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java.lang.Objectde.jstacs.algorithms.alignment.cost.AffineCosts
public class AffineCosts
This class implements affine gap costs, i.e., the costs for starting a new gap are given by start
, and
the costs for elongating a gap by one position are given by elong
.
Constructor Summary | |
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AffineCosts(double start,
Costs c)
This constructor creates a new instance of cost using affine gap costs. |
Method Summary | |
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double |
getCostFor(Sequence s1,
Sequence s2,
int i,
int j)
Returns the costs for the alignment of s1(i) and
s2(j) . |
double |
getElongateCosts()
Returns the costs to elongate a gap by one position. |
double |
getGapCosts()
Returns the costs for a gap. |
double |
getGapCostsFor(int length)
Returns the costs for a gap of length length . |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public AffineCosts(double start, Costs c)
c
,
while the costs for a start of a gap are given by start
.
start
- the costs for starting a gapc
- the cost for match, mismatch and gap elongationMethod Detail |
---|
public double getElongateCosts()
public double getGapCostsFor(int length)
length
.
length
- the length of the gap
public double getCostFor(Sequence s1, Sequence s2, int i, int j)
Costs
s1(i)
and
s2(j)
.
getCostFor
in interface Costs
s1
- the first sequences2
- the second sequencei
- the index in the first sequencej
- the index in the second sequence
Sequence.discreteVal(int)
public double getGapCosts()
Costs
getGapCosts
in interface Costs
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