pal.distance
Class DistanceMatrix

java.lang.Object
  pal.distance.DistanceMatrix

All Implemented Interfaces:

IdGroup, java.io.Serializable

Direct Known Subclasses:

AlignmentDistanceMatrix, JukesCantorDistanceMatrix, ReadDistanceMatrix, SUPGMADistanceMatrix, TreeDistanceMatrix

public class DistanceMatrix

extends java.lang.Object

implements java.io.Serializable, IdGroup

storage for pairwise distance matrices.

features: - printing in in PHYLIP format, - computation of (weighted) squared distance to other distance matrix - Fills in all of array...

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class pal.misc.IdGroup

IdGroup.Utils

Constructor Summary

DistanceMatrix()
constructor

DistanceMatrix(DistanceMatrix dm)
constructor that takes a distance matrix and clones the distances but uses the same idGroup.

DistanceMatrix(DistanceMatrix dm, IdGroup subset)
constructor that takes a distance matrix and clones the distances, of a the identifiers in idGroup.

DistanceMatrix(double[][] distance, IdGroup idGroup)
constructor taking distances array and IdGroup

Method Summary

double	absoluteDistance(DistanceMatrix mat) compute absolute distance to second distance matrix
void	addDistance(int i, int j, double delta) Adds a delta to both upper and lower triangle distances.
double[][]	getClonedDistances() Returns the distances as a 2-dimensional array of doubles.
int	getClosestIndex(int fromIndex, int[] exclusion)
int	getClosestIndex(java.lang.String fromID, java.lang.String[] exclusion)
double	getDistance(int row, int col)
protected double[][]	getDistances() Returns the distances as a 2-dimensional array of doubles (in the actual array used to store the distances)
int	getIdCount() Returns the number of identifiers in this group
Identifier	getIdentifier(int i) Returns the ith identifier.
IdGroup	getIdGroup() Deprecated. distance matrix now implements IdGroup
int	getSize() Returns the number of rows and columns that the distance matrix has.
boolean	isSymmetric() test whether this matrix is a symmetric distance matrix
double	meanDistance() Returns the mean pairwise distance of this matrix
void	printPHYLIP(java.io.PrintWriter out) print alignment (PHYLIP format)
void	setDistance(int i, int j, double dist) Sets both upper and lower triangles.
protected void	setDistances(double[][] matrix)
void	setIdentifier(int i, Identifier ident) Sets the ith identifier.
protected void	setIdGroup(IdGroup base)
double	squaredDistance(DistanceMatrix mat, boolean weighted) compute squared distance to second distance matrix
java.lang.String	toString() returns representation of this alignment as a string
int	whichIdNumber(java.lang.String name) returns the index of the identifier with the given name.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

DistanceMatrix

public DistanceMatrix()

constructor

DistanceMatrix

public DistanceMatrix(double[][] distance,
                      IdGroup idGroup)

constructor taking distances array and IdGroup

DistanceMatrix

public DistanceMatrix(DistanceMatrix dm)

constructor that takes a distance matrix and clones the distances but uses the same idGroup.

DistanceMatrix

public DistanceMatrix(DistanceMatrix dm,
                      IdGroup subset)

constructor that takes a distance matrix and clones the distances, of a the identifiers in idGroup.

Method Detail

printPHYLIP

public void printPHYLIP(java.io.PrintWriter out)

print alignment (PHYLIP format)

toString

public java.lang.String toString()

returns representation of this alignment as a string

squaredDistance

public double squaredDistance(DistanceMatrix mat,
                              boolean weighted)

compute squared distance to second distance matrix

absoluteDistance

public double absoluteDistance(DistanceMatrix mat)

compute absolute distance to second distance matrix

getSize

public int getSize()

Returns the number of rows and columns that the distance matrix has.

getClonedDistances

public final double[][] getClonedDistances()

Returns the distances as a 2-dimensional array of doubles. Matrix is cloned first so it can be altered freely.

getDistances

protected final double[][] getDistances()

Returns the distances as a 2-dimensional array of doubles (in the actual array used to store the distances)

getDistance

public final double getDistance(int row,
                                int col)

setDistance

public void setDistance(int i,
                        int j,
                        double dist)

Sets both upper and lower triangles.

addDistance

public void addDistance(int i,
                        int j,
                        double delta)

Adds a delta to both upper and lower triangle distances.

meanDistance

public double meanDistance()

Returns the mean pairwise distance of this matrix

getIdentifier

public Identifier getIdentifier(int i)

Description copied from interface: IdGroup

Returns the ith identifier.

Specified by:

getIdentifier in interface IdGroup

setIdentifier

public void setIdentifier(int i,
                          Identifier ident)

Description copied from interface: IdGroup

Sets the ith identifier.

Specified by:

setIdentifier in interface IdGroup

getIdCount

public int getIdCount()

Description copied from interface: IdGroup

Returns the number of identifiers in this group

Specified by:

getIdCount in interface IdGroup

whichIdNumber

public int whichIdNumber(java.lang.String name)

Description copied from interface: IdGroup

returns the index of the identifier with the given name.

Specified by:

whichIdNumber in interface IdGroup

getIdGroup

public IdGroup getIdGroup()

Deprecated. distance matrix now implements IdGroup

Return id group of this alignment.

isSymmetric

public boolean isSymmetric()

test whether this matrix is a symmetric distance matrix

getClosestIndex

public int getClosestIndex(java.lang.String fromID,
                           java.lang.String[] exclusion)

Parameters:

fromID - the thing (taxa,sequence) from which we want to find the closest (excluding self)

Returns:

the index of the thing closest to the specified

getClosestIndex

public int getClosestIndex(int fromIndex,
                           int[] exclusion)

Parameters:

fromIndex - the index of the thing (taxa,sequence) from which we want to find the closest (excluding self)

Returns:

the index of the member closes to the specified

setIdGroup

protected final void setIdGroup(IdGroup base)

setDistances

protected final void setDistances(double[][] matrix)