1 /* $Id: psiblast_args.cpp 571333 2018-09-25 13:30:42Z fongah2 $
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 psiblast_args.cpp
31 * Implementation of the PSI-BLAST command line arguments
32 */
33 #include <ncbi_pch.hpp>
34 #include <algo/blast/blastinput/psiblast_args.hpp>
35 #include <algo/blast/api/psiblast_options.hpp>
36 #include <algo/blast/blastinput/blast_input_aux.hpp>
37 #include <algo/blast/api/phiblast_prot_options.hpp>
38 #include <algo/blast/api/version.hpp>
39
40 BEGIN_NCBI_SCOPE
41 BEGIN_SCOPE(blast)
42 USING_SCOPE(objects);
43
CPsiBlastAppArgs()44 CPsiBlastAppArgs::CPsiBlastAppArgs()
45 {
46 bool const kQueryIsProtein = true;
47 bool const kFilterByDefault = false;
48 static const string kProgram("psiblast");
49 CRef<IBlastCmdLineArgs> arg;
50 arg.Reset(new CProgramDescriptionArgs(kProgram,
51 "Position-Specific Iterated BLAST"));
52 m_Args.push_back(arg);
53 m_ClientId = kProgram + " " + CBlastVersion().Print();
54
55 static const char kDefaultTask[] = "psiblast";
56 SetTask(kDefaultTask);
57
58 m_BlastDbArgs.Reset(new CBlastDatabaseArgs);
59 m_BlastDbArgs->SetIPGFilteringSupport(true);
60 arg.Reset(m_BlastDbArgs);
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 m_HspFilteringArgs.Reset(new CHspFilteringArgs);
80 arg.Reset(m_HspFilteringArgs);
81 m_Args.push_back(arg);
82
83 arg.Reset(new CWindowSizeArg);
84 m_Args.push_back(arg);
85
86 m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein));
87 arg.Reset(m_QueryOptsArgs);
88 m_Args.push_back(arg);
89
90 m_FormattingArgs.Reset(new CFormattingArgs);
91 arg.Reset(m_FormattingArgs);
92 m_Args.push_back(arg);
93
94 m_MTArgs.Reset(new CMTArgs);
95 arg.Reset(m_MTArgs);
96 m_Args.push_back(arg);
97
98 m_RemoteArgs.Reset(new CRemoteArgs);
99 arg.Reset(m_RemoteArgs);
100 m_Args.push_back(arg);
101
102 arg.Reset(new CCompositionBasedStatsArgs);
103 m_Args.push_back(arg);
104
105 arg.Reset(new CGapTriggerArgs(kQueryIsProtein));
106 m_Args.push_back(arg);
107
108 m_PsiBlastArgs.Reset(new CPsiBlastArgs(CPsiBlastArgs::eProteinDb));
109 arg.Reset(m_PsiBlastArgs);
110 m_Args.push_back(arg);
111
112 arg.Reset(new CPssmEngineArgs);
113 m_Args.push_back(arg);
114
115 arg.Reset(new CPhiBlastArgs);
116 m_Args.push_back(arg);
117
118 m_DebugArgs.Reset(new CDebugArgs);
119 arg.Reset(m_DebugArgs);
120 m_Args.push_back(arg);
121 }
122
123 CRef<CBlastOptionsHandle>
x_CreateOptionsHandle(CBlastOptions::EAPILocality locality,const CArgs & args)124 CPsiBlastAppArgs::x_CreateOptionsHandle(CBlastOptions::EAPILocality locality,
125 const CArgs& args)
126 {
127 if (args.Exist(kArgPHIPatternFile) && args[kArgPHIPatternFile])
128 return CRef<CBlastOptionsHandle>(new CPHIBlastProtOptionsHandle(locality));
129 else
130 return CRef<CBlastOptionsHandle>(new CPSIBlastOptionsHandle(locality));
131 }
132
133 size_t
GetNumberOfIterations() const134 CPsiBlastAppArgs::GetNumberOfIterations() const
135 {
136 return m_PsiBlastArgs->GetNumberOfIterations();
137 }
138
139 CRef<objects::CPssmWithParameters>
GetInputPssm() const140 CPsiBlastAppArgs::GetInputPssm() const
141 {
142 return m_PsiBlastArgs->GetInputPssm();
143 }
144
145 void
SetInputPssm(CRef<objects::CPssmWithParameters> pssm)146 CPsiBlastAppArgs::SetInputPssm(CRef<objects::CPssmWithParameters> pssm)
147 {
148 m_PsiBlastArgs->SetInputPssm(pssm);
149 }
150
151 void
SetNumberOfIterations(unsigned int num_iters)152 CPsiBlastAppArgs::SetNumberOfIterations(unsigned int num_iters)
153 {
154 m_PsiBlastArgs->SetNumberOfIterations(num_iters);
155 }
156
157 int
GetQueryBatchSize() const158 CPsiBlastAppArgs::GetQueryBatchSize() const
159 {
160 bool is_remote = (m_RemoteArgs.NotEmpty() && m_RemoteArgs->ExecuteRemotely());
161 return blast::GetQueryBatchSize(ePSIBlast, m_IsUngapped, is_remote);
162 }
163
164 bool
SaveCheckpoint() const165 CPsiBlastAppArgs::SaveCheckpoint() const
166 {
167 return m_PsiBlastArgs->RequiresCheckPointOutput();
168 }
169
170 CNcbiOstream*
GetCheckpointStream()171 CPsiBlastAppArgs::GetCheckpointStream()
172 {
173 return m_PsiBlastArgs->GetCheckPointOutputStream();
174 }
175
176 bool
SaveAsciiPssm() const177 CPsiBlastAppArgs::SaveAsciiPssm() const
178 {
179 return m_PsiBlastArgs->RequiresAsciiPssmOutput();
180 }
181
182 CNcbiOstream*
GetAsciiPssmStream()183 CPsiBlastAppArgs::GetAsciiPssmStream()
184 {
185 return m_PsiBlastArgs->GetAsciiMatrixOutputStream();
186 }
187
188 bool
GetSaveLastPssm() const189 CPsiBlastAppArgs::GetSaveLastPssm() const
190 {
191 return m_PsiBlastArgs->GetSaveLastPssm();
192 }
193
194 END_SCOPE(blast)
195 END_NCBI_SCOPE
196
197