Package org.biojava.bio.program.homologene

Class SimpleOrthoPairSet

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.program.homologene.AbstractOrthoPairSet

org.biojava.bio.program.homologene.SimpleOrthoPairSet

All Implemented Interfaces:

OrthoPairSet, Changeable

public class SimpleOrthoPairSet
extends AbstractOrthoPairSet

a no-frills implementation of a Homologene Group

Author:

David Huen

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	SimpleOrthoPairSet.Iterator

Field Summary

Fields inherited from interface org.biojava.bio.program.homologene.OrthoPairSet

MODIFY

Constructor Summary

Constructors

Constructor	Description
SimpleOrthoPairSet()

Method Summary

Modifier and Type	Method	Description
void	addOrthoPair(OrthoPair orthology)	adds a specified OrthoPair relationship to this group.
double	getMinIdentity()	get the lowest level of identity observed in this Group
String	getName()	retrieves name of this group.
Set	getTaxa()	get the taxa represented in this group
OrthoPairSet.Iterator	iterator()	returns an iterator to the members of this set
void	removeOrthoPair(OrthoPair orthology)	removes a specified OrthoPair relationship from this group.
void	setName(String name)	set the name of this group.
int	size()	returns an iterator to the contents of the set. /** no. of entries in this Homologene group

Methods inherited from class org.biojava.bio.program.homologene.AbstractOrthoPairSet

filter

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleOrthoPairSet

public SimpleOrthoPairSet()

Method Detail

getName

public String getName()

Description copied from interface: OrthoPairSet

retrieves name of this group. Homologene itself does not assign names or identifiers to groups.

setName

public void setName(String name)

Description copied from interface: OrthoPairSet

set the name of this group.

addOrthoPair

public void addOrthoPair(OrthoPair orthology)
                  throws ChangeVetoException

Description copied from interface: OrthoPairSet

adds a specified OrthoPair relationship to this group.

Throws:

ChangeVetoException

removeOrthoPair

public void removeOrthoPair(OrthoPair orthology)
                     throws ChangeVetoException

Description copied from interface: OrthoPairSet

removes a specified OrthoPair relationship from this group.

Throws:

ChangeVetoException

iterator

public OrthoPairSet.Iterator iterator()

Description copied from interface: OrthoPairSet

returns an iterator to the members of this set

getMinIdentity

public double getMinIdentity()

Description copied from interface: OrthoPairSet

get the lowest level of identity observed in this Group

size

public int size()

Description copied from interface: OrthoPairSet

returns an iterator to the contents of the set. /** no. of entries in this Homologene group

getTaxa

public Set getTaxa()

Description copied from interface: OrthoPairSet

get the taxa represented in this group