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
|
// Author: Mark Chaisson
#pragma once
#include <alignment/algorithms/alignment/sdp/SDPFragment.hpp>
#include <alignment/algorithms/anchoring/BasicEndpoint.hpp>
#include <alignment/datastructures/anchoring/ClusterList.hpp>
#include <alignment/datastructures/anchoring/MatchPos.hpp>
#include <alignment/tuples/DNATuple.hpp>
#include <alignment/tuples/TupleList.hpp>
#include <vector>
//
// Define a list of buffers that are meant to grow to high-water
// marks, and not shrink down past that. The memory is reused rather
// than having multiple calls to new.
//
class MappingBuffers
{
public:
std::vector<int> hpInsScoreMat, insScoreMat;
std::vector<int> kbandScoreMat;
std::vector<Arrow> hpInsPathMat, insPathMat;
std::vector<Arrow> kbandPathMat;
std::vector<int> scoreMat;
std::vector<Arrow> pathMat;
std::vector<int> affineScoreMat;
std::vector<Arrow> affinePathMat;
std::vector<ChainedMatchPos> matchPosList;
std::vector<ChainedMatchPos> rcMatchPosList;
std::vector<BasicEndpoint<ChainedMatchPos> > globalChainEndpointBuffer;
std::vector<Fragment> sdpFragmentSet, sdpPrefixFragmentSet, sdpSuffixFragmentSet;
TupleList<PositionDNATuple> sdpCachedTargetTupleList;
TupleList<PositionDNATuple> sdpCachedTargetPrefixTupleList;
TupleList<PositionDNATuple> sdpCachedTargetSuffixTupleList;
std::vector<int> sdpCachedMaxFragmentChain;
std::vector<double> probMat;
std::vector<double> optPathProbMat;
std::vector<float> lnSubPValueMat;
std::vector<float> lnInsPValueMat;
std::vector<float> lnDelPValueMat;
std::vector<float> lnMatchPValueMat;
std::vector<int> clusterNumBases;
ClusterList clusterList;
ClusterList revStrandClusterList;
void Reset(void);
};
inline void MappingBuffers::Reset(void)
{
std::vector<int>().swap(hpInsScoreMat);
std::vector<int>().swap(insScoreMat);
std::vector<int>().swap(kbandScoreMat);
std::vector<Arrow>().swap(hpInsPathMat);
std::vector<Arrow>().swap(insPathMat);
std::vector<Arrow>().swap(kbandPathMat);
std::vector<int>().swap(scoreMat);
std::vector<Arrow>().swap(pathMat);
std::vector<ChainedMatchPos>().swap(matchPosList);
std::vector<ChainedMatchPos>().swap(rcMatchPosList);
std::vector<BasicEndpoint<ChainedMatchPos> >().swap(globalChainEndpointBuffer);
std::vector<Fragment>().swap(sdpFragmentSet);
std::vector<Fragment>().swap(sdpPrefixFragmentSet);
std::vector<Fragment>().swap(sdpSuffixFragmentSet);
sdpCachedTargetTupleList.Reset();
sdpCachedTargetPrefixTupleList.Reset();
sdpCachedTargetSuffixTupleList.Reset();
std::vector<int>().swap(sdpCachedMaxFragmentChain);
std::vector<double>().swap(probMat);
std::vector<double>().swap(optPathProbMat);
std::vector<float>().swap(lnSubPValueMat);
std::vector<float>().swap(lnInsPValueMat);
std::vector<float>().swap(lnDelPValueMat);
std::vector<float>().swap(lnMatchPValueMat);
std::vector<int>().swap(clusterNumBases);
}
|
