org.biojava.bio.program.homologene
Interface OrthoPairSet

All Known Implementing Classes:
AbstractOrthoPairSet, SimpleOrthoPairSet

public interface OrthoPairSet

represents the Homologene Group.


Nested Class Summary
static interface OrthoPairSet.Iterator
           
 
Field Summary
static ChangeType MODIFY
           
 
Method Summary
 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.
 

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