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java.lang.Object | +--org.biojava.stats.svm.tools.SuffixTreeKernel
Computes the dot-product of two suffix-trees as the sum of the products of the counts of all nodes they have in common.
This implementation allows you to scale the sub-space for each word length independantly.
Inner Class Summary | |
static interface |
SuffixTreeKernel.DepthScaler
Encapsulates the scale factor to apply at a given depth. |
static class |
SuffixTreeKernel.MultipleScalar
Scale using a multiple of two DepthScalers. |
static class |
SuffixTreeKernel.NullModelScaler
Scales by 4^depth - equivalent to dividing by a probablistic flatt prior null model |
static class |
SuffixTreeKernel.SelectionScalar
Scale using a BitSet to allow/dissalow depths. |
static class |
SuffixTreeKernel.UniformScaler
Scale all depths by 1.0 |
Constructor Summary | |
SuffixTreeKernel()
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Method Summary | |
double |
evaluate(java.lang.Object a,
java.lang.Object b)
Calculate the dot product between the SuffixTrees a and b. |
SuffixTreeKernel.DepthScaler |
getDepthScaler()
Retrieve the current DepthScaler. |
void |
setDepthScaler(SuffixTreeKernel.DepthScaler depthScaler)
Change the current DepthScaler to depthScaler. |
java.lang.String |
toString()
|
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
wait,
wait,
wait |
Constructor Detail |
public SuffixTreeKernel()
Method Detail |
public SuffixTreeKernel.DepthScaler getDepthScaler()
public void setDepthScaler(SuffixTreeKernel.DepthScaler depthScaler)
depthScaler
- the new DepthScaler to usepublic double evaluate(java.lang.Object a, java.lang.Object b)
This is the sum of the dot products of each subspace for a given word length. Each subspace is scaled using the DepthScaler returned by getDepthScaler.
a
- the first Objectb
- the second Objectpublic java.lang.String toString()
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