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java.lang.Objectde.jstacs.utils.PFMComparator.PFMDistance
public abstract static class PFMComparator.PFMDistance
This interface declares a method for comparing different PFMs. If the PFMs are identical the value 0 should be returned, otherwise some positive value. Ideally, each distance has to be length-normalized.
Constructor Summary | |
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PFMComparator.PFMDistance()
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Method Summary | |
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double |
compare(double[][] pfm1,
double[][] pfm2,
int minimalOverlap)
This method compares two PFMs, pfm1 and pfm2 . |
double |
getDistance(double[][] pfm1,
double[][] pfm2,
int offset)
This method computes the distance between two PFMs. |
protected abstract double |
getDistance(double[][] pfm1,
double[][] pfm2,
int l1,
int l2)
Computes the mean distance between the overlapping parts of pfm1 and pfm2 starting at the offsets
l1 and l2 , respectively. |
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 PFMComparator.PFMDistance()
Method Detail |
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public final double getDistance(double[][] pfm1, double[][] pfm2, int offset)
pfm1
- the first PFMpfm2
- the second PFMoffset
- the offset for the alignment of the PFMs
protected abstract double getDistance(double[][] pfm1, double[][] pfm2, int l1, int l2)
pfm1
and pfm2
starting at the offsets
l1
and l2
, respectively.
pfm1
- the first PFMpfm2
- the second PFMl1
- the offset for the first PFMl2
- the offset for the second PFM
public double compare(double[][] pfm1, double[][] pfm2, int minimalOverlap)
pfm1
and pfm2
.
The method tests all alignments of the PFMs with an overlap of mininmalOverlap
consecutive positions.
pfm1
- the first PFMpfm2
- the second PFMminimalOverlap
- the minimal number of consecutive positions in an alignment
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