NCBI C++ ToolKit
deltablast_options.hpp
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1 #ifndef ALGO_BLAST_API___DELTABLAST_OPTIONS__HPP
2 #define ALGO_BLAST_API___DELTABLAST_OPTIONS__HPP
3 
4 /* $Id: deltablast_options.hpp 52627 2012-01-12 18:51:12Z boratyng $
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
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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: Greg Boratyn
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32 
33 /// @file deltablast_options.hpp
34 /// Declares the CDeltaBlastOptionsHandle class.
35 
36 
38 
39 /** @addtogroup AlgoBlast
40  *
41  * @{
42  */
43 
45 BEGIN_SCOPE(blast)
46 
47 /// Handle to the protein-protein options to the BLAST algorithm.
48 ///
49 /// Adapter class for protein-protein BLAST comparisons.
50 /// Exposes an interface to allow manipulation the options that are relevant to
51 /// this type of search.
53 {
54 public:
55 
56  /// Creates object with default options set
58  /// Destructor
60 
61  /******************* DELTA BLAST options ***********************/
62 
63  /// Get e-value threshold for including domains in Pssm calculation
64  /// @return E-value cutoff for domains
65  double GetDomainInclusionThreshold(void) const
66  { return m_Opts->GetDomainInclusionThreshold(); }
67 
68  /// Set e-value threshold for including domains in Pssm calculation
69  /// @param th E-value cutoff for domains [in]
71  { m_Opts->SetDomainInclusionThreshold(th); }
72 
73  /// Get e-value threshold for including sequences in Pssm calculation
74  /// @return E-value cutoff for sequences
75  ///
76  /// Same as GetInclusionThreshold().It was added for clear distinction
77  /// between Psi and Delta Blast inclusion thresholds
78  double GetPSIInclusionThreshold(void) const
79  {return GetInclusionThreshold(); }
80 
81  /// Set e-value threshold for including sequences in Pssm calculation
82  /// @param th E-value cutoff for sequences [in]
83  ///
84  /// Same as SetInclusionThreshold().It was added for clear distinction
85  /// between Psi and Delta Blast inclusion thresholds
87  { SetInclusionThreshold(th); }
88 
89 protected:
90 
91  /// Set the program and service name for remote blast
93  {
94  m_Opts->SetRemoteProgramAndService_Blast3("blastp", "delta_blast");
95  }
96 
97  /// Override the parent class' default for filtering query sequence (i.e.:
98  /// no filtering applied to the query by default)
99  virtual void SetQueryOptionDefaults();
100 
101  /// Override the parent class' defaults for gapped extension (i.e.:
102  /// composition based statistics 1)
103  virtual void SetGappedExtensionDefaults();
104 
105  /// Sets Delta Blast defaults
106  void SetDeltaBlastDefaults();
107 
108 private:
109  /// Disallow copy constructor
111  /// Disallow assignment operator
113 };
114 
115 END_SCOPE(blast)
117 
118 
119 /* @} */
120 
121 #endif /* ALGO_BLAST_API___DELTABLAST_OPTIONS__HPP */
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
Definition: blast_export.h:65
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 protein-protein options to the BLAST algorithm.
Handle to the protein-protein options to the BLAST algorithm.
void SetDomainInclusionThreshold(double th)
Set e-value threshold for including domains in Pssm calculation.
CDeltaBlastOptionsHandle(const CDeltaBlastOptionsHandle &rhs)
Disallow copy constructor.
CDeltaBlastOptionsHandle & operator=(const CDeltaBlastOptionsHandle &rhs)
Disallow assignment operator.
virtual void SetRemoteProgramAndService_Blast3()
Set the program and service name for remote blast.
void SetPSIInclusionThreshold(double th)
Set e-value threshold for including sequences in Pssm calculation.
double GetPSIInclusionThreshold(void) const
Get e-value threshold for including sequences in Pssm calculation.
double GetDomainInclusionThreshold(void) const
Get e-value threshold for including domains in Pssm calculation.
#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
<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n th
Declares the CPSIBlastOptionsHandle class.
Modified on Thu May 30 12:21:44 2024 by modify_doxy.py rev. 669887