NCBI C++ ToolKit
kblastp_args.cpp
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1 /* $Id: kblastp_args.cpp 77530 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.
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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>
39 
41 BEGIN_SCOPE(blast)
43 
45 {
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 
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 
104  const CArgs& args)
105 {
107 }
108 
109 int
111 {
112  return 10000;
113 }
114 
115 END_SCOPE(blast)
117 
Declares singleton objects to store the version and reference for the BLAST engine.
Declares the CBlastAdvancedProteinOptionsHandle class.
Declares the BLAST exception class.
Auxiliary classes/functions for BLAST input library.
CArgs –.
Definition: ncbiargs.hpp:379
Argument class to collect database/subject arguments.
Definition: blast_args.hpp:889
EAPILocality
Enumerates the possible contexts in which objects of this type can be used.
Handle to the protein-protein options to the BLAST algorithm.
Keeps track of the version of the BLAST engine in the NCBI C++ toolkit.
Definition: version.hpp:53
Argument class for collecting composition based statistics options.
Definition: blast_args.hpp:397
Argument class to collect debugging options.
Argument class for collecting filtering options.
Definition: blast_args.hpp:333
Argument class to collect formatting options, use this to create a CBlastFormat object.
Argument class for general search BLAST algorithm options: evalue, gap penalties, query filter string...
Definition: blast_args.hpp:292
Handles command line arguments for blastp binary.
virtual CRef< CBlastOptionsHandle > x_CreateOptionsHandle(CBlastOptions::EAPILocality locality, const CArgs &args)
@inheritDoc
virtual int GetQueryBatchSize() const
@inheritDoc
Argument class to collect options specific to KBLASTP.
Definition: blast_args.hpp:670
Argument class to collect multi-threaded arguments.
Argument class to retrieve and set the scoring matrix name BLAST algorithm option.
Definition: blast_args.hpp:278
Argument class to populate an application's name and description.
Definition: blast_args.hpp:178
Argument class to collect query options.
Definition: blast_args.hpp:775
CRef –.
Definition: ncbiobj.hpp:618
Argument class to retrieve input and output streams for a command line program.
Definition: blast_args.hpp:110
Argument class to retrieve and set the window size BLAST algorithm option.
Definition: blast_args.hpp:223
Argument class to retrieve and set the word threshold BLAST algorithm option.
Definition: blast_args.hpp:251
virtual string Print(void) const
Print version information.
Definition: version.hpp:59
void Reset(void)
Reset reference object.
Definition: ncbiobj.hpp:773
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define END_SCOPE(ns)
End the previously defined scope.
Definition: ncbistl.hpp:75
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define BEGIN_SCOPE(ns)
Define a new scope.
Definition: ncbistl.hpp:72
USING_SCOPE(objects)
Main argument class for KBLASTP application.
Modified on Sat May 18 11:40:14 2024 by modify_doxy.py rev. 669887