pal.tree
public class TreeDistanceMatrix extends DistanceMatrix
IdGroup.Utils
Constructor and Description |
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TreeDistanceMatrix(Tree t)
compute induced distance matrix using actual branch lengths
(using tree-induced order of sequences)
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TreeDistanceMatrix(Tree t,
boolean countEdges,
double epsilon)
compute induced distance matrix
(using tree-induced order of sequences)
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TreeDistanceMatrix(Tree t,
IdGroup idGroup)
compute induced distance matrix using actual branch lengths
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TreeDistanceMatrix(Tree t,
IdGroup idGroup,
boolean countEdges,
double epsilon)
compute induced distance matrix
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Modifier and Type | Method and Description |
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void |
recompute(Tree t) |
absoluteDistance, addDistance, getClonedDistances, getClosestIndex, getClosestIndex, getDistance, getDistances, getIdCount, getIdentifier, getIdGroup, getSize, isSymmetric, meanDistance, printPHYLIP, setDistance, setDistances, setIdentifier, setIdGroup, squaredDistance, toString, whichIdNumber
public TreeDistanceMatrix(Tree t, IdGroup idGroup, boolean countEdges, double epsilon)
idGroup
- sequence order for the matrixt
- treecountEdges
- boolean variable deciding whether the actual
branch lengths are used in computing the distance
or whether simply all edges larger or equal a certain
threshold length are counted (each with weight 1.0)epsilon
- minimum branch length for a which an edge is countedpublic TreeDistanceMatrix(Tree t, IdGroup idGroup)
idGroup
- sequence order for the matrixt
- treepublic TreeDistanceMatrix(Tree t, boolean countEdges, double epsilon)
t
- treecountEdges
- boolean variable deciding whether the actual
branch lengths are used in computing the distance
or whether simply all edges larger or equal a certain
threshold length are counted (each with weight 1.0)epsilon
- minimum branch length for a which an edge is countedpublic TreeDistanceMatrix(Tree t)
t
- treepublic void recompute(Tree t)