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java.lang.Objectde.jstacs.algorithms.Alignment.SimpleCosts
public static class Alignment.SimpleCosts
Class for simple costs with costs mismatch
for a mismatch,
costs start
to start a new gap, elong
to
elongate a gap by one position, and costs of 0
for a match
Nested Class Summary |
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Nested classes/interfaces inherited from interface de.jstacs.algorithms.Alignment.Costs |
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Alignment.Costs.Direction |
Constructor Summary | |
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Alignment.SimpleCosts(double mismatch,
double start,
double elong)
Creates a new instance of simple costs with costs mismatch for a mismatch, costs start to
start a new gap, elong to elongate a gap by one
position, and costs of 0 for a match |
Method Summary | |
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double |
getCostFor(Sequence s1,
Sequence s2,
int i,
int j,
Alignment.Costs.Direction from)
Returns the costs for the alignment if s1(i) and s2(j) coming from from . |
double |
getElongateCosts()
Returns the costs to elongate a gap by one position |
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 Alignment.SimpleCosts(double mismatch, double start, double elong)
mismatch
for a mismatch, costs start
to
start a new gap, elong
to elongate a gap by one
position, and costs of 0
for a match
mismatch
- the mismatch costsstart
- the costs to start a gapelong
- the costs to elongate a gapMethod Detail |
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public double getCostFor(Sequence s1, Sequence s2, int i, int j, Alignment.Costs.Direction from)
Alignment.Costs
from
.
getCostFor
in interface Alignment.Costs
s1
- the first sequences2
- the second sequencei
- the index in the first sequencej
- the index in the second sequencefrom
- the direction within the DP-matrix
public double getElongateCosts()
Alignment.Costs
getElongateCosts
in interface Alignment.Costs
public double getGapCostsFor(int length)
Alignment.Costs
length
.
getGapCostsFor
in interface Alignment.Costs
length
- the length of the gap
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