/usr/include/ngs/adapter/ReadCollectionItf.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 | /*===========================================================================
*
* 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_adapt_read_collectionitf_
#define _hpp_ngs_adapt_read_collectionitf_
#ifndef _hpp_ngs_adapt_refcount_
#include <ngs/adapter/Refcount.hpp>
#endif
#ifndef _h_ngs_itf_read_collectionitf_
#include <ngs/itf/ReadCollectionItf.h>
#endif
namespace ngs_adapt
{
/*----------------------------------------------------------------------
* forwards
*/
class ReadItf;
class StringItf;
class ReadGroupItf;
class ReferenceItf;
class AlignmentItf;
/*----------------------------------------------------------------------
* ReadCollectionItf
*/
class ReadCollectionItf : public Refcount < ReadCollectionItf, NGS_ReadCollection_v1 >
{
public:
virtual StringItf * getName () const = 0;
virtual ReadGroupItf * getReadGroups () const = 0;
virtual bool hasReadGroup ( const char * spec ) const = 0;
virtual ReadGroupItf * getReadGroup ( const char * spec ) const = 0;
virtual ReferenceItf * getReferences () const = 0;
virtual bool hasReference ( const char * spec ) const = 0;
virtual ReferenceItf * getReference ( const char * spec ) const = 0;
virtual AlignmentItf * getAlignment ( const char * alignmentId ) const = 0;
virtual AlignmentItf * getAlignments ( bool wants_primary, bool wants_secondary ) const = 0;
virtual uint64_t getAlignmentCount ( bool wants_primary, bool wants_secondary ) const = 0;
virtual AlignmentItf * getAlignmentRange ( uint64_t first, uint64_t count, bool wants_primary, bool wants_secondary ) const = 0;
virtual ReadItf * getRead ( const char * readId ) const = 0;
virtual ReadItf * getReads ( bool wants_full, bool wants_partial, bool wants_unaligned ) const = 0;
virtual uint64_t getReadCount ( bool wants_full, bool wants_partial, bool wants_unaligned ) const = 0;
virtual ReadItf * getReadRange ( uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned ) const = 0;
protected:
ReadCollectionItf ();
static NGS_ReadCollection_v1_vt ivt;
private:
static NGS_String_v1 * CC get_name ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err );
static NGS_ReadGroup_v1 * CC get_read_groups ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err );
static bool CC has_read_group ( const NGS_ReadCollection_v1 * self, const char * spec );
static NGS_ReadGroup_v1 * CC get_read_group ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err,
const char * spec );
static NGS_Reference_v1 * CC get_references ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err );
static bool CC has_reference ( const NGS_ReadCollection_v1 * self, const char * spec );
static NGS_Reference_v1 * CC get_reference ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err,
const char * spec );
static NGS_Alignment_v1 * CC get_alignment ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err,
const char * alignmentId );
static NGS_Alignment_v1 * CC get_alignments ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err,
bool wants_primary, bool wants_secondary );
static uint64_t CC get_align_count ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err,
bool wants_primary, bool wants_secondary );
static NGS_Alignment_v1 * CC get_align_range ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err,
uint64_t first, uint64_t count, bool wants_primary, bool wants_secondary );
static NGS_Read_v1 * CC get_read ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err,
const char * readId );
static NGS_Read_v1 * CC get_reads ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err,
bool wants_full, bool wants_partial, bool wants_unaligned );
static uint64_t CC get_read_count ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err,
bool wants_full, bool wants_partial, bool wants_unaligned );
static NGS_Read_v1 * CC get_read_range ( const NGS_ReadCollection_v1 * self, NGS_ErrBlock_v1 * err,
uint64_t first, uint64_t count, bool wants_full, bool wants_partial, bool wants_unaligned );
};
} // namespace ngs_adapt
#endif // _hpp_ngs_adapt_read_collectionitf_
|