NCBI C++ ToolKit
blast_advprot_options.cpp
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1 /* $Id: blast_advprot_options.cpp 39958 2008-11-03 20:57:20Z camacho $
2  * ===========================================================================
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26  * Authors: Tom Madden
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29 
30 /// @file blast_advprot_options.cpp
31 /// Implements the CBlastAdvancedProteinOptionsHandle class.
32 
33 #include <ncbi_pch.hpp>
35 
36 
37 /** @addtogroup AlgoBlast
38  *
39  * @{
40  */
41 
42 
44 BEGIN_SCOPE(blast)
45 
47  : CBlastProteinOptionsHandle(locality)
48 {
49  SetDefaults();
50  m_Opts->SetProgram(eBlastp);
51 }
52 
53 void
55 {
60 }
61 
62 void
64 {
66  SetSegFiltering(false); // disable SEG filtering because of eCompositionMatrixAdjust mode
67 }
68 
69 
70 END_SCOPE(blast)
72 
73 
74 /* @} */
Declares the CBlastAdvancedProteinOptionsHandle class.
@ eBlastp
Protein-Protein.
Definition: blast_types.hpp:59
Handle to the Advanced BLASTP options.
EAPILocality
Enumerates the possible contexts in which objects of this type can be used.
Handle to the protein-protein options to the BLAST algorithm.
@ eCompositionMatrixAdjust
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence pro...
virtual void SetGappedExtensionDefaults()
Overrides GappedExtensionDefaults for protein options.
void SetCompositionBasedStats(ECompoAdjustModes mode)
virtual void SetGappedExtensionDefaults()
Overrides SetGappedExtensionDefaults for advanced blastp options.
CRef< CBlastOptions > m_Opts
Data type this class controls access to.
virtual void SetQueryOptionDefaults()
Overrides QueryOptionDefaults for protein options.
virtual void SetQueryOptionDefaults()
Overrides SetQueryOptionDefaults for advanced blastp options to disable filtering.
bool GetSegFiltering() const
void SetSegFiltering(bool val)
Enable SEG filtering.
void SetSmithWatermanMode(bool m=true)
#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
#define _ASSERT
Modified on Fri Jul 19 17:13:23 2024 by modify_doxy.py rev. 669887