get_ref_bases ( const NGS_ReferenceSequence_v1 * self, NGS_ErrBlock_v1 * err,
uint64_t offset, uint64_t length );
static NGS_String_v1 * CC get_ref_chunk ( const NGS_ReferenceSequence_v1 * self, NGS_ErrBlock_v1 * err,
uint64_t offset, uint64_t length );
};
} // namespace ngs_adapt
#endif // _hpp_ngs_adapt_referencesequenceitf_
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