1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
|
#ifndef ALGO_BLAST_CORE___BLAST_PROGRAM__H
#define ALGO_BLAST_CORE___BLAST_PROGRAM__H
/* $Id: blast_program.h,v 1.1 2005/06/08 17:25:37 madden Exp $
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's offical duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author: Christiam Camacho / Ilya Dondoshansky
*
*/
/** @file blast_program.h
* Definitions for various programs supported by core BLAST
*/
#include <algo/blast/core/ncbi_std.h>
#ifdef __cplusplus
extern "C" {
#endif
/* Low-level preprocessor definitions: these are not intended to be used
* directly, use the EBlastProgramType enumeration below */
/** This bit is on if the query is protein */
#define PROTEIN_QUERY_MASK (0x1<<0)
/** This bit is on if the subject is protein */
#define PROTEIN_SUBJECT_MASK (0x1<<1)
/** This bit is on if the query is nucleotide */
#define NUCLEOTIDE_QUERY_MASK (0x1<<2)
/** This bit is on if the subject is nucleotide */
#define NUCLEOTIDE_SUBJECT_MASK (0x1<<3)
/** This bit is on if the query is translated */
#define TRANSLATED_QUERY_MASK (0x1<<4)
/** This bit is on if the subject is translated */
#define TRANSLATED_SUBJECT_MASK (0x1<<5)
/** This bit is on if the query is a PSSM (PSI-BLAST) */
#define PSSM_QUERY_MASK (0x1<<6)
/** This bit is on if the subject is a PSSM (RPS-BLAST) */
#define PSSM_SUBJECT_MASK (0x1<<7)
/* This bit is on if the query includes a pattern (PHI-BLAST) */
#define PATTERN_QUERY_MASK (0x1<<8)
/******************** Main BLAST program definitions ***********************/
/** Defines the engine's notion of the different applications of the BLAST
* algorithm */
typedef enum {
eBlastTypeBlastp = (PROTEIN_QUERY_MASK | PROTEIN_SUBJECT_MASK),
eBlastTypeBlastn = (NUCLEOTIDE_QUERY_MASK | NUCLEOTIDE_SUBJECT_MASK),
eBlastTypeBlastx = (NUCLEOTIDE_QUERY_MASK | PROTEIN_SUBJECT_MASK |
TRANSLATED_QUERY_MASK),
eBlastTypeTblastn = (PROTEIN_QUERY_MASK | NUCLEOTIDE_SUBJECT_MASK |
TRANSLATED_SUBJECT_MASK),
eBlastTypeTblastx = (NUCLEOTIDE_QUERY_MASK | NUCLEOTIDE_SUBJECT_MASK
| TRANSLATED_QUERY_MASK
| TRANSLATED_SUBJECT_MASK),
eBlastTypePsiBlast = (PSSM_QUERY_MASK | eBlastTypeBlastp),
eBlastTypePsiTblastn = (PSSM_QUERY_MASK | eBlastTypeTblastn),
eBlastTypeRpsBlast = (PSSM_SUBJECT_MASK | eBlastTypeBlastp),
eBlastTypeRpsTblastn = (PSSM_SUBJECT_MASK | eBlastTypeBlastx),
eBlastTypePhiBlastp = (PATTERN_QUERY_MASK | eBlastTypeBlastp),
eBlastTypePhiBlastn = (PATTERN_QUERY_MASK | eBlastTypeBlastn),
eBlastTypeUndefined = 0x0
} EBlastProgramType;
/************* Functions to classify programs by query **********************/
/** Returns true if the query is protein
* @param p program type [in]
*/
Boolean Blast_QueryIsProtein(EBlastProgramType p);
/** Returns true if the query is nucleotide
* @param p program type [in]
*/
Boolean Blast_QueryIsNucleotide(EBlastProgramType p);
/** Returns true if the query is PSSM
* @param p program type [in]
*/
Boolean Blast_QueryIsPssm(EBlastProgramType p);
/************* Functions to classify programs by subject **********************/
/** Returns true if the subject is protein
* @param p program type [in]
*/
Boolean Blast_SubjectIsProtein(EBlastProgramType p);
/** Returns true if the subject is nucleotide
* @param p program type [in]
*/
Boolean Blast_SubjectIsNucleotide(EBlastProgramType p);
/** Returns true if the subject is PSSM
* @param p program type [in]
*/
Boolean Blast_SubjectIsPssm(EBlastProgramType p);
/************* Functions to classify programs by translation *****************/
/** Returns true if the query is translated
* @param p program type [in]
*/
Boolean Blast_QueryIsTranslated(EBlastProgramType p);
/** Returns true if the subject is translated
* @param p program type [in]
*/
Boolean Blast_SubjectIsTranslated(EBlastProgramType p);
/************* Functions to classify special BLAST programs *****************/
/** Returns true if program is PSI-BLAST (i.e.: involves a PSSM as query)
* @param p program type [in]
*/
Boolean Blast_ProgramIsPsiBlast(EBlastProgramType p);
/** Returns true if program is PHI-BLAST (i.e.: involves a pattern)
* @param p program type [in]
*/
Boolean Blast_ProgramIsPhiBlast(EBlastProgramType p);
/** Returns true if program is RPS-BLAST (i.e.: involves a PSSM as subject)
* @param p program type [in]
*/
Boolean Blast_ProgramIsRpsBlast(EBlastProgramType p);
#ifdef __cplusplus
}
#endif
#endif /* !ALGO_BLAST_CORE__BLAST_PROGRAM__H */
|
