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java.lang.Objectpal.distance.PairwiseDistance
public class PairwiseDistance
determines the (observed and ML) distance between a pair of sequences
Field Summary | |
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double |
distance
last estimated distance |
double |
distanceSE
last estimate standard error of a distance |
Constructor Summary | |
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PairwiseDistance(SitePattern sp)
Constructor 1 (estimate observed distances only) |
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PairwiseDistance(SitePattern sp,
SubstitutionModel m)
Constructor 2 (uses evolutionary model) |
Method Summary | |
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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 |
void |
updateModel(SubstitutionModel m)
update model of substitution |
void |
updateSitePattern(SitePattern sp)
update site pattern |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public double distance
public double distanceSE
Constructor Detail |
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public PairwiseDistance(SitePattern sp)
sp
- site patternpublic PairwiseDistance(SitePattern sp, SubstitutionModel m)
sp
- site patternm
- evolutionary modelMethod Detail |
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public 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 sequence
public double getDistance(byte[] s1, byte[] s2)
s1
- site pattern of first sequences2
- site pattern of second sequence
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