NCBI C++ ToolKit
matrix_freq_ratios.h
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1 #ifndef ALGO_BLAST_CORE___MATRIX_FREQ_RATIOS__H
2 #define ALGO_BLAST_CORE___MATRIX_FREQ_RATIOS__H
3 
4 /* $Id: matrix_freq_ratios.h 63475 2014-07-02 13:40:24Z madden $
5  * ===========================================================================
6  *
7  * PUBLIC DOMAIN NOTICE
8  * National Center for Biotechnology Information
9  *
10  * This software/database is a "United States Government Work" under the
11  * terms of the United States Copyright Act. It was written as part of
12  * the author's official duties as a United States Government employee and
13  * thus cannot be copyrighted. This software/database is freely available
14  * to the public for use. The National Library of Medicine and the U.S.
15  * Government have not placed any restriction on its use or reproduction.
16  *
17  * Although all reasonable efforts have been taken to ensure the accuracy
18  * and reliability of the software and data, the NLM and the U.S.
19  * Government do not and cannot warrant the performance or results that
20  * may be obtained by using this software or data. The NLM and the U.S.
21  * Government disclaim all warranties, express or implied, including
22  * warranties of performance, merchantability or fitness for any particular
23  * purpose.
24  *
25  * Please cite the author in any work or product based on this material.
26  *
27  * ===========================================================================
28  *
29  * Author: Christiam Camacho
30  *
31  */
32 
33 /** @file matrix_freq_ratios.h
34  * Interface to retrieve the frequency ratios for various scoring matrices.
35  *
36  * See explanation in p 2996 of Nucleic Acids Research, 2001, Vol 29, No 14.
37  */
38 
40 
41 #ifdef __cplusplus
42 extern "C" {
43 #endif
44 
45 /** Stores the frequency ratios along with their bit scale factor */
46 typedef struct SFreqRatios {
47 
48  /** The actual frequency ratios */
49  double** data;
50 
51  /** Used to multiply the values in the above matrix to obtain scores in bit
52  * units */
54 
56 
57 /** Retrive the matrix's frequency ratios.
58  * @param matrix_name Available options include:
59  * BLOSUM62
60  * BLOSUM62_20
61  * BLOSUM62_20A
62  * BLOSUM62_20B
63  * BLOSUM45
64  * BLOSUM80
65  * BLOSUM50
66  * BLOSUM90
67  * PAM30
68  * PAM70
69  * PAM250
70  * @return NULL on error
71  */
73 _PSIMatrixFrequencyRatiosNew(const char* matrix_name);
74 
75 /** Deallocate the frequency ratios structure */
78 
79 #ifdef __cplusplus
80 }
81 #endif
82 
83 #endif /* !ALGO_BLAST_CORE__MATRIX_FREQ_RATIOS__H */
Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent ...
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
Definition: blast_export.h:65
struct SFreqRatios SFreqRatios
Stores the frequency ratios along with their bit scale factor.
SFreqRatios * _PSIMatrixFrequencyRatiosFree(SFreqRatios *freq_ratios)
Deallocate the frequency ratios structure.
SFreqRatios * _PSIMatrixFrequencyRatiosNew(const char *matrix_name)
Retrive the matrix's frequency ratios.
Stores the frequency ratios along with their bit scale factor.
double ** data
The actual frequency ratios.
int bit_scale_factor
Used to multiply the values in the above matrix to obtain scores in bit units.
Modified on Mon May 20 05:04:18 2024 by modify_doxy.py rev. 669887