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
|
/*******************************************************************************
* $Id: DNAMemorySML.cpp,v 1.3 2004/03/01 02:40:08 darling Exp $
* This file is copyright 2002-2007 Aaron Darling and authors listed in the AUTHORS file.
* Please see the file called COPYING for licensing, copying, and modification
* Please see the file called COPYING for licensing details.
* **************
******************************************************************************/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libGenome/gnSequence.h"
#include "libMems/DNAMemorySML.h"
using namespace std;
using namespace genome;
namespace mems {
DNAMemorySML::DNAMemorySML(const uint8* table, const uint32 alpha_bits) :
MemorySML( table, alpha_bits )
{}
DNAMemorySML& DNAMemorySML::operator=(const DNAMemorySML& msa ){
MemorySML::operator=(msa);
return *this;
}
DNAMemorySML* DNAMemorySML::Clone() const{
DNAMemorySML *bdsa = new DNAMemorySML();
(*bdsa) = *this;
return bdsa;
}
uint64 DNAMemorySML::GetMer(gnSeqI position) const{
return GetDnaMer( position );
}
uint64 DNAMemorySML::GetSeedMer( gnSeqI offset ) const{
return GetDnaSeedMer( offset );
}
void DNAMemorySML::FillSML(const gnSequence& seq, vector<bmer>& sml_array)
{
FillDnaSML(seq, sml_array);
}
} // namespace mems
|
