1 /* $Id: blastx_args.cpp 631557 2021-05-19 13:52:41Z ivanov $
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 blastx_args.cpp
31 * Implementation of the BLASTX command line arguments
32 */
33
34 #include <ncbi_pch.hpp>
35 #include <algo/blast/blastinput/blastx_args.hpp>
36 #include <algo/blast/api/blastx_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
CBlastxAppArgs()44 CBlastxAppArgs::CBlastxAppArgs()
45 {
46 CRef<IBlastCmdLineArgs> arg;
47 static const string kProgram("blastx");
48 arg.Reset(new CProgramDescriptionArgs(kProgram,
49 "Translated Query-Protein 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[] = "blastx";
55 SetTask(kDefaultTask);
56 set<string> tasks;
57 tasks.insert(kDefaultTask);
58 tasks.insert("blastx-fast");
59 arg.Reset(new CTaskCmdLineArgs(tasks, kDefaultTask));
60 m_Args.push_back(arg);
61
62 m_BlastDbArgs.Reset(new CBlastDatabaseArgs);
63 m_BlastDbArgs->SetDatabaseMaskingSupport(true);
64 m_BlastDbArgs->SetIPGFilteringSupport(true);
65 arg.Reset(m_BlastDbArgs);
66 m_Args.push_back(arg);
67
68 m_StdCmdLineArgs.Reset(new CStdCmdLineArgs);
69 arg.Reset(m_StdCmdLineArgs);
70 m_Args.push_back(arg);
71
72 // N.B.: query is not protein because the options are applied on the
73 // translated query
74 arg.Reset(new CGenericSearchArgs( !kQueryIsProtein ));
75 m_Args.push_back(arg);
76
77 //Disable until OOF is supported in align manager
78 //SB-1043
79 //arg.Reset(new CFrameShiftArgs);
80 //m_Args.push_back(arg);
81
82 arg.Reset(new CLargestIntronSizeArgs);
83 m_Args.push_back(arg);
84
85 // N.B.: query is not protein because the filtering is applied on the
86 // translated query
87 arg.Reset(new CFilteringArgs( !kQueryIsProtein ));
88 m_Args.push_back(arg);
89
90 arg.Reset(new CMatrixNameArg);
91 m_Args.push_back(arg);
92
93 arg.Reset(new CWordThresholdArg);
94 m_Args.push_back(arg);
95
96 m_HspFilteringArgs.Reset(new CHspFilteringArgs);
97 arg.Reset(m_HspFilteringArgs);
98 m_Args.push_back(arg);
99
100 arg.Reset(new CWindowSizeArg);
101 m_Args.push_back(arg);
102
103 arg.Reset(new CGappedArgs);
104 m_Args.push_back(arg);
105
106 m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein));
107 arg.Reset(m_QueryOptsArgs);
108 m_Args.push_back(arg);
109
110 arg.Reset(new CGeneticCodeArgs(CGeneticCodeArgs::eQuery));
111 m_Args.push_back(arg);
112
113 m_FormattingArgs.Reset(new CFormattingArgs);
114 arg.Reset(m_FormattingArgs);
115 m_Args.push_back(arg);
116
117 m_MTArgs.Reset(new CMTArgs(CThreadable::kMinNumThreads, CMTArgs::eSplitByDB));
118 arg.Reset(m_MTArgs);
119 m_Args.push_back(arg);
120
121 m_RemoteArgs.Reset(new CRemoteArgs);
122 arg.Reset(m_RemoteArgs);
123 m_Args.push_back(arg);
124
125 arg.Reset(new CCompositionBasedStatsArgs);
126 m_Args.push_back(arg);
127
128 m_DebugArgs.Reset(new CDebugArgs);
129 arg.Reset(m_DebugArgs);
130 m_Args.push_back(arg);
131 }
132
133 CRef<CBlastOptionsHandle>
x_CreateOptionsHandle(CBlastOptions::EAPILocality locality,const CArgs & args)134 CBlastxAppArgs::x_CreateOptionsHandle(CBlastOptions::EAPILocality locality,
135 const CArgs& args)
136 {
137 _ASSERT(args.Exist(kTask));
138 _ASSERT(args[kTask].HasValue());
139 return x_CreateOptionsHandleWithTask(locality, args[kTask].AsString());
140 }
141
142 int
GetQueryBatchSize() const143 CBlastxAppArgs::GetQueryBatchSize() const
144 {
145 bool is_remote = (m_RemoteArgs.NotEmpty() && m_RemoteArgs->ExecuteRemotely());
146 return blast::GetQueryBatchSize(eBlastx, m_IsUngapped, is_remote);
147 }
148
149 /// Get the input stream
150 CNcbiIstream&
GetInputStream()151 CBlastxNodeArgs::GetInputStream()
152 {
153 if ( !m_InputStream ) {
154 abort();
155 }
156 return *m_InputStream;
157 }
158 /// Get the output stream
159 CNcbiOstream&
GetOutputStream()160 CBlastxNodeArgs::GetOutputStream()
161 {
162 return m_OutputStream;
163 }
164
CBlastxNodeArgs(const string & input)165 CBlastxNodeArgs::CBlastxNodeArgs(const string & input)
166 {
167 m_InputStream = new CNcbiIstrstream(input.c_str(), input.length());
168 }
169
~CBlastxNodeArgs()170 CBlastxNodeArgs::~CBlastxNodeArgs()
171 {
172 if (m_InputStream) {
173 free(m_InputStream);
174 m_InputStream = NULL;
175 }
176 }
177
178 int
GetQueryBatchSize() const179 CBlastxNodeArgs::GetQueryBatchSize() const
180 {
181 bool is_remote = (m_RemoteArgs.NotEmpty() && m_RemoteArgs->ExecuteRemotely());
182 return blast::GetQueryBatchSize(eBlastx, m_IsUngapped, is_remote);
183 }
184
185 CRef<CBlastOptionsHandle>
x_CreateOptionsHandle(CBlastOptions::EAPILocality locality,const CArgs & args)186 CBlastxNodeArgs::x_CreateOptionsHandle(CBlastOptions::EAPILocality locality, const CArgs& args)
187 {
188 return CBlastxAppArgs::x_CreateOptionsHandle(locality, args);
189 }
190
191 END_SCOPE(blast)
192 END_NCBI_SCOPE
193
194