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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.program.homologene.AbstractOrthoPairSet
org.biojava.bio.program.homologene.SimpleOrthoPairSet
public class SimpleOrthoPairSet
a no-frills implementation of a Homologene Group
Nested Class Summary | |
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class |
SimpleOrthoPairSet.Iterator
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Field Summary |
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Fields inherited from interface org.biojava.bio.program.homologene.OrthoPairSet |
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MODIFY |
Constructor Summary | |
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SimpleOrthoPairSet()
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Method Summary | |
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void |
addOrthoPair(OrthoPair orthology)
adds a specified OrthoPair relationship to this group. |
double |
getMinIdentity()
get the lowest level of identity observed in this Group |
java.lang.String |
getName()
retrieves name of this group. |
java.util.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(java.lang.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 |
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filter |
Methods inherited from class org.biojava.utils.AbstractChangeable |
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addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SimpleOrthoPairSet()
Method Detail |
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public java.lang.String getName()
OrthoPairSet
public void setName(java.lang.String name)
OrthoPairSet
public void addOrthoPair(OrthoPair orthology) throws ChangeVetoException
OrthoPairSet
ChangeVetoException
public void removeOrthoPair(OrthoPair orthology) throws ChangeVetoException
OrthoPairSet
ChangeVetoException
public OrthoPairSet.Iterator iterator()
OrthoPairSet
public double getMinIdentity()
OrthoPairSet
public int size()
OrthoPairSet
public java.util.Set getTaxa()
OrthoPairSet
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