NCBI C++ ToolKit
tblastx_options.cpp
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1 /* $Id: tblastx_options.cpp 33815 2007-05-04 17:18:18Z kazimird $
2  * ===========================================================================
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26  * Authors: Christiam Camacho
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29 
30 /// @file tblastx_options.cpp
31 /// Implements the CTBlastxOptionsHandle class.
32 
33 #include <ncbi_pch.hpp>
36 #include "blast_setup.hpp"
37 
38 /** @addtogroup AlgoBlast
39  *
40  * @{
41  */
42 
43 
45 BEGIN_SCOPE(blast)
46 
48  : CBlastProteinOptionsHandle(locality)
49 {
50  SetDefaults();
51  m_Opts->SetProgram(eTblastx);
52 }
53 
54 void
56 {
59 }
60 
61 void
63 {
67 }
68 
69 void
71 {
73  m_Opts->SetGappedMode(false);
74 }
75 
76 void
78 {
81 }
82 
83 void
85 {
89 }
90 
91 void
93 {
95 }
96 
97 END_SCOPE(blast)
99 
100 
101 /* @} */
#define BLAST_WORD_THRESHOLD_TBLASTX
default threshold (tblastx)
#define BLAST_GAP_X_DROPOFF_FINAL_TBLASTX
default dropoff for tblastx
#define BLAST_GENETIC_CODE
Default genetic code for query and/or database.
#define BLAST_GAP_X_DROPOFF_TBLASTX
default dropoff for tblastx
Internal auxiliary setup classes/functions for C++ BLAST APIs.
@ eTblastx
Translated nucl-Translated nucl.
Definition: blast_types.hpp:62
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-translated nucleotide options to the BLAST algorithm.
virtual void SetGappedExtensionDefaults()
Overrides GappedExtensionDefaults for protein options.
void SetStrandOption(objects::ENa_strand s)
virtual void SetHitSavingOptionsDefaults()
Overrides HitSavingOptionsDefaults for protein options.
void SetQueryOptionDefaults()
Overrides QueryOptionDefaults for tblastx options.
void SetHitSavingOptionsDefaults()
Overrides HitSavingOptionsDefaults for tblastx options.
void SetSubjectSequenceOptionsDefaults()
Overrides SubjectSequenceOptionsDefaults for tblastx options.
void SetQueryGeneticCode(int gc)
void SetLookupTableDefaults()
Overrides LookupTableDefaults for tblastx options.
CRef< CBlastOptions > m_Opts
Data type this class controls access to.
void SetWordThreshold(double w)
Sets WordThreshold.
void SetSumStatisticsMode(bool m=true)
void SetGapXDropoffFinal(double x)
virtual void SetLookupTableDefaults()
Overrides LookupTableDefaults for protein options.
virtual void SetQueryOptionDefaults()
Overrides QueryOptionDefaults for protein options.
void SetGapXDropoff(double x)
void SetGappedExtensionDefaults()
Overrides GappedExtensionDefaults for tblastx options.
virtual void SetScoringOptionsDefaults()
Overrides ScoringOptionsDefaults for protein options.
void SetDbGeneticCode(int gc)
void SetGappedMode(bool m=true)
void SetScoringOptionsDefaults()
Overrides ScoringOptionsDefaults for tblastx options.
#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
Declares the CTBlastxOptionsHandle class.
Modified on Tue Apr 23 07:38:01 2024 by modify_doxy.py rev. 669887