java.io.Serializable
public class PairwiseDistance
extends java.lang.Object
implements java.io.Serializable
Modifier and Type | Field | Description |
---|---|---|
double |
distance |
last estimated distance
|
double |
distanceSE |
last estimate standard error of a distance
|
Constructor | Description |
---|---|
PairwiseDistance(SitePattern sp) |
Constructor 1 (estimate observed distances only)
|
PairwiseDistance(SitePattern sp,
SubstitutionModel m) |
Constructor 2 (uses evolutionary model)
|
Modifier and Type | Method | Description |
---|---|---|
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
|
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