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
|
/*******************************************************************************
* $Id: MemorySML.cpp,v 1.8 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 "libMems/MemorySML.h"
#include <algorithm>
using namespace std;
using namespace genome;
namespace mems {
MemorySML::MemorySML(const uint8* table, const uint32 alpha_bits ){
header.alphabet_bits = alpha_bits;
memcpy(header.translation_table, table, UINT8_MAX);
header.version = 0;
}
MemorySML::MemorySML(const MemorySML& msa){
*this = msa;
}
MemorySML& MemorySML::operator=(const MemorySML& msa ) {
SortedMerList::operator=( msa );
positions = msa.positions;
return *this;
}
MemorySML* MemorySML::Clone() const{
return new MemorySML(*this);
}
void MemorySML::Clear(){
SortedMerList::Clear();
positions.clear();
}
void MemorySML::Create(const gnSequence& seq, const uint64 seed ){
SortedMerList::Create(seq, seed);
vector<bmer> sml_array;
boolean is_spaced_seed = header.seed_length != header.seed_weight;
if( is_spaced_seed )
FillDnaSeedSML( seq, sml_array );
else
FillSML( seq, sml_array );
sort( sml_array.begin(), sml_array.end(), &bmer_lessthan );
positions.reserve( sml_array.size() );
for(gnSeqI merI = 0; merI < sml_array.size(); merI++ ){
positions.push_back( sml_array[merI].position );
}
}
boolean MemorySML::Read(vector<bmer>& readVector, gnSeqI size, gnSeqI offset )
{
readVector.clear();
if( offset > positions.size() )
return false;
gnSeqI last_mer = offset + size;
boolean success = true;
if( last_mer > positions.size() ){
last_mer = positions.size();
success = false;
}
bmer cur_mer;
for(gnSeqI merI = offset; merI < last_mer; merI++){
cur_mer.position = positions[merI];
cur_mer.mer = GetSeedMer( cur_mer.position );
readVector.push_back( cur_mer );
}
return success;
}
void MemorySML::Merge(SortedMerList& sa, SortedMerList& sa2){
}
bmer MemorySML::operator[](gnSeqI index)
{
bmer cur_mer;
cur_mer.position = positions[index];
cur_mer.mer = GetSeedMer( cur_mer.position );
return cur_mer;
}
} // namespace mems
|
