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

Go to the SVN repository for this file.

1 /* $Id: psiblast_options.cpp 62310 2014-04-01 15:13:51Z 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  * Authors: Kevin Bealer
27  *
28  */
29 
30 /// @file psiblast_options.cpp
31 /// Implements the CPSIBlastOptionsHandle 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 
48 {
49  SetDefaults();
50  m_Opts->SetProgram(ePSIBlast);
51  if (m_Opts->GetLocality() == CBlastOptions::eRemote) {
52  return;
53  }
54  SetPSIBlastDefaults();
55 }
56 
57 void
59 {
60  m_Opts->ClearFilterOptions(); // turn off all filtering.
61 }
62 
64 {
67 }
68 
70 {
75 }
76 
77 END_SCOPE(blast)
79 
80 
81 /* @} */
#define PSI_INCLUSION_ETHRESH
Defaults for PSI-BLAST and DELTA-BLAST options.
#define PSI_PSEUDO_COUNT_CONST
Pseudo-count constant for PSI-BLAST.
#define BLAST_GENETIC_CODE
Default genetic code for query and/or database.
#define BLAST_WORD_THRESHOLD_TBLASTN
default neighboring threshold (tblastn/rpstblastn)
Internal auxiliary setup classes/functions for C++ BLAST APIs.
@ ePSIBlast
PSI Blast.
Definition: blast_types.hpp:67
@ ePSITblastn
PSI Tblastn.
Definition: blast_types.hpp:68
Handle to the Advanced BLASTP options.
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.
void SetInclusionThreshold(double u)
void SetPseudoCount(int u)
CRef< CBlastOptions > m_Opts
Data type this class controls access to.
void SetWordThreshold(double w)
Sets WordThreshold.
void SetProgram(EProgram p)
Sets the task this object is best suited for.
void SetDbGeneticCode(int gc)
virtual void SetQueryOptionDefaults()
Override the parent class' default for filtering query sequence (i.e.
void SetPSITblastnDefaults()
Sets default options for psi tblastn search.
void SetSmithWatermanMode(bool m=true)
void SetPSIBlastDefaults()
Sets PSIBlastDefaults.
#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
Declares the CPSIBlastOptionsHandle class.
Modified on Tue Apr 23 07:38:26 2024 by modify_doxy.py rev. 669887