1 #ifndef NGALIGN_INTERFACE__HPP
2 #define NGALIGN_INTERFACE__HPP
3 
4 /*  $Id: ngalign_interface.hpp 408317 2013-07-29 18:47:05Z grichenk $
5  * ===========================================================================
6  *
7  *                            PUBLIC DOMAIN NOTICE
8  *               National Center for Biotechnology Information
9  *
10  *  This software/database is a "United States Government Work" under the
11  *  terms of the United States Copyright Act.  It was written as part of
12  *  the author's official duties as a United States Government employee and
13  *  thus cannot be copyrighted.  This software/database is freely available
14  *  to the public for use. The National Library of Medicine and the U.S.
15  *  Government have not placed any restriction on its use or reproduction.
16  *
17  *  Although all reasonable efforts have been taken to ensure the accuracy
18  *  and reliability of the software and data, the NLM and the U.S.
19  *  Government do not and cannot warrant the performance or results that
20  *  may be obtained by using this software or data. The NLM and the U.S.
21  *  Government disclaim all warranties, express or implied, including
22  *  warranties of performance, merchantability or fitness for any particular
23  *  purpose.
24  *
25  *  Please cite the author in any work or product based on this material.
26  *
27  * ===========================================================================
28  *
29  * Authors:  Nathan Bouk
30  *
31  * File Description:
32  *
33  */
34 
35 #include <corelib/ncbistd.hpp>
36 #include <corelib/ncbiobj.hpp>
37 #include <objects/seqloc/Na_strand.hpp>
38 
39 #include <algo/align/ngalign/result_set.hpp>
40 
41 
42 BEGIN_NCBI_SCOPE
43 
44 BEGIN_SCOPE(objects)
45     class CScope;
46     class CSeq_align;
47     class CSeq_align_set;
48     class CSeq_id;
49 END_SCOPE(objects)
50 
51 BEGIN_SCOPE(blast)
52     class IQueryFactory;
53     class CLocalDbAdapter;
54     class CBlastOptionsHandle;
55     class CSearchResultSet;
56     class CSearchResults;
57 END_SCOPE(blast)
58 
59 class CSeqMasker;
60 
61 
62 typedef CRef<objects::CSeq_align_set> TAlignSetRef;
63 typedef CRef<blast::CSearchResultSet> TResultsSetRef;
64 typedef CRef<CAlignResultsSet>  TAlignResultsRef;
65 
66 
67 class ISequenceSet : public CObject
68 {
69 public:
70     virtual CRef<blast::IQueryFactory> CreateQueryFactory(
71             objects::CScope& Scope, const blast::CBlastOptionsHandle& BlastOpts) = 0;
72     virtual CRef<blast::IQueryFactory> CreateQueryFactory(
73             objects::CScope& Scope, const blast::CBlastOptionsHandle& BlastOpts,
74             const CAlignResultsSet& Alignments, int Threshold) = 0;
75     virtual CRef<blast::CLocalDbAdapter> CreateLocalDbAdapter(
76             objects::CScope& Scope, const blast::CBlastOptionsHandle& BlastOpts) = 0;
77 };
78 
79 
80 
81 class IAlignmentFactory : public CObject
82 {
83 public:
84     virtual string GetName() const = 0;
85     virtual TAlignResultsRef GenerateAlignments(objects::CScope& Scope,
86                                                 ISequenceSet* Querys,
87                                                 ISequenceSet* Subjects,
88                                                 TAlignResultsRef AccumResults) = 0;
89 };
90 
91 
92 // Low Ranks are better.
93 class IAlignmentFilter : public CObject
94 {
95 public:
96     virtual void FilterAlignments(TAlignResultsRef In,
97                                   TAlignResultsRef Out,
98                                   objects::CScope& Scope) = 0;
99     virtual unsigned int GetFilterRank() const = 0;
100 
101     static const char* KFILTER_SCORE;
102 };
103 
104 
105 
106 class IAlignmentScorer : public CObject
107 {
108 public:
109     virtual void ScoreAlignments(TAlignResultsRef Alignments,
110                                  objects::CScope& Scope) = 0;
111 };
112 
113 
114 
115 
116 END_NCBI_SCOPE
117 
118 #endif
119