org.biojava.bio.program.homologene

Interface OrthoPairSet

All Known Implementing Classes:

AbstractOrthoPairSet, SimpleOrthoPairSet

public interface OrthoPairSet

represents the Homologene Group.

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static interface	OrthoPairSet.Iterator

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	MODIFY

Method Summary

Methods

Modifier and Type	Method and Description
void	addOrthoPair(OrthoPair orthology) adds a specified OrthoPair relationship to this group.
OrthoPairSet	filter(OrthoPairFilter filter) filter an OrthoPairSet
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

Field Detail

MODIFY

static final ChangeType MODIFY

Method Detail

getName

String getName()

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

setName

void setName(String name)

set the name of this group.

addOrthoPair

void addOrthoPair(OrthoPair orthology)
                  throws ChangeVetoException

adds a specified OrthoPair relationship to this group.

Throws:

ChangeVetoException

removeOrthoPair

void removeOrthoPair(OrthoPair orthology)
                     throws ChangeVetoException

removes a specified OrthoPair relationship from this group.

Throws:

ChangeVetoException

size

int size()

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

iterator

OrthoPairSet.Iterator iterator()

returns an iterator to the members of this set

getTaxa

Set getTaxa()

get the taxa represented in this group

getMinIdentity

double getMinIdentity()

get the lowest level of identity observed in this Group

filter

OrthoPairSet filter(OrthoPairFilter filter)

filter an OrthoPairSet