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
|
#include <alignment/simulator/LengthHistogram.hpp>
int LengthHistogram::Read(std::string &inName)
{
std::ifstream in;
CrucialOpen(inName, in, std::ios::in);
return Read(in);
}
int LengthHistogram::Read(std::ifstream &in)
{
while (in) {
int length, count;
in >> length;
in >> count;
lengthHistogram.data.push_back(length);
if (lengthHistogram.cdf.size() == 0) {
lengthHistogram.cdf.push_back(count);
} else {
lengthHistogram.cdf.push_back(lengthHistogram.cdf[lengthHistogram.cdf.size() - 1] +
count);
}
}
return 1;
}
void LengthHistogram::GetRandomLength(int &length) { lengthHistogram.SelectRandomValue(length); }
void LengthHistogram::BuildFromAlignmentLengths(std::vector<int> &lengths)
{
sort(lengths.begin(), lengths.end());
for (size_t f = 0, i = 1; i < lengths.size(); i++) {
if (lengths[i] != lengths[f]) {
lengthHistogram.data.push_back(lengths[f]);
lengthHistogram.cdf.push_back(i);
f = i;
}
}
if (lengths.size() != 0) {
lengthHistogram.data.push_back(lengths[lengths.size() - 1]);
lengthHistogram.cdf.push_back(lengths.size());
}
/* Tests:
* indices 0 1 2 3 4 5 6
* lengths: 1 3 5 9 10 10 11
* lengthHistogram.data: 1 3 5 9 10 11
* lengthHistogram.cdf : 1 2 3 4 6 7
*
* lengths: 1 3 5 9 10 11
* lengthHistogram.data: 1 3 5 9 10 11
* lengthHistogram.cdf : 1 2 3 4 5 6
*
* lengths: 10
* lengthHistogram.data: 10
* lengthHistogram.cdf : 1
*/
}
|
