1 /* $Id: kblastp_args.cpp 533962 2017-04-21 12:57:45Z 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
20 * purpose.
21 *
22 * Please cite the author in any work or product based on this material.
23 *
24 * ===========================================================================
25 *
26 * Author: Tom Madden
27 *
28 */
29
30 /** @file kblastp_args.cpp
31 * Implementation of the BLASTP command line arguments
32 */
33 #include <ncbi_pch.hpp>
34 #include <algo/blast/blastinput/kblastp_args.hpp>
35 #include <algo/blast/api/blast_advprot_options.hpp>
36 #include <algo/blast/api/blast_exception.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
CKBlastpAppArgs()44 CKBlastpAppArgs::CKBlastpAppArgs()
45 {
46 CRef<IBlastCmdLineArgs> arg;
47 static const string kProgram("kblastp");
48 arg.Reset(new CProgramDescriptionArgs(kProgram, "Protein-Protein BLAST"));
49 const bool kQueryIsProtein = true;
50 bool const kFilterByDefault = false;
51 m_Args.push_back(arg);
52 m_ClientId = kProgram + " " + CBlastVersion().Print();
53
54 m_BlastDbArgs.Reset(new CBlastDatabaseArgs(false, false, false, false, true));
55 m_BlastDbArgs->SetDatabaseMaskingSupport(false);
56 arg.Reset(m_BlastDbArgs);
57 m_Args.push_back(arg);
58
59 m_KBlastpArgs.Reset(new CKBlastpArgs);
60 arg.Reset(m_KBlastpArgs);
61 m_Args.push_back(arg);
62
63 m_StdCmdLineArgs.Reset(new CStdCmdLineArgs);
64 arg.Reset(m_StdCmdLineArgs);
65 m_Args.push_back(arg);
66
67 arg.Reset(new CGenericSearchArgs(kQueryIsProtein));
68 m_Args.push_back(arg);
69
70 arg.Reset(new CFilteringArgs(kQueryIsProtein, kFilterByDefault));
71 m_Args.push_back(arg);
72
73 arg.Reset(new CMatrixNameArg);
74 m_Args.push_back(arg);
75
76 arg.Reset(new CWordThresholdArg);
77 m_Args.push_back(arg);
78
79 arg.Reset(new CWindowSizeArg);
80 m_Args.push_back(arg);
81
82 m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein));
83 arg.Reset(m_QueryOptsArgs);
84 m_Args.push_back(arg);
85
86 m_FormattingArgs.Reset(new CFormattingArgs);
87 arg.Reset(m_FormattingArgs);
88 m_Args.push_back(arg);
89
90 m_MTArgs.Reset(new CMTArgs);
91 arg.Reset(m_MTArgs);
92 m_Args.push_back(arg);
93
94 arg.Reset(new CCompositionBasedStatsArgs);
95 m_Args.push_back(arg);
96
97 m_DebugArgs.Reset(new CDebugArgs);
98 arg.Reset(m_DebugArgs);
99 m_Args.push_back(arg);
100 }
101
102 CRef<CBlastOptionsHandle>
x_CreateOptionsHandle(CBlastOptions::EAPILocality locality,const CArgs & args)103 CKBlastpAppArgs::x_CreateOptionsHandle(CBlastOptions::EAPILocality locality,
104 const CArgs& args)
105 {
106 return CRef<CBlastOptionsHandle>(new CBlastProteinOptionsHandle(locality));
107 }
108
109 int
GetQueryBatchSize() const110 CKBlastpAppArgs::GetQueryBatchSize() const
111 {
112 return 10000;
113 }
114
115 END_SCOPE(blast)
116 END_NCBI_SCOPE
117
118