org.biojava.bio.program.homologene
Class SimpleOrthoPairSet

java.lang.Object
  extended by org.biojava.utils.AbstractChangeable
      extended by org.biojava.bio.program.homologene.AbstractOrthoPairSet
          extended by 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
 class SimpleOrthoPairSet.Iterator
           
 
Field Summary
 
Fields inherited from interface org.biojava.bio.program.homologene.OrthoPairSet
MODIFY
 
Constructor Summary
SimpleOrthoPairSet()
           
 
Method Summary
 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.
 
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