/usr/include/ngs/ReferenceSequence.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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 | /*===========================================================================
*
* 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.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#ifndef _hpp_ngs_reference_sequence_
#define _hpp_ngs_reference_sequence_
#ifndef _hpp_ngs_error_msg_
#include <ngs/ErrorMsg.hpp>
#endif
#ifndef _hpp_ngs_stringref_
#include <ngs/StringRef.hpp>
#endif
#include <stdint.h>
namespace ngs
{
/*----------------------------------------------------------------------
* forwards and typedefs
*/
typedef class ReferenceSequenceItf * ReferenceSequenceRef;
/*======================================================================
* ReferenceSequence
* represents a reference sequence
*/
class ReferenceSequence
{
public:
/* getCanonicalName
* returns the accessioned name of reference, e.g. "NC_000001.11"
*/
String getCanonicalName () const
throw ( ErrorMsg );
/* getIsCircular
* returns true if reference is circular
*/
bool getIsCircular () const
throw ( ErrorMsg );
/* getLength
* returns the length of the reference sequence
*/
uint64_t getLength () const
throw ( ErrorMsg );
/* getReferenceBases
* return sub-sequence bases for Reference
* "offset" is zero-based
*/
String getReferenceBases ( uint64_t offset ) const
throw ( ErrorMsg );
String getReferenceBases ( uint64_t offset, uint64_t length ) const
throw ( ErrorMsg );
/* getReferenceChunk
* return largest contiguous chunk available of
* sub-sequence bases for Reference
* "offset" is zero-based
*
* NB - actual returned sequence may be shorter
* than requested.
*/
StringRef getReferenceChunk ( uint64_t offset ) const
throw ( ErrorMsg );
StringRef getReferenceChunk ( uint64_t offset, uint64_t length ) const
throw ( ErrorMsg );
public:
// C++ support
ReferenceSequence & operator = ( ReferenceSequenceRef ref )
throw ();
ReferenceSequence ( ReferenceSequenceRef ref )
throw ();
ReferenceSequence & operator = ( const ReferenceSequence & obj )
throw ( ErrorMsg );
ReferenceSequence ( const ReferenceSequence & obj )
throw ( ErrorMsg );
~ ReferenceSequence ()
throw ();
protected:
ReferenceSequenceRef self;
};
} // namespace ngs
#ifndef _inl_ngs_reference_sequence_
#include <ngs/inl/ReferenceSequence.hpp>
#endif
#endif // _hpp_ngs_reference_sequence_
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