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
|
#include <alignment/datastructures/anchoring/AnchorParameters.hpp>
AnchorParameters::AnchorParameters()
{
branchQualityThreshold = 0;
minMatchLength = 0;
maxMatchScore = 0;
expand = 0;
contextAlignLength = 0;
useLookupTable = true;
numBranches = 0;
maxAnchorsPerPosition = 1000;
advanceExactMatches = 0;
maxLCPLength = 0; // 0 Defaults to full lcp length
stopMappingOnceUnique = false;
removeEncompassedMatches = false;
verbosity = 0;
lcpBoundsOutPtr = NULL;
branchExpand = 0;
}
AnchorParameters &AnchorParameters::Assign(const AnchorParameters &rhs)
{
//
// Manually handle assignment in case there is some deep copy
// that is necessary eventually.
//
branchQualityThreshold = rhs.branchQualityThreshold;
minMatchLength = rhs.minMatchLength;
maxMatchScore = rhs.maxMatchScore;
expand = rhs.expand;
contextAlignLength = rhs.contextAlignLength;
numBranches = rhs.numBranches;
maxAnchorsPerPosition = rhs.maxAnchorsPerPosition;
advanceExactMatches = rhs.advanceExactMatches;
maxLCPLength = rhs.maxLCPLength;
stopMappingOnceUnique = rhs.stopMappingOnceUnique;
verbosity = rhs.verbosity;
removeEncompassedMatches = rhs.removeEncompassedMatches;
branchExpand = rhs.branchExpand;
return *this;
}
AnchorParameters &AnchorParameters::operator=(const AnchorParameters &rhs)
{
return this->Assign(rhs);
}
|
