pal.distance
public class PairwiseDistance extends java.lang.Object implements java.io.Serializable
Modifier and Type | Field and Description |
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double |
distance
last estimated distance
|
double |
distanceSE
last estimate standard error of a distance
|
Constructor and Description |
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PairwiseDistance(SitePattern sp)
Constructor 1 (estimate observed distances only)
|
PairwiseDistance(SitePattern sp,
SubstitutionModel m)
Constructor 2 (uses evolutionary model)
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Modifier and Type | Method and Description |
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double |
getDistance(byte[] s1,
byte[] s2)
compute distance between two sequences (not necessarly
in the given alignment but with the same weights in the site pattern)
|
double |
getDistance(int s1,
int s2)
compute distance between two sequences in the given alignment
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void |
updateModel(SubstitutionModel m)
update model of substitution
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void |
updateSitePattern(SitePattern sp)
update site pattern
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public double distance
public double distanceSE
public PairwiseDistance(SitePattern sp)
sp
- site patternpublic PairwiseDistance(SitePattern sp, SubstitutionModel m)
sp
- site patternm
- evolutionary modelpublic void updateModel(SubstitutionModel m)
model
- of substitutionpublic void updateSitePattern(SitePattern sp)
site
- patternpublic double getDistance(int s1, int s2)
s1
- number of first sequences2
- number of second sequencepublic double getDistance(byte[] s1, byte[] s2)
s1
- site pattern of first sequences2
- site pattern of second sequence