softparsmap
Class PreferredTree

java.lang.Object
  ooc.LinkedTagInstance
      softparsmap.PreferredTree

All Implemented Interfaces:

java.util.Comparator, Dependencies

Direct Known Subclasses:

PreferredTreeStandard

public abstract class PreferredTree

extends LinkedTagInstance

implements java.util.Comparator

Classes extending this abstract class are used by task ComputeRoot to choose the preferred gene tree.

Constructor Summary

PreferredTree()

Method Summary

abstract java.lang.String	getDesc(GeneNode geneTree) Returns the data used in the given gene tree that is used to choose the preferred tree.
GeneNode	getFreeGeneTree() Returns the free gene tree.
SpeciesNode	getSpeciesTree() Returns the rooted species tree.
void	setFreeGeneTree(GeneNode freeGeneTree)
void	setSpeciesTree(SpeciesNode speciesTree)

Methods inherited from class ooc.LinkedTagInstance

containsKey, get, getAttribute, getAttributeBoolean, getAttributeDouble, getAttributeFloat, getAttributeInteger, getAttributeList, getAttributeRef, getAttributeShort, getAttributeString, getAttributeTag, getChildIterator, getChildIteratorByName, getContainer, getContainerTag, getFirstChildTagByName, getTag, getTagId, getTagInstance, getTagInstance, getTagRef, hasAttributeValue, hasChildTagByName, hasChildTags, hasTag, isMutable, keySet, put, remove, setTag, setupInstance

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.util.Comparator

compare, equals

Constructor Detail

PreferredTree

public PreferredTree()

Method Detail

getFreeGeneTree

public GeneNode getFreeGeneTree()

Returns the free gene tree.

Returns:

the free gene tree.

See Also:

GeneNode

setFreeGeneTree

public void setFreeGeneTree(GeneNode freeGeneTree)

getSpeciesTree

public SpeciesNode getSpeciesTree()

Returns the rooted species tree.

Returns:

the rooted species tree.

See Also:

SpeciesNode

setSpeciesTree

public void setSpeciesTree(SpeciesNode speciesTree)

getDesc

public abstract java.lang.String getDesc(GeneNode geneTree)

Returns the data used in the given gene tree that is used to choose the preferred tree.

Parameters:

geneTree - is the given gene tree.

Returns:

the data used to choose the preferred tree.