NCBI C++ ToolKit
rpstblastn_options.hpp
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1 #ifndef ALGO_BLAST_API___RPSTBLASTN_OPTIONS__HPP
2 #define ALGO_BLAST_API___RPSTBLASTN_OPTIONS__HPP
3 
4 /* $Id: rpstblastn_options.hpp 63585 2014-07-11 17:28:33Z madden $
5  * ===========================================================================
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7  * PUBLIC DOMAIN NOTICE
8  * National Center for Biotechnology Information
9  *
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11  * terms of the United States Copyright Act. It was written as part of
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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.
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29  * Authors: Jason Papadopoulos
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32 
33 /// @file rpstblastn_options.hpp
34 /// Declares the CRPSTBlastnOptionsHandle class.
35 
37 
38 /** @addtogroup AlgoBlast
39  *
40  * @{
41  */
42 
44 BEGIN_SCOPE(blast)
45 
46 /// Handle to the options for translated nucleotide-RPS blast
47 ///
48 /// Adapter class for translated nucleotide - RPS BLAST searches.
49 /// Exposes an interface to allow manipulation the options that are relevant to
50 /// this type of search.
51 
54 {
55 public:
56 
57  /// Creates object with default options set
60 
61  /******************* Subject sequence options *******************/
62  /// Returns DbGeneticCode
63  int GetDbGeneticCode() const {
64  return m_Opts->GetDbGeneticCode();
65  }
66  /// Sets DbGeneticCode
67  /// @param gc DbGeneticCode [in]
68  void SetDbGeneticCode(int gc) {
69  m_Opts->SetDbGeneticCode(gc);
70  }
71 
72 protected:
73  /// Set the program and service name for remote blast.
75  {
76  m_Opts->SetRemoteProgramAndService_Blast3("tblastn", "rpsblast");
77  }
78 
79  /// Overrides SubjectSequenceOptionsDefaults for RPS-TBLASTN options
80  void SetQueryOptionDefaults();
81 
82  /// Overrides SetGappedExtensionDefaults for RPS-TBLASTN options
83  void SetGappedExtensionDefaults();
84 
85 private:
86  /// Disallow copy constructor
88  /// Disallow assignment operator
90 };
91 
92 END_SCOPE(blast)
94 
95 
96 /* @} */
97 
98 #endif /* ALGO_BLAST_API___RPSTBLASTN_OPTIONS__HPP */
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
Definition: blast_export.h:65
Declares the CBlastRPSOptionsHandle class.
EAPILocality
Enumerates the possible contexts in which objects of this type can be used.
@ eLocal
To be used for running BLAST locally.
Handle to the rpsblast options to the BLAST algorithm.
Handle to the options for translated nucleotide-RPS blast.
void SetDbGeneticCode(int gc)
Sets DbGeneticCode.
CRPSTBlastnOptionsHandle(const CRPSTBlastnOptionsHandle &rhs)
Disallow copy constructor.
int GetDbGeneticCode() const
Returns DbGeneticCode.
virtual void SetRemoteProgramAndService_Blast3()
Set the program and service name for remote blast.
CRPSTBlastnOptionsHandle & operator=(const CRPSTBlastnOptionsHandle &rhs)
Disallow assignment operator.
#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
Modified on Tue May 21 11:02:06 2024 by modify_doxy.py rev. 669887