NCBI C++ ToolKit
blastx_options.cpp
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1 /* $Id: blastx_options.cpp 55051 2012-07-10 12:20:47Z madden $
2  * ===========================================================================
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5  * National Center for Biotechnology Information
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26  * Authors: Christiam Camacho
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29 
30 /// @file blastx_options.cpp
31 /// Implements the CBlastxOptionsHandle class.
32 
33 #include <ncbi_pch.hpp>
36 
37 
38 /** @addtogroup AlgoBlast
39  *
40  * @{
41  */
42 
43 
45 BEGIN_SCOPE(blast)
46 
48  : CBlastProteinOptionsHandle(locality)
49 {
50  SetDefaults();
51  m_Opts->SetProgram(eBlastx);
52 }
53 
54 void
56 {
59 }
60 
61 void
63 {
67  SetSegFiltering(false); // disable SEG filtering because of eCompositionMatrixAdjust mode
68 }
69 
70 void
72 {
77 }
78 
79 void
81 {
83 }
84 
85 void
87 {
90 }
91 
92 END_SCOPE(blast)
94 
95 
96 /* @} */
#define BLAST_WORD_THRESHOLD_BLASTX
default threshold (blastx)
#define BLAST_GENETIC_CODE
Default genetic code for query and/or database.
@ eBlastx
Translated nucl-Protein.
Definition: blast_types.hpp:60
Declares the CBlastxOptionsHandle class.
EAPILocality
Enumerates the possible contexts in which objects of this type can be used.
Handle to the protein-protein options to the BLAST algorithm.
Handle to the translated nucleotide-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)
void SetStrandOption(objects::ENa_strand s)
virtual void SetHitSavingOptionsDefaults()
Overrides HitSavingOptionsDefaults for protein options.
void SetScoringOptionsDefaults()
Overrides ScoringOptionsDefaults for blastx options.
void SetQueryGeneticCode(int gc)
void SetHitSavingOptionsDefaults()
Overrides HitSavingOptionsDefaults for blastx options.
CRef< CBlastOptions > m_Opts
Data type this class controls access to.
void SetWordThreshold(double w)
Sets WordThreshold.
void SetSumStatisticsMode(bool m=true)
void SetGappedExtensionDefaults()
Overrides SetGappedExtensionDefaults for blastx option.
virtual void SetLookupTableDefaults()
Overrides LookupTableDefaults for protein options.
virtual void SetQueryOptionDefaults()
Overrides QueryOptionDefaults for protein options.
virtual void SetScoringOptionsDefaults()
Overrides ScoringOptionsDefaults for protein options.
void SetQueryOptionDefaults()
Overrides QueryOptionDefaults for blastx options.
void SetLookupTableDefaults()
Overrides LookupTableDefaults for blastx options.
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
@ eNa_strand_both
in forward orientation
Definition: Na_strand_.hpp:68
#define _ASSERT
Modified on Wed Apr 17 13:09:29 2024 by modify_doxy.py rev. 669887