Package jebl.evolution.distances
Interface DistanceMatrix
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- All Known Implementing Classes:
BasicDistanceMatrix
,F84DistanceMatrix
,HKYDistanceMatrix
,JukesCantorDistanceMatrix
,SequenceAlignmentsDistanceMatrix
,TamuraNeiDistanceMatrix
public interface DistanceMatrix
- Version:
- $Id: DistanceMatrix.java 186 2006-01-24 00:41:22Z pepster $
- Author:
- Andrew Rambaut, Alexei Drummond
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Method Summary
All Methods Instance Methods Abstract 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> taxa)
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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Method Detail
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getSize
int getSize()
Gets the size of the matrix (which is square), i.e., number of rows or columns.- Returns:
- the size
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getTaxa
java.util.List<Taxon> getTaxa()
- Returns:
- the list of taxa that the state values correspond to.
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getDistance
double getDistance(int row, int column)
Gets the distance at a particular row and column- Parameters:
row
- the row indexcolumn
- the column index- Returns:
- the distance
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getDistance
double getDistance(Taxon taxonRow, Taxon taxonColumn)
Gets the distance between 2 taxa- Parameters:
taxonRow
-taxonColumn
-- Returns:
- the distance
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getSubmatrix
DistanceMatrix getSubmatrix(java.util.Collection<Taxon> taxa)
Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).- Parameters:
taxa
-- Returns:
- the new submatrix
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getDistances
double[][] getDistances()
Gets a 2-dimensional array containing the distances- Returns:
- the distances
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