NCBI C++ ToolKit
cn3d_pssm.hpp
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1 /* $Id: cn3d_pssm.hpp 33815 2007-05-04 17:18:18Z kazimird $
2 * ===========================================================================
3 *
4 * PUBLIC DOMAIN NOTICE
5 * National Center for Biotechnology Information
6 *
7 * This software/database is a "United States Government Work" under the
8 * terms of the United States Copyright Act. It was written as part of
9 * the author's official duties as a United States Government employee and
10 * thus cannot be copyrighted. This software/database is freely available
11 * to the public for use. The National Library of Medicine and the U.S.
12 * Government have not placed any restriction on its use or reproduction.
13 *
14 * Although all reasonable efforts have been taken to ensure the accuracy
15 * and reliability of the software and data, the NLM and the U.S.
16 * Government do not and cannot warrant the performance or results that
17 * may be obtained by using this software or data. The NLM and the U.S.
18 * Government disclaim all warranties, express or implied, including
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20 * purpose.
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22 * Please cite the author in any work or product based on this material.
23 *
24 * ===========================================================================
25 *
26 * Authors: Paul Thiessen
27 *
28 * File Description:
29 * new C++ PSSM construction
30 *
31 * ===========================================================================
32 */
33 
34 #ifndef CN3D_PSSM__HPP
35 #define CN3D_PSSM__HPP
36 
37 #include <corelib/ncbistd.hpp>
38 #include <corelib/ncbistre.hpp>
39 
40 #include <vector>
41 
43 
45 BEGIN_SCOPE(cd_utils)
46 class PssmMaker;
47 END_SCOPE(cd_utils)
49 
50 
51 BEGIN_SCOPE(Cn3D)
52 
54 
56 private:
58  ncbi::CRef < ncbi::objects::CPssmWithParameters > pssm;
59 
60  // store an unpacked matrix for efficient access (e.g. for GetPSSMScore())
61  typedef std::vector < int > Column;
62  std::vector < Column > scaledMatrix;
64  std::vector < int > master2consensus, consensus2master;
65  void UnpackMatrix(ncbi::cd_utils::PssmMaker& pm);
66 
67 public:
69 
70  int GetPSSMScore(unsigned char ncbistdaa, unsigned int realMasterIndex) const;
71  void OutputPSSM(ncbi::CNcbiOstream& os, const std::string& title) const;
72 
73  const ncbi::objects::CPssmWithParameters& GetPSSM(void) const { return *pssm; }
74  int MapConsensusToMaster(unsigned int consensusIndex) const { return consensus2master[consensusIndex]; }
75 };
76 
77 END_SCOPE(Cn3D)
78 
79 #endif // CN3D_PSSM__HPP
User-defined methods of the data storage class.
const ncbi::objects::CPssmWithParameters & GetPSSM(void) const
Definition: cn3d_pssm.hpp:73
std::vector< Column > scaledMatrix
Definition: cn3d_pssm.hpp:62
std::vector< int > master2consensus
Definition: cn3d_pssm.hpp:64
ncbi::CRef< ncbi::objects::CPssmWithParameters > pssm
Definition: cn3d_pssm.hpp:58
std::vector< int > Column
Definition: cn3d_pssm.hpp:61
int scalingFactor
Definition: cn3d_pssm.hpp:63
PSSMWrapper(const BlockMultipleAlignment *bma)
Definition: cn3d_pssm.cpp:63
void UnpackMatrix(ncbi::cd_utils::PssmMaker &pm)
Definition: cn3d_pssm.cpp:212
std::vector< int > consensus2master
Definition: cn3d_pssm.hpp:64
int GetPSSMScore(unsigned char ncbistdaa, unsigned int realMasterIndex) const
Definition: cn3d_pssm.cpp:315
const BlockMultipleAlignment * multiple
Definition: cn3d_pssm.hpp:57
void OutputPSSM(ncbi::CNcbiOstream &os, const std::string &title) const
Definition: cn3d_pssm.cpp:265
int MapConsensusToMaster(unsigned int consensusIndex) const
Definition: cn3d_pssm.hpp:74
Include a standard set of the NCBI C++ Toolkit most basic headers.
string
Definition: cgiapp.hpp:687
#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
IO_PREFIX::ostream CNcbiOstream
Portable alias for ostream.
Definition: ncbistre.hpp:149
NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.
Modified on Wed Apr 17 13:08:50 2024 by modify_doxy.py rev. 669887