NCBI C++ ToolKit
deltablast_options.cpp
Go to the documentation of this file.

Go to the SVN repository for this file.

1 /* $Id: deltablast_options.cpp 52298 2011-12-14 20:08:44Z boratyng $
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  * Authors: Greg Boratyn
27  *
28  */
29 
30 /// @file deltablast_options.cpp
31 /// Implements the CDeltaBlastOptionsHandle class.
32 
33 #include <ncbi_pch.hpp>
35 #include "blast_setup.hpp"
36 
37 /** @addtogroup AlgoBlast
38  *
39  * @{
40  */
41 
42 
44 BEGIN_SCOPE(blast)
45 
47  : CPSIBlastOptionsHandle(locality)
48 {
49  SetDefaults();
50  m_Opts->SetProgram(eDeltaBlast);
51  if (m_Opts->GetLocality() == CBlastOptions::eRemote) {
52  return;
53  }
54  SetDeltaBlastDefaults();
55 }
56 
57 void
59 {
60  m_Opts->ClearFilterOptions(); // turn off all filtering.
61 }
62 
64 {
67 }
68 
70 {
73 }
74 
75 END_SCOPE(blast)
77 
78 
79 /* @} */
#define DELTA_INCLUSION_ETHRESH
Inclusion threshold for DELTA-BLAST.
#define PSI_PSEUDO_COUNT_CONST
Pseudo-count constant for PSI-BLAST.
Internal auxiliary setup classes/functions for C++ BLAST APIs.
@ eDeltaBlast
Delta Blast.
Definition: blast_types.hpp:71
EAPILocality
Enumerates the possible contexts in which objects of this type can be used.
@ eRemote
To be used when running BLAST remotely.
Handle to the protein-protein options to the BLAST algorithm.
Handle to the protein-protein options to the BLAST algorithm.
@ eCompositionBasedStats
Composition-based statistics as in NAR 29:2994-3005, 2001.
Declares the CDeltaBlastOptionsHandle class.
void SetInclusionThreshold(double u)
void SetCompositionBasedStats(ECompoAdjustModes mode)
virtual void SetQueryOptionDefaults()
Override the parent class' default for filtering query sequence (i.e.
void SetPseudoCount(int u)
void SetDeltaBlastDefaults()
Sets Delta Blast defaults.
virtual void SetGappedExtensionDefaults()
Overrides SetGappedExtensionDefaults for advanced blastp options.
CRef< CBlastOptions > m_Opts
Data type this class controls access to.
virtual void SetGappedExtensionDefaults()
Override the parent class' defaults for gapped extension (i.e.
#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
Modified on Sun Apr 14 05:29:10 2024 by modify_doxy.py rev. 669887