java.lang.Object
- pal.distance.DistanceMatrix

All Implemented Interfaces:

java.io.Serializable, IdGroup

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...

Version:

$Id: DistanceMatrix.java,v 1.11 2003/07/20 02:36:08 matt Exp $

Author:

Korbinian Strimmer, Alexei Drummond

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from interface pal.misc.IdGroup
  IdGroup.Utils

Constructor Summary

Constructors
Constructor	Description
`DistanceMatrix()`	constructor
`DistanceMatrix(double[][] distance, IdGroup idGroup)`	constructor taking distances array and IdGroup
`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.

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`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
    
    Overrides:
    
    toString in class java.lang.Object
  - 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)
    
    exlcusion - indexes of things that should not be considered, may be null
    
    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)
    
    exlcusion - indexes of things that should not be considered, may be null
    
    Returns:
    
    the index of the member closes to the specified
  - setIdGroup
```
protected final void setIdGroup(IdGroup base)
```
  - setDistances
```
protected final void setDistances(double[][] matrix)
```

Class DistanceMatrix

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.IdGroup

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

DistanceMatrix

DistanceMatrix

DistanceMatrix

DistanceMatrix

Method Detail

printPHYLIP

toString

squaredDistance

absoluteDistance

getSize

getClonedDistances

getDistances

getDistance

setDistance

addDistance

meanDistance

getIdentifier

setIdentifier

getIdCount

whichIdNumber

getIdGroup

isSymmetric

getClosestIndex

getClosestIndex

setIdGroup

setDistances