rapgreen

Class TreeReconciler

java.lang.Object

rapgreen.TreeReconciler

public class TreeReconciler
extends java.lang.Object

Tree reconciliation class.

This class manages the 3 entities (species tree, gene tree and reconciled tree), during the reconciliation process.

Field Summary

Fields

Modifier and Type	Field and Description
static double	geneCollapseThreshold Gene tree branch collapse threshold, in term of branch support, initialized to 0.95
static double	geneDepthThreshold Depth threshold, under which no duplications are predicted (polymorphism / sequencing error).
Tree	geneTree The gene tree
static int	kLevel K-level for subtree neighbor measure.
Tree	reconciledTree The reconciled tree
static double	speciesCollapseThreshold Species tree branch collapse threshold, in term of length, initialized to 10.0.
Tree	speciesTree The species tree

Constructor Summary

Constructors

Constructor and Description
TreeReconciler(Tree geneTree, Tree speciesTree) Standard constructor, from species and gene trees, constructing reconciled tree.

Method Summary

Methods

Modifier and Type	Method and Description
Tree	advanceInLosses(Tree r, Tree g) Return the next not-loss event
boolean	areCongruent(Tree g, Tree r, java.util.Vector congruentGeneNodes, java.util.Vector congruentReconciledNodes, java.util.Vector congruentReconciledLengths) Return true if the two nodes are congruent.
boolean	areMutuallyIncluded(Tree g, Tree r) Return true if the taxa under the two nodes are mutually included
int	cardinality(Tree r) Return the number of not-loss sons
int	findReductionCandidat(Tree g, Tree r) Return the index of a possible candidat
void	parseSpecies(Tree rootedGeneTree) Parse labels to extract species name, and put it into pretreated structures
int	reconciliation(Tree g, Tree r) Recursive method that reconcile gene and reconciled tree (initialized with species tree topology)
void	removeUselessSubtrees(Tree tree, java.util.Vector vector) Parse labels to extract species name, and put it into pretreated structures
boolean	sonExclusion(Tree g) Return true if g respect the condition of son exclusion (mandatory to be congruent to a species tree).

Methods inherited from class java.lang.Object

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

Field Detail

geneCollapseThreshold

public static double geneCollapseThreshold

Gene tree branch collapse threshold, in term of branch support, initialized to 0.95

speciesCollapseThreshold

public static double speciesCollapseThreshold

Species tree branch collapse threshold, in term of length, initialized to 10.0. No effect if species tree does not have branch lengths

geneDepthThreshold

public static double geneDepthThreshold

Depth threshold, under which no duplications are predicted (polymorphism / sequencing error).

kLevel

public static int kLevel

K-level for subtree neighbor measure.

geneTree

public Tree geneTree

The gene tree

speciesTree

public Tree speciesTree

The species tree

reconciledTree

public Tree reconciledTree

The reconciled tree

Constructor Detail

TreeReconciler

public TreeReconciler(Tree geneTree,
              Tree speciesTree)

Standard constructor, from species and gene trees, constructing reconciled tree.

Parameters:

geneTree - The tree representing gene family evolution history

speciesTree - The global species tree

Method Detail

parseSpecies

public void parseSpecies(Tree rootedGeneTree)

Parse labels to extract species name, and put it into pretreated structures

removeUselessSubtrees

public void removeUselessSubtrees(Tree tree,
                         java.util.Vector vector)

Parse labels to extract species name, and put it into pretreated structures

Parameters:

tree - The species tree to clean

vector - The list of allowed taxa

reconciliation

public int reconciliation(Tree g,
                 Tree r)

Recursive method that reconcile gene and reconciled tree (initialized with species tree topology)

Parameters:

g - The tree representing gene family evolution history

r - The tree to reconcile

Returns:

The number of duplications needed.

areCongruent

public boolean areCongruent(Tree g,
                   Tree r,
                   java.util.Vector congruentGeneNodes,
                   java.util.Vector congruentReconciledNodes,
                   java.util.Vector congruentReconciledLengths)

Return true if the two nodes are congruent.

Parameters:

g - The tree representing gene family evolution history

r - The tree to reconcile

congruentGeneNodes - the list of subnode after reduction in the gene tree

congruentReconciledNodes - the list of subnode after reduction in the reconciled tree

congruentReconciledLengths - the list of cumuled lengths of congruent reconciled nodes

Returns:

True if the two nodes are congruent

sonExclusion

public boolean sonExclusion(Tree g)

Return true if g respect the condition of son exclusion (mandatory to be congruent to a species tree).

Parameters:

g - The tree representing gene family evolution history

Returns:

True g respect the son exclusion, or false otherwise.

cardinality

public int cardinality(Tree r)

Return the number of not-loss sons

Parameters:

r - The tree to reconcile

Returns:

Number of sons.

findReductionCandidat

public int findReductionCandidat(Tree g,
                        Tree r)

Return the index of a possible candidat

Parameters:

g - The tree representing gene family evolution history

r - The tree to reconcile

Returns:

Index between positive for gene tree and negative for reconciled tree.

areMutuallyIncluded

public boolean areMutuallyIncluded(Tree g,
                          Tree r)

Return true if the taxa under the two nodes are mutually included

Parameters:

g - The tree representing gene family evolution history

r - The tree to reconcile

Returns:

True of the taxa are mutually included, or false otherwise.

advanceInLosses

public Tree advanceInLosses(Tree r,
                   Tree g)

Return the next not-loss event

Parameters:

r - The tree

Returns:

The next not-loss event.