1 /*  $Id: blastx_options.cpp 368583 2012-07-10 12:20:47Z madden $
2  * ===========================================================================
3  *
4  *                            PUBLIC DOMAIN NOTICE
5  *               National Center for Biotechnology Information
6  *
7  *  This software/database is a "United States Government Work" under the
8  *  terms of the United States Copyright Act.  It was written as part of
9  *  the author's official duties as a United States Government employee and
10  *  thus cannot be copyrighted.  This software/database is freely available
11  *  to the public for use. The National Library of Medicine and the U.S.
12  *  Government have not placed any restriction on its use or reproduction.
13  *
14  *  Although all reasonable efforts have been taken to ensure the accuracy
15  *  and reliability of the software and data, the NLM and the U.S.
16  *  Government do not and cannot warrant the performance or results that
17  *  may be obtained by using this software or data. The NLM and the U.S.
18  *  Government disclaim all warranties, express or implied, including
19  *  warranties of performance, merchantability or fitness for any particular
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22  *  Please cite the author in any work or product based on this material.
23  *
24  * ===========================================================================
25  *
26  * Authors:  Christiam Camacho
27  *
28  */
29 
30 /// @file blastx_options.cpp
31 /// Implements the CBlastxOptionsHandle class.
32 
33 #include <ncbi_pch.hpp>
34 #include <algo/blast/api/blastx_options.hpp>
35 #include <objects/seqloc/Na_strand.hpp>
36 
37 
38 /** @addtogroup AlgoBlast
39  *
40  * @{
41  */
42 
43 
44 BEGIN_NCBI_SCOPE
BEGIN_SCOPE(blast)45 BEGIN_SCOPE(blast)
46 
47 CBlastxOptionsHandle::CBlastxOptionsHandle(EAPILocality locality)
48     : CBlastProteinOptionsHandle(locality)
49 {
50     SetDefaults();
51     m_Opts->SetProgram(eBlastx);
52 }
53 
54 void
SetLookupTableDefaults()55 CBlastxOptionsHandle::SetLookupTableDefaults()
56 {
57     CBlastProteinOptionsHandle::SetLookupTableDefaults();
58     m_Opts->SetWordThreshold(BLAST_WORD_THRESHOLD_BLASTX);
59 }
60 
61 void
SetQueryOptionDefaults()62 CBlastxOptionsHandle::SetQueryOptionDefaults()
63 {
64     CBlastProteinOptionsHandle::SetQueryOptionDefaults();
65     m_Opts->SetStrandOption(objects::eNa_strand_both);
66     m_Opts->SetQueryGeneticCode(BLAST_GENETIC_CODE);
67     SetSegFiltering(false); // disable SEG filtering because of eCompositionMatrixAdjust mode
68 }
69 
70 void
SetGappedExtensionDefaults()71 CBlastxOptionsHandle::SetGappedExtensionDefaults()
72 {
73     CBlastProteinOptionsHandle::SetGappedExtensionDefaults();
74     m_Opts->SetCompositionBasedStats(eCompositionMatrixAdjust);
75     m_Opts->SetSmithWatermanMode(false);
76     _ASSERT(!m_Opts->GetSegFiltering());
77 }
78 
79 void
SetScoringOptionsDefaults()80 CBlastxOptionsHandle::SetScoringOptionsDefaults()
81 {
82     CBlastProteinOptionsHandle::SetScoringOptionsDefaults();
83 }
84 
85 void
SetHitSavingOptionsDefaults()86 CBlastxOptionsHandle::SetHitSavingOptionsDefaults()
87 {
88     CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults();
89     m_Opts->SetSumStatisticsMode();
90 }
91 
92 END_SCOPE(blast)
93 END_NCBI_SCOPE
94 
95 
96 /* @} */
97