1 /* $Id: tblastx_args.cpp 500404 2016-05-04 14:59:01Z camacho $
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
20 * purpose.
21 *
22 * Please cite the author in any work or product based on this material.
23 *
24 * ===========================================================================
25 *
26 * Author: Christiam Camacho
27 *
28 */
29
30 /** @file tblastx_args.cpp
31 * Implementation of the TBLASTX command line arguments
32 */
33
34 #include <ncbi_pch.hpp>
35 #include <algo/blast/blastinput/tblastx_args.hpp>
36 #include <algo/blast/api/tblastx_options.hpp>
37 #include <algo/blast/blastinput/blast_input_aux.hpp>
38 #include <algo/blast/api/version.hpp>
39
40 BEGIN_NCBI_SCOPE
41 BEGIN_SCOPE(blast)
42 USING_SCOPE(objects);
43
CTblastxAppArgs()44 CTblastxAppArgs::CTblastxAppArgs()
45 {
46 CRef<IBlastCmdLineArgs> arg;
47 static const string kProgram("tblastx");
48 arg.Reset(new CProgramDescriptionArgs(kProgram,
49 "Translated Query-Translated Subject BLAST"));
50 const bool kQueryIsProtein = false;
51 m_Args.push_back(arg);
52 m_ClientId = kProgram + " " + CBlastVersion().Print();
53
54 static const char kDefaultTask[] = "tblastx";
55 SetTask(kDefaultTask);
56
57 m_BlastDbArgs.Reset(new CBlastDatabaseArgs);
58 m_BlastDbArgs->SetDatabaseMaskingSupport(true);
59 arg.Reset(m_BlastDbArgs);
60 m_Args.push_back(arg);
61
62 m_StdCmdLineArgs.Reset(new CStdCmdLineArgs);
63 arg.Reset(m_StdCmdLineArgs);
64 m_Args.push_back(arg);
65
66 // N.B.: query is not protein because the options are applied on the
67 // translated query
68 arg.Reset(new CGenericSearchArgs( !kQueryIsProtein, false, false, true));
69 m_Args.push_back(arg);
70
71 /*arg.Reset(new CFrameShiftArgs);
72 m_Args.push_back(arg);*/
73
74 arg.Reset(new CLargestIntronSizeArgs);
75 m_Args.push_back(arg);
76
77 // N.B.: this is because the filtering is applied on the translated query
78 arg.Reset(new CFilteringArgs( !kQueryIsProtein ));
79 m_Args.push_back(arg);
80
81 arg.Reset(new CMatrixNameArg);
82 m_Args.push_back(arg);
83
84 arg.Reset(new CWordThresholdArg);
85 m_Args.push_back(arg);
86
87 m_HspFilteringArgs.Reset(new CHspFilteringArgs);
88 arg.Reset(m_HspFilteringArgs);
89 m_Args.push_back(arg);
90
91 arg.Reset(new CWindowSizeArg);
92 m_Args.push_back(arg);
93
94 m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein));
95 arg.Reset(m_QueryOptsArgs);
96 m_Args.push_back(arg);
97
98 arg.Reset(new CGeneticCodeArgs(CGeneticCodeArgs::eQuery));
99 m_Args.push_back(arg);
100
101 arg.Reset(new CGeneticCodeArgs(CGeneticCodeArgs::eDatabase));
102 m_Args.push_back(arg);
103
104 m_FormattingArgs.Reset(new CFormattingArgs);
105 arg.Reset(m_FormattingArgs);
106 m_Args.push_back(arg);
107
108 m_MTArgs.Reset(new CMTArgs);
109 arg.Reset(m_MTArgs);
110 m_Args.push_back(arg);
111
112 m_RemoteArgs.Reset(new CRemoteArgs);
113 arg.Reset(m_RemoteArgs);
114 m_Args.push_back(arg);
115
116 m_DebugArgs.Reset(new CDebugArgs);
117 arg.Reset(m_DebugArgs);
118 m_Args.push_back(arg);
119 }
120
121 CRef<CBlastOptionsHandle>
x_CreateOptionsHandle(CBlastOptions::EAPILocality locality,const CArgs &)122 CTblastxAppArgs::x_CreateOptionsHandle(CBlastOptions::EAPILocality locality,
123 const CArgs& /*args*/)
124 {
125 return CRef<CBlastOptionsHandle>(new CTBlastxOptionsHandle(locality));
126 }
127
128 int
GetQueryBatchSize() const129 CTblastxAppArgs::GetQueryBatchSize() const
130 {
131 bool is_remote = (m_RemoteArgs.NotEmpty() && m_RemoteArgs->ExecuteRemotely());
132 return blast::GetQueryBatchSize(eTblastx, m_IsUngapped, is_remote);
133 }
134
135 END_SCOPE(blast)
136 END_NCBI_SCOPE
137
138