softparsmap
Class MuNode

java.lang.Object
  softparsmap.Node
      softparsmap.GeneNode
          softparsmap.MuNode

All Implemented Interfaces:

java.lang.Comparable

public class MuNode

extends GeneNode

This class contains the code that implements the soft interpretation of gene duplication and loss. When inserting species splits this class will also be used when reducing uncertainties.

Method Summary

SpeciesNode	getM() See the m-map in the article.
java.util.Set	getMM() See the M-map in the article.
java.util.Set	getSL() See the SL function in the article.
boolean	isEdgeWeak() Returns true if the edge for this node is weak, else false.

Methods inherited from class softparsmap.GeneNode

cloneNode, cloneTree, collapsedEdges, collapseEdges, countDuplications, countGeneLosses, countMutation, countStrongEdges, duplicatedNode, findLeaf, findLeaf, findNode, findNodeForUnrootedSplit, getChildIterator, getCollapsedEdge, getDuplicatedNodes, getDuplicationsNode, getEdgeType, getEdgeValue, getFamily, getGeneLossesNode, getInternalNodes, getPropertyFile, hasFamily, hasM, hasMM, hasSL, insertSpeciesTreeSplits, nextNode, nextNode, pruneOneChildNodes, reroot, rerootThis, resolveUncertainties, rootedEquals, setCollapsedEdge, setEdge, setEdgeType, setEdgeValue, setFamily, setFamilyTree, setNewLabel

Methods inherited from class softparsmap.Node

addChild, compareTo, equals, findLCA, getChildren, getLabel, getLeaves, getMap, getNodes, getParent, getRoot, getSplits, hasChildren, hashCode, isBinaryTree, isConsistentWith, isRoot, nextUnique, numChildren, removeChild, setMap, setNextUnique, toString, toStringAll, toStringTable, toStringTree

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Method Detail

getM

public SpeciesNode getM()

Description copied from class: GeneNode

See the m-map in the article.

Overrides:

getM in class GeneNode

Returns:

the mapped species node

getMM

public java.util.Set getMM()

Description copied from class: GeneNode

See the M-map in the article.

Overrides:

getMM in class GeneNode

Returns:

a set of species nodes.

See Also:

SpeciesNode

getSL

public java.util.Set getSL()

Description copied from class: GeneNode

See the SL function in the article.

Overrides:

getSL in class GeneNode

Returns:

a set of species nodes.

See Also:

SpeciesNode

isEdgeWeak

public boolean isEdgeWeak()

Description copied from class: GeneNode

Returns true if the edge for this node is weak, else false.

Overrides:

isEdgeWeak in class GeneNode

Returns:

true if the edge for this node is weak, else false.