Package jebl.evolution.distances
Class BasicDistanceMatrix
- java.lang.Object
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- jebl.evolution.distances.BasicDistanceMatrix
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- All Implemented Interfaces:
DistanceMatrix
- Direct Known Subclasses:
F84DistanceMatrix
,HKYDistanceMatrix
,JukesCantorDistanceMatrix
,SequenceAlignmentsDistanceMatrix
,TamuraNeiDistanceMatrix
public class BasicDistanceMatrix extends java.lang.Object implements DistanceMatrix
- Version:
- $Id: BasicDistanceMatrix.java 842 2007-11-12 22:33:48Z twobeers $
- Author:
- Andrew Rambaut, Alexei Drummond
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Constructor Summary
Constructors Constructor Description BasicDistanceMatrix(java.util.Collection<Taxon> taxa, double[][] distances)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
getDistance(int row, int column)
Gets the distance at a particular row and columndouble
getDistance(Taxon taxonRow, Taxon taxonColumn)
Gets the distance between 2 taxadouble[][]
getDistances()
Gets a 2-dimensional array containing the distancesint
getSize()
Gets the size of the matrix (which is square), i.e., number of rows or columns.DistanceMatrix
getSubmatrix(java.util.Collection<Taxon> taxonSubset)
Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).java.util.List<Taxon>
getTaxa()
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Constructor Detail
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BasicDistanceMatrix
public BasicDistanceMatrix(java.util.Collection<Taxon> taxa, double[][] distances)
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Method Detail
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getSize
public int getSize()
Gets the size of the matrix (which is square), i.e., number of rows or columns.- Specified by:
getSize
in interfaceDistanceMatrix
- Returns:
- the size
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getTaxa
public java.util.List<Taxon> getTaxa()
- Specified by:
getTaxa
in interfaceDistanceMatrix
- Returns:
- the list of taxa that the state values correspond to.
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getDistance
public double getDistance(int row, int column)
Gets the distance at a particular row and column- Specified by:
getDistance
in interfaceDistanceMatrix
- Parameters:
row
- the row indexcolumn
- the column index- Returns:
- the distance
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getDistance
public double getDistance(Taxon taxonRow, Taxon taxonColumn)
Gets the distance between 2 taxa- Specified by:
getDistance
in interfaceDistanceMatrix
- Parameters:
taxonRow
-taxonColumn
-- Returns:
- the distance
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getSubmatrix
public DistanceMatrix getSubmatrix(java.util.Collection<Taxon> taxonSubset)
Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).- Specified by:
getSubmatrix
in interfaceDistanceMatrix
- Parameters:
taxonSubset
-- Returns:
- the new submatrix
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getDistances
public double[][] getDistances()
Gets a 2-dimensional array containing the distances- Specified by:
getDistances
in interfaceDistanceMatrix
- Returns:
- the distances
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