NCBI C++ ToolKit
alignment_scorer.hpp
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1 #ifndef NGALIGN_ALIGNMENT_SCORER__HPP
2 #define NGALIGN_ALIGNMENT_SCORER__HPP
3 
4 /* $Id: alignment_scorer.hpp 59290 2013-08-09 15:01:46Z whlavina $
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>
38 
41 #include <objmgr/scope.hpp>
45 
46 
48 
49 
51 
53  class CScope;
54  class CSeq_align;
55  class CSeq_align_set;
56  class CSeq_id;
57  class CDense_seg;
59 
60 
61 
63 {
64 public:
65  enum EOptions {
68  eDefault = eNone
69  };
70  typedef int TOptions;
71 
73  : m_Options(options) { ; }
74 
75  void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope);
76 
77 private:
79 };
80 
81 
83 {
84 public:
86 
87  void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope);
88 };
89 
90 
92 {
93 public:
95 
96  void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope);
97 };
98 
99 
101 {
102 public:
104 
105  void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope);
106 };
107 
108 
110 {
111 public:
112  CWeightedIdentityScorer(double K = 0.02) : m_K(K) { ; }
113 
114  void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope);
115 
116 private:
117  double m_K;
118 };
119 
120 
122 {
123 public:
124  CHangScorer() { ; }
125 
126  void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope);
127 
128 private:
129 };
130 
131 
132 
134 {
135 public:
136  COverlapScorer(TSeqPos Slop=10) : m_Slop(Slop) { ; }
137 
138  void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope);
139 
140 private:
142 };
143 
144 
146 {
147 public:
148  CClippedScorer(double K = 0.02) : m_K(K) { ; }
149 
150  void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope);
151 
152 private:
153  double m_K;
154 };
155 
156 
158 {
159 public:
161 
162  void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope& Scope);
163 
164 private:
165 
167  list<CRef<objects::CSeq_id> >& CompIds);
169  TSeqPos Start, TSeqPos Stop,
170  list<CRef<objects::CSeq_id> >& CompIds);
172  TSeqPos Start, TSeqPos Stop,
173  list<CRef<objects::CSeq_id> >& CompIds);
174 
175  void x_GetCompList(const objects::CSeq_id& Id,
176  TSeqPos Start, TSeqPos Stop,
177  list<CRef<objects::CSeq_id> >& CompIds,
178  objects::CScope& Scope);
179 
180  bool x_CompareCompLists(list<CRef<objects::CSeq_id> >& QueryIds,
181  list<CRef<objects::CSeq_id> >& SubjectIds);
182 
183 };
184 
185 
186 
187 
189 
190 #endif
@ eNone
None specified.
Definition: blast_def.h:326
CBioseq_Handle –.
CBlastScorer(TOptions options=eDefault)
CClippedScorer(double K=0.02)
void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)
void x_GetCompList(const objects::CSeq_id &Id, TSeqPos Start, TSeqPos Stop, list< CRef< objects::CSeq_id > > &CompIds, objects::CScope &Scope)
void x_GetSeqHistCompList(CBioseq_Handle Handle, TSeqPos Start, TSeqPos Stop, list< CRef< objects::CSeq_id > > &CompIds)
void x_GetDeltaExtCompList(CBioseq_Handle Handle, TSeqPos Start, TSeqPos Stop, list< CRef< objects::CSeq_id > > &CompIds)
void x_GetUserCompList(CBioseq_Handle Handle, list< CRef< objects::CSeq_id > > &CompIds)
void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)
bool x_CompareCompLists(list< CRef< objects::CSeq_id > > &QueryIds, list< CRef< objects::CSeq_id > > &SubjectIds)
void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)
void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)
void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)
COverlapScorer(TSeqPos Slop=10)
void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)
void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)
CRef –.
Definition: ncbiobj.hpp:618
CScope –.
Definition: scope.hpp:92
void ScoreAlignments(TAlignResultsRef Alignments, objects::CScope &Scope)
CWeightedIdentityScorer(double K=0.02)
Include a standard set of the NCBI C++ Toolkit most basic headers.
unsigned int TSeqPos
Type for sequence locations and lengths.
Definition: ncbimisc.hpp:875
@ eDefault
Definition: ncbi_types.h:112
#define Handle
Definition: ncbistd.hpp:119
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define END_SCOPE(ns)
End the previously defined scope.
Definition: ncbistl.hpp:75
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define BEGIN_SCOPE(ns)
Define a new scope.
Definition: ncbistl.hpp:72
Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.
Modified on Mon Jun 17 05:11:00 2024 by modify_doxy.py rev. 669887