public final class AffineGap extends Object implements Gap
A+(B * GapLegth)
.
This class is immutable and thread-safe.
Substitution
,
Wikipedia - Gap
PenaltyConstructor and Description |
---|
AffineGap(float startValue,
float gapValue)
Constructs a constant gap function that assigns a penalty of
startValue + gapValue * gapLenght to a gap. |
Modifier and Type | Method and Description |
---|---|
float |
max()
Returns the minimum value a gap can have.
|
float |
min()
Returns the maximum value a gap can have.
|
String |
toString() |
float |
value(int fromIndex,
int toIndex)
Returns the penalty for creating a gap from
fromIndex to
toIndex -1 . |
public AffineGap(float startValue, float gapValue)
startValue + gapValue * gapLenght
to a gap. .startValue
- a non-positive initial penalty for creating a gapgapValue
- a non-positive constant gap valuepublic final float value(int fromIndex, int toIndex)
Gap
fromIndex
to
toIndex -1
. The value must be non-positive.public final float max()
Gap
public final float min()
Gap
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