1 /*===========================================================================
2 *
3 *                            PUBLIC DOMAIN NOTICE
4 *               National Center for Biotechnology Information
5 *
6 *  This software/database is a "United States Government Work" under the
7 *  terms of the United States Copyright Act.  It was written as part of
8 *  the author's official duties as a United States Government employee and
9 *  thus cannot be copyrighted.  This software/database is freely available
10 *  to the public for use. The National Library of Medicine and the U.S.
11 *  Government have not placed any restriction on its use or reproduction.
12 *
13 *  Although all reasonable efforts have been taken to ensure the accuracy
14 *  and reliability of the software and data, the NLM and the U.S.
15 *  Government do not and cannot warrant the performance or results that
16 *  may be obtained by using this software or data. The NLM and the U.S.
17 *  Government disclaim all warranties, express or implied, including
18 *  warranties of performance, merchantability or fitness for any particular
19 *  purpose.
20 *
21 *  Please cite the author in any work or product based on this material.
22 *
23 * ===========================================================================
24 *
25 */
26 
27 #ifndef _hpp_ngs_itf_referenceitf_
28 #define _hpp_ngs_itf_referenceitf_
29 
30 #ifndef _hpp_ngs_itf_refcount_
31 #include <ngs/itf/Refcount.hpp>
32 #endif
33 
34 struct NGS_Reference_v1;
35 
36 namespace ngs
37 {
38 
39     /*----------------------------------------------------------------------
40      * forwards
41      */
42     class StringItf;
43     class PileupItf;
44     class AlignmentItf;
45 
46     /*----------------------------------------------------------------------
47      * Reference
48      */
49     class ReferenceItf : public Refcount < ReferenceItf, NGS_Reference_v1 >
50     {
51     public:
52 
53         StringItf * getCommonName () const
54             NGS_THROWS ( ErrorMsg );
55         StringItf * getCanonicalName () const
56             NGS_THROWS ( ErrorMsg );
57         bool getIsCircular () const
58             NGS_THROWS ( ErrorMsg );
59         bool getIsLocal () const
60             NGS_THROWS ( ErrorMsg );
61         uint64_t getLength () const
62             NGS_THROWS ( ErrorMsg );
63         StringItf * getReferenceBases ( uint64_t offset ) const
64             NGS_THROWS ( ErrorMsg );
65         StringItf * getReferenceBases ( uint64_t offset, uint64_t length ) const
66             NGS_THROWS ( ErrorMsg );
67         StringItf * getReferenceChunk ( uint64_t offset ) const
68             NGS_THROWS ( ErrorMsg );
69         StringItf * getReferenceChunk ( uint64_t offset, uint64_t length ) const
70             NGS_THROWS ( ErrorMsg );
71         uint64_t getAlignmentCount () const
72             NGS_THROWS ( ErrorMsg );
73         uint64_t getAlignmentCount ( uint32_t categories ) const
74             NGS_THROWS ( ErrorMsg );
75         AlignmentItf * getAlignment ( const char * alignmentId ) const
76             NGS_THROWS ( ErrorMsg );
77         AlignmentItf * getAlignments ( uint32_t categories ) const
78             NGS_THROWS ( ErrorMsg );
79         AlignmentItf * getAlignmentSlice ( int64_t start, uint64_t length ) const
80             NGS_THROWS ( ErrorMsg );
81         AlignmentItf * getAlignmentSlice ( int64_t start, uint64_t length, uint32_t categories ) const
82             NGS_THROWS ( ErrorMsg );
83         AlignmentItf * getFilteredAlignmentSlice ( int64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
84             NGS_THROWS ( ErrorMsg );
85         PileupItf * getPileups ( uint32_t categories ) const
86             NGS_THROWS ( ErrorMsg );
87         PileupItf * getFilteredPileups ( uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
88             NGS_THROWS ( ErrorMsg );
89         PileupItf * getPileupSlice ( int64_t start, uint64_t length ) const
90             NGS_THROWS ( ErrorMsg );
91         PileupItf * getPileupSlice ( int64_t start, uint64_t length, uint32_t categories ) const
92             NGS_THROWS ( ErrorMsg );
93         PileupItf * getFilteredPileupSlice ( int64_t start, uint64_t length, uint32_t categories, uint32_t filters, int32_t mappingQuality ) const
94             NGS_THROWS ( ErrorMsg );
95         bool nextReference ()
96             NGS_THROWS ( ErrorMsg );
97     };
98 
99 } // namespace ngs
100 
101 #endif // _hpp_ngs_itf_referenceitf_
102