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
|
#include "myutils.h"
#include "chime.h"
#include "ultra.h"
#include <set>
void AddTargets(Ultra &U, const SeqData &Query, set<unsigned> &TargetIndexes);
void GetChunkInfo(unsigned L, unsigned &Length, vector<unsigned> &Los)
{
Los.clear();
if (L <= opt_minchunk)
{
Length = L;
Los.push_back(0);
return;
}
Length = (L - 1)/opt_chunks + 1;
if (Length < opt_minchunk)
Length = opt_minchunk;
unsigned Lo = 0;
for (;;)
{
if (Lo + Length >= L)
{
Lo = L - Length - 1;
Los.push_back(Lo);
return;
}
Los.push_back(Lo);
Lo += Length;
}
}
void GetCandidateParents(Ultra &U, const SeqData &QSD, float AbQ,
vector<unsigned> &Parents)
{
Parents.clear();
set<unsigned> TargetIndexes;
unsigned QL = QSD.L;
SeqData QuerySD = QSD;
unsigned ChunkLength;
vector<unsigned> ChunkLos;
GetChunkInfo(QL, ChunkLength, ChunkLos);
unsigned ChunkCount = SIZE(ChunkLos);
for (unsigned ChunkIndex = 0; ChunkIndex < ChunkCount; ++ChunkIndex)
{
unsigned Lo = ChunkLos[ChunkIndex];
asserta(Lo + ChunkLength <= QL);
const byte *Chunk = QSD.Seq + Lo;
// THIS MESSES UP --self!!
//char Prefix[32];
//sprintf(Prefix, "%u|", Lo);
//string ChunkLabel = string(Prefix) + string(QSD.Label);
//QuerySD.Label = ChunkLabel.c_str();
QuerySD.Seq = Chunk;
QuerySD.L = ChunkLength;
AddTargets(U, QuerySD, TargetIndexes);
Lo += ChunkLength;
}
for (set<unsigned>::const_iterator p = TargetIndexes.begin();
p != TargetIndexes.end(); ++p)
{
unsigned TargetIndex = *p;
bool Accept = true;
if (AbQ > 0.0f)
{
const char *TargetLabel = U.GetSeedLabel(TargetIndex);
float AbT = GetAbFromLabel(string(TargetLabel));
if (AbT > 0.0f && AbT < opt_abskew*AbQ)
Accept = false;
}
if (Accept)
Parents.push_back(TargetIndex);
}
}
|
