public abstract static class PFMComparator.PFMDistance extends Object
Constructor and Description |
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PFMDistance() |
Modifier and Type | Method and Description |
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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. |
public final double getDistance(double[][] pfm1, double[][] pfm2, int offset)
pfm1
- the first PFMpfm2
- the second PFMoffset
- the offset for the alignment of the PFMsprotected 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 PFMpublic 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