NCBI C++ ToolKit
nw_pssm_aligner.hpp
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1 #ifndef ALGO___NW_PSSM_ALIGNER__HPP
2 #define ALGO___NW_PSSM_ALIGNER__HPP
3 
4 /* $Id: nw_pssm_aligner.hpp 35543 2007-09-24 15:37:09Z papadopo $
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 * Author: Jason Papadopoulos
30 *
31 * File Description:
32 * CPSSMAligner class definition
33 *
34 * CPSSMAligner encapsulates a generic global (Needleman-Wunsch)
35 * alignment algorithm with affine gap penalty model and position-
36 * specific scoring for one or both input sequences.
37 *
38 */
39 
40 #include <corelib/ncbistd.hpp>
41 #include <corelib/ncbiobj.hpp>
42 #include <corelib/ncbi_limits.hpp>
45 
46 #include <vector>
47 #include <string>
48 
49 
50 /** @addtogroup AlgoAlignRoot
51  *
52  * @{
53  */
54 
55 
57 
58 
59 // Needleman Wunsch algorithm with position-specific scoring
60 //
61 
63 {
64 public:
65  // ctors
66  CPSSMAligner();
67 
68  CPSSMAligner(const CNWAligner::TScore** pssm1, size_t len1,
69  const char* seq2, size_t len2);
70 
71  CPSSMAligner(const double** freq1, size_t len1,
72  const double** freq2, size_t len2,
73  const SNCBIPackedScoreMatrix* scoremat,
74  const int scale = 1);
75 
76  virtual ~CPSSMAligner(void) {}
77 
78  // Compute the alignment
79  virtual CNWAligner::TScore Run(void);
80 
81  // Setters
82  void SetSequences(const char* seq1, size_t len1,
83  const char* seq2, size_t len2,
84  bool verify = true);
85 
86  void SetSequences(const CNWAligner::TScore** pssm1, size_t len1,
87  const char* seq2, size_t len2,
88  bool verify = true);
89 
90  void SetSequences(const double** freq1, size_t len1,
91  const double** freq2, size_t len2,
92  const int scale = 1);
93 
94  void SetScoreMatrix(const SNCBIPackedScoreMatrix* scoremat);
95 
96  void SetFreqScale(const int scale) {m_FreqScale = scale;}
97 
98  void SetWg (TScore value) // gap opening
99  {
100  m_StartWg = m_Wg = m_EndWg = value;
101  }
102  void SetWs (TScore value) // gap extension
103  {
104  m_StartWs = m_Ws = m_EndWs = value;
105  }
106  void SetStartWg(TScore value) { m_StartWg = value; } // gap opening
107  void SetStartWs(TScore value) { m_StartWs = value; } // gap extension
108  void SetEndWg(TScore value) { m_EndWg = value; } // gap opening
109  void SetEndWs(TScore value) { m_EndWs = value; } // gap extension
110 
111  // Getters
112  const CNWAligner::TScore** GetPssm1() const {return m_Pssm1;}
113  const char* GetSeq1() const {return m_Seq1;}
114  const double** GetFreq1() const {return m_Freq1;}
115  const double** GetFreq2() const {return m_Freq2;}
116  int GetFreqScale() const {return m_FreqScale;}
117 
118  TScore GetStartWg() const { return m_StartWg; }
119  TScore GetStartWs() const { return m_StartWs; }
120  TScore GetEndWg() const { return m_EndWg; }
121  TScore GetEndWs() const { return m_EndWs; }
123 
124  virtual TScore ScoreFromTranscript(const TTranscript& transcript,
125  size_t start1 = 0,
126  size_t start2 = 0) const;
127 
128 protected:
129 
130  // only NCBIstdaa alphabet supported
131  static const int kPSSM_ColumnSize = 28;
132 
133  // Source sequences
134  const TScore** m_Pssm1;
135  const double** m_Freq1;
136 
137  const char* m_Seq2;
138  const double** m_Freq2;
139 
140  // scale factor for position frequencies
142 
143  TScore m_StartWg;// gap opening penalty for initial gaps
144  TScore m_StartWs;// gap extension penalty for initial gaps
145  TScore m_EndWg; // gap opening penalty for terminal gaps
146  TScore m_EndWs; // gap extension penalty for terminal gaps
147 
148  // core dynamic programming
149  virtual TScore x_Align (SAlignInOut* data);
150  TScore x_AlignProfile (SAlignInOut* data);
151  TScore x_AlignPSSM (SAlignInOut* data);
152 
153  // retrieve transcript symbol for a one-character diag
154  virtual ETranscriptSymbol x_GetDiagTS(size_t i1, size_t i2) const;
155 
156  double m_DScoreMatrix[kPSSM_ColumnSize][kPSSM_ColumnSize];
157 };
158 
159 
161 
162 
163 /* @} */
164 
165 #endif /* ALGO___NW_PSSM_ALIGNER__HPP */
Include a standard set of the NCBI C++ Toolkit most basic headers.
char data[12]
Definition: iconv.c:80
void SetStartWg(TScore value)
const CNWAligner::TScore ** GetPssm1() const
const double ** GetFreq1() const
const char * GetSeq1() const
int GetFreqScale() const
virtual TScore x_Align(SAlignInOut *data)
Definition: nw_aligner.cpp:229
virtual TScore ScoreFromTranscript(const TTranscript &transcript, size_t start1=kMax_UInt, size_t start2=kMax_UInt) const
virtual ETranscriptSymbol x_GetDiagTS(size_t i1, size_t i2) const
Definition: nw_aligner.cpp:707
const char * m_Seq1
Definition: nw_aligner.hpp:295
const double ** GetFreq2() const
virtual void SetSequences(const char *seq1, size_t len1, const char *seq2, size_t len2, bool verify=true)
Definition: nw_aligner.cpp:140
SNCBIFullScoreMatrix m_ScoreMatrix
Definition: nw_aligner.hpp:281
void SetEndWs(TScore value)
TScore GetStartWs() const
const double ** m_Freq2
SNCBIFullScoreMatrix & GetMatrix()
const double ** m_Freq1
void SetFreqScale(const int scale)
const char * m_Seq2
virtual TScore Run(void)
Definition: nw_aligner.cpp:503
void SetEndWg(TScore value)
TScore GetEndWg() const
virtual ~CPSSMAligner(void)
TScore GetEndWs() const
void SetScoreMatrix(const SNCBIPackedScoreMatrix *scoremat)
void SetWs(TScore value)
TScore GetStartWg() const
void SetWg(TScore value)
void SetStartWs(TScore value)
const TScore ** m_Pssm1
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define NCBI_XALGOALIGN_EXPORT
Definition: ncbi_export.h:985
const GenericPointer< typename T::ValueType > T2 value
Definition: pointer.h:1227
#define verify(expr)
Definition: ncbi_assert.h:51
Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.
Modified on Tue Jun 25 13:30:48 2024 by modify_doxy.py rev. 669887