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
|
/* $Id: hashset.hpp,v 1.3 2007/07/11 20:49:29 rotmistr 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 official 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: Kirill Rotmistrovsky
*
* ========================================================================= */
#ifndef EPCR_HASHSET__HPP
#define EPCR_HASHSET__HPP
#include <epcr/build_cfg.h>
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(EPCR_SCOPE)
class CHashSet;
class CHashSet
{
public:
// stl-style typedefs
typedef Uint4 hash_type;
typedef Uint4 size_type;
typedef Uint4 bits_type;
// ncbi-style typedefs
typedef hash_type THashValue;
typedef size_type TSize;
typedef bits_type TBitMask;
TSize GetWordSize() const { return m_WdSize; }
TSize GetWordCount() const { return m_Period; }
TBitMask GetWord( TSize id ) const { return m_Word[id]; }
TBitMask GetMask( TSize id ) const { return m_Mask[id]; }
THashValue GetValue( TSize id ) const { return m_Hash[id]; }
THashValue GetTableSize( TSize id ) const
{ return m_TbSize[id]; }
THashValue GetAmbiquityMask() const { return m_AmbMask; }
THashValue operator [] ( TSize id ) const
{ return GetValue( id ); }
bool Begin( const char * ptr );
bool Next() { // inline
if( End() ) return false;
m_AmbMask <<= 1;
unsigned char nt = sm_HashId[ int(*m_Ptr) ];
if( nt > 3 ) /* ambiquos */ { m_AmbMask |= 1; nt = 0; }
// Circular 'rotation' with update of values
if( m_Period == 1 ) {
m_Hash[0] = m_Mask[0] & ( ( m_Hash[0] << 2 ) | nt );
} else {
hash_type x = m_Hash[ m_Period - 1 ];
for( size_type t = m_Period - 1; t > 0; --t ) {
m_Hash[t] = m_Mask[t] & ( ( m_Hash[ t - 1 ] << 2 ) | nt );
}
m_Hash[0] = x & m_Mask[0];
}
++m_Offset;
++m_Ptr;
return true;
};
bool Good() const;
bool Good( TSize id ) const { return ( m_Word[id] & m_AmbMask ) == 0; }
bool End() const { return m_Ptr == 0 || *m_Ptr == 0; }
TSize GetPosition() const { return m_Offset; }
const char * GetPtr() const { return m_Ptr; }
virtual ~CHashSet() throw ();
CHashSet( TSize wdsize = 0, TSize period = 0 );
CHashSet( const CHashSet& );
CHashSet& operator = ( const CHashSet& s );
protected:
void _intl_free();
void _intl_copy( const CHashSet& s );
protected:
const char * m_Ptr; // Pointer to current position
// of string being processed
TSize m_Offset; // Current offset in original string
TSize m_WdSize; // Wordsize
TSize m_Period; // Number of words to be used
TSize * m_TbSize; // Hash table sizes for each word;
// used by users
TBitMask m_AmbMask; // Mask showing ambiquity positions
TBitMask * m_Word; // Words; needed for ambiquity test
THashValue * m_Hash; // Current hash values for each word
THashValue * m_Mask; // Masks for each word;
// used for value update
protected:
static unsigned char sm_HashId[];
};
END_SCOPE(EPCR_SCOPE)
END_NCBI_SCOPE
#endif
/*
* $Log: hashset.hpp,v $
* Revision 1.3 2007/07/11 20:49:29 rotmistr
* Made 64bit-compatible
*
* Revision 1.2 2004/02/04 21:23:22 rotmistr
* - gcc-3.3.2 compatible
* - better postfiltering for reverse-e-PCR for discontiguos words
* - cgi added, that supports:
* -- contig to chromosome mapping
* -- simple mapviewer links
* -- unists links
* -- discontiguos words
*
* Revision 1.1.1.1 2003/12/23 18:17:27 rotmistr
* Package that includes e-PCR, reverse e-PCR, and sequence data preparation
* program for reverse e-PCR looks ready
*
*/
|
