com.hfg.bio.phylogeny

Class DistanceMatrix

java.lang.Object

com.hfg.bio.phylogeny.DistanceMatrix

All Implemented Interfaces:

Cloneable

public class DistanceMatrix
extends Object
implements Cloneable

Simple distance matrix container. Can read Phylip-format matrices or general matrices where the identifiers do not contain whitespace.

Most commonly constructed via a multiple sequence alignment:

    DistanceMatrix matrix = msa.getDistanceMatrix(new UncorrectedModel());
   

Phylip-formatted matrix example:

    String testMatrix =
       "   14\n" +
       "Mouse     \n" +
       "Bovine      1.7043\n" +
       "Lemur       2.0235  1.1901\n" +
       "Tarsier     2.1378  1.3287  1.2905\n" +
       "Squir Monk  1.5232  1.2423  1.3199  1.7878\n" +
       "Jpn Macaq   1.8261  1.2508  1.3887  1.3137  1.0642\n" +
       "Rhesus Mac  1.9182  1.2536  1.4658  1.3788  1.1124  0.1022\n" +
       "Crab-E.Mac  2.0039  1.3066  1.4826  1.3826  0.9832  0.2061  0.2681\n";

    DistanceMatrix matrix = new DistanceMatrix(testMatrix);
   

General matrix example:

    String testMatrix =
             "# Subunit distance matrix\n" +
             "Alpha      0.000 1.000 2.000 3.000 3.000\n" +
             "Beta       1.000 0.000 2.000 3.000 3.000\n" +
             "Gamma      2.000 2.000 0.000 3.000 3.000\n" +
             "Delta      3.000 3.000 0.000 0.000 1.000\n" +
             "Epsilon    3.000 3.000 3.000 1.000 0.000\n\n";

    DistanceMatrix matrix = new DistanceMatrix(testMatrix);
   

See the Phylip Distance matrix programs page for the description of the Phylip distance matrix format.

Constructor Summary

Constructors

Constructor and Description
DistanceMatrix()
DistanceMatrix(File inMatrix)
DistanceMatrix(int inInitialSize)
DistanceMatrix(String inMatrix)

Method Summary

Modifier and Type	Method and Description
void	addKey(String inKey)
void	changeKey(String inOldKey, String inNewKey) Changes the key name inOldKey to inNewKey.
DistanceMatrix	clone()
Float	getDistance(String inKey1, String inKey2)
String	getNearestNeighbor(String inKey)
float	getNetDivergence(String inKey)
Edge<String>	getShortestEdge() Returns the Edge with the shortest distance.
List<Edge<String>>	getSortedEdges(String inSeqId) Returns the Edges for the specified sequence sorted shortest to longest.
boolean	isConsumable()
boolean	isConsumed()
Collection<String>	keySet()
int	numKeys()
void	removeKey(String inKey)
void	removeKeys(Set<String> inKeys)
void	setDistance(String inKey1, String inKey2, Float inDistance)
DistanceMatrix	setIsConsumable(boolean inValue)
DistanceMatrix	setIsConsumed()
int	size()

Methods inherited from class java.lang.Object

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

Constructor Detail

DistanceMatrix

public DistanceMatrix()

DistanceMatrix

public DistanceMatrix(int inInitialSize)

DistanceMatrix

public DistanceMatrix(String inMatrix)

DistanceMatrix

public DistanceMatrix(File inMatrix)
               throws IOException

Throws:

IOException

Method Detail

setIsConsumable

public DistanceMatrix setIsConsumable(boolean inValue)

isConsumable

public boolean isConsumable()

setIsConsumed

public DistanceMatrix setIsConsumed()

isConsumed

public boolean isConsumed()

addKey

public void addKey(String inKey)

removeKey

public void removeKey(String inKey)

removeKeys

public void removeKeys(Set<String> inKeys)

changeKey

public void changeKey(String inOldKey,
                      String inNewKey)

Changes the key name inOldKey to inNewKey. Can be useful in re-expanding names after replacing them in order to comply with the 10-character Phylip format limitation.

Parameters:

inOldKey - the old matrix key

inNewKey - the new matrix key

setDistance

public void setDistance(String inKey1,
                        String inKey2,
                        Float inDistance)

getDistance

public Float getDistance(String inKey1,
                         String inKey2)

size

public int size()

numKeys

public int numKeys()

keySet

public Collection<String> keySet()

getNetDivergence

public float getNetDivergence(String inKey)

getNearestNeighbor

public String getNearestNeighbor(String inKey)

getShortestEdge

public Edge<String> getShortestEdge()

Returns the Edge with the shortest distance. If multiple edges are found with the same distance, no guarantee is made as to which one will be returned.

Returns:

the Edge with the shortest distance

getSortedEdges

public List<Edge<String>> getSortedEdges(String inSeqId)

Returns the Edges for the specified sequence sorted shortest to longest.

Parameters:

inSeqId - the id (key) of the sequence for which Edges should be retrieved

Returns:

the Edges for the specified sequence sorted shortest to longest

clone

public DistanceMatrix clone()

Overrides:

clone in class Object