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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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 
46 
48  : CBlastProteinOptionsHandle(locality)
49 {
50  SetDefaults();
51  m_Opts->SetProgram(eBlastx);
52 }
53 
54 void
56 {
59 }
60 
61 void
63 {
65  m_Opts->SetStrandOption(objects::eNa_strand_both);
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 
94 
95 
96 /* @} */
Handle to the protein-protein options to the BLAST algorithm.
void SetSegFiltering(bool val)
Enable SEG filtering.
#define END_SCOPE(ns)
End the previously defined scope.
Definition: ncbistl.hpp:73
EAPILocality
Enumerates the possible contexts in which objects of this type can be used.
virtual void SetQueryOptionDefaults()
Overrides QueryOptionDefaults for protein options.
#define BLAST_WORD_THRESHOLD_BLASTX
default threshold (blastx)
void SetQueryOptionDefaults()
Overrides QueryOptionDefaults for blastx options.
Declares the CBlastxOptionsHandle class.
#define BLAST_GENETIC_CODE
Default genetic code for query and/or database.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:101
void SetStrandOption(objects::ENa_strand s)
void SetWordThreshold(double w)
Sets WordThreshold.
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence pro...
Translated nucl-Protein.
Definition: blast_types.hpp:60
void SetSmithWatermanMode(bool m=true)
CRef< CBlastOptions > m_Opts
Data type this class controls access to.
void SetCompositionBasedStats(ECompoAdjustModes mode)
virtual void SetScoringOptionsDefaults()
Overrides ScoringOptionsDefaults for protein options.
void SetQueryGeneticCode(int gc)
virtual void SetGappedExtensionDefaults()
Overrides GappedExtensionDefaults for protein options.
void SetLookupTableDefaults()
Overrides LookupTableDefaults for blastx options.
void SetScoringOptionsDefaults()
Overrides ScoringOptionsDefaults for blastx options.
Handle to the translated nucleotide-protein options to the BLAST algorithm.
#define _ASSERT
virtual void SetLookupTableDefaults()
Overrides LookupTableDefaults for protein options.
#define BEGIN_SCOPE(ns)
Define a new scope.
Definition: ncbistl.hpp:70
bool GetSegFiltering() const
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:98
void SetSumStatisticsMode(bool m=true)
void SetGappedExtensionDefaults()
Overrides SetGappedExtensionDefaults for blastx option.
virtual void SetHitSavingOptionsDefaults()
Overrides HitSavingOptionsDefaults for protein options.
void SetHitSavingOptionsDefaults()
Overrides HitSavingOptionsDefaults for blastx options.
Modified on Wed Feb 10 16:11:27 2016 by modify_doxy.py rev. 426318