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
a no-frills implementation of a Homologene Group
- Author:
- David Huen
-
Nested Class Summary
Nested Classes -
Field Summary
Fields inherited from interface org.biojava.bio.program.homologene.OrthoPairSet
MODIFY
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addOrthoPair
(OrthoPair orthology) adds a specified OrthoPair relationship to this group.double
get the lowest level of identity observed in this GroupgetName()
retrieves name of this group.getTaxa()
get the taxa represented in this groupiterator()
returns an iterator to the members of this setvoid
removeOrthoPair
(OrthoPair orthology) removes a specified OrthoPair relationship from this group.void
set the name of this group.int
size()
returns an iterator to the contents of the set. /** no. of entries in this Homologene groupMethods 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
-
Constructor Details
-
SimpleOrthoPairSet
public SimpleOrthoPairSet()
-
-
Method Details
-
getName
Description copied from interface:OrthoPairSet
retrieves name of this group. Homologene itself does not assign names or identifiers to groups. -
setName
Description copied from interface:OrthoPairSet
set the name of this group. -
addOrthoPair
Description copied from interface:OrthoPairSet
adds a specified OrthoPair relationship to this group.- Throws:
ChangeVetoException
-
removeOrthoPair
Description copied from interface:OrthoPairSet
removes a specified OrthoPair relationship from this group.- Throws:
ChangeVetoException
-
iterator
Description copied from interface:OrthoPairSet
returns an iterator to the members of this set -
getMinIdentity
Description copied from interface:OrthoPairSet
get the lowest level of identity observed in this Group -
size
Description copied from interface:OrthoPairSet
returns an iterator to the contents of the set. /** no. of entries in this Homologene group -
getTaxa
Description copied from interface:OrthoPairSet
get the taxa represented in this group
-