1 /* $Id: deltablast_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: Greg Boratyn
27 *
28 */
29
30 /** @file deltablast_args.cpp
31 * Implementation of the DELTA-BLAST command line arguments
32 */
33 #include <ncbi_pch.hpp>
34 #include <algo/blast/blastinput/deltablast_args.hpp>
35 #include <algo/blast/api/deltablast_options.hpp>
36 #include <algo/blast/blastinput/blast_input_aux.hpp>
37 #include <algo/blast/api/version.hpp>
38
39 BEGIN_NCBI_SCOPE
40 BEGIN_SCOPE(blast)
41 USING_SCOPE(objects);
42
CDeltaBlastAppArgs()43 CDeltaBlastAppArgs::CDeltaBlastAppArgs()
44 {
45 static const string kProgram("deltablast");
46 CRef<IBlastCmdLineArgs> arg;
47 arg.Reset(new CProgramDescriptionArgs(kProgram, "Domain enhanced lookup "
48 "time accelarated BLAST"));
49
50 m_Args.push_back(arg);
51
52 bool const kQueryIsProtein = true;
53 bool const kFilterByDefault = false;
54 bool const kIsDeltaBlast = true;
55 bool const kIsCBS2and3Supported = false;
56 m_ClientId = kProgram + " " + CBlastVersion().Print();
57
58 static const char kDefaultTask[] = "deltablast";
59 SetTask(kDefaultTask);
60
61 m_BlastDbArgs.Reset(new CBlastDatabaseArgs);
62 arg.Reset(m_BlastDbArgs);
63 m_Args.push_back(arg);
64
65 m_StdCmdLineArgs.Reset(new CStdCmdLineArgs);
66 arg.Reset(m_StdCmdLineArgs);
67 m_Args.push_back(arg);
68
69 arg.Reset(new CGenericSearchArgs(kQueryIsProtein));
70 m_Args.push_back(arg);
71
72 arg.Reset(new CFilteringArgs(kQueryIsProtein, kFilterByDefault));
73 m_Args.push_back(arg);
74
75 arg.Reset(new CMatrixNameArg);
76 m_Args.push_back(arg);
77
78 arg.Reset(new CWordThresholdArg);
79 m_Args.push_back(arg);
80
81 m_HspFilteringArgs.Reset(new CHspFilteringArgs);
82 arg.Reset(m_HspFilteringArgs);
83 m_Args.push_back(arg);
84
85 arg.Reset(new CWindowSizeArg);
86 m_Args.push_back(arg);
87
88 m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein));
89 arg.Reset(m_QueryOptsArgs);
90 m_Args.push_back(arg);
91
92 m_FormattingArgs.Reset(new CFormattingArgs);
93 arg.Reset(m_FormattingArgs);
94 m_Args.push_back(arg);
95
96 m_MTArgs.Reset(new CMTArgs);
97 arg.Reset(m_MTArgs);
98 m_Args.push_back(arg);
99
100 m_RemoteArgs.Reset(new CRemoteArgs);
101 arg.Reset(m_RemoteArgs);
102 m_Args.push_back(arg);
103
104 arg.Reset(new CCompositionBasedStatsArgs(kIsCBS2and3Supported,
105 kDfltArgCompBasedStatsDelta));
106 m_Args.push_back(arg);
107
108 arg.Reset(new CGapTriggerArgs(kQueryIsProtein));
109 m_Args.push_back(arg);
110
111 m_PsiBlastArgs.Reset(new CPsiBlastArgs(CPsiBlastArgs::eProteinDb,
112 kIsDeltaBlast));
113 arg.Reset(m_PsiBlastArgs);
114 m_Args.push_back(arg);
115
116 arg.Reset(new CPssmEngineArgs(kIsDeltaBlast));
117 m_Args.push_back(arg);
118
119 m_DeltaBlastArgs.Reset(new CDeltaBlastArgs());
120 arg.Reset(m_DeltaBlastArgs);
121 m_Args.push_back(arg);
122
123 m_DebugArgs.Reset(new CDebugArgs);
124 arg.Reset(m_DebugArgs);
125 m_Args.push_back(arg);
126 }
127
128 int
GetQueryBatchSize(void) const129 CDeltaBlastAppArgs::GetQueryBatchSize(void) const
130 {
131 bool is_remote = (m_RemoteArgs.NotEmpty() && m_RemoteArgs->ExecuteRemotely());
132 return blast::GetQueryBatchSize(eDeltaBlast, m_IsUngapped, is_remote);
133 }
134
135 CRef<CBlastOptionsHandle>
x_CreateOptionsHandle(CBlastOptions::EAPILocality locality,const CArgs & args)136 CDeltaBlastAppArgs::x_CreateOptionsHandle(CBlastOptions::EAPILocality locality,
137 const CArgs& args)
138 {
139 return CRef<CBlastOptionsHandle>(new CDeltaBlastOptionsHandle(locality));
140 }
141
142 bool
GetSaveLastPssm(void) const143 CDeltaBlastAppArgs::GetSaveLastPssm(void) const
144 {
145 return m_PsiBlastArgs->GetSaveLastPssm();
146 }
147
148
149 END_SCOPE(blast)
150 END_NCBI_SCOPE
151
152