Package org.biojava.nbio.alignment

Class GuideTree.Node

java.lang.Object

org.biojava.nbio.alignment.GuideTree.Node

All Implemented Interfaces:

TreeNode, GuideTreeNode<S,C>

Enclosing class:

GuideTree<S extends Sequence<C>,C extends Compound>

public class GuideTree.Node
extends Object
implements GuideTreeNode<S,C>

Implements a data structure for the node in a guide tree used during progressive multiple sequence alignment.

Method Summary

Modifier and Type	Method	Description
Enumeration<GuideTreeNode<S,C>>	children()
boolean	getAllowsChildren()
GuideTreeNode<S,C>	getChild1()	Returns the first child node of this node.
GuideTreeNode<S,C>	getChild2()	Returns the second child node of this node.
GuideTreeNode<S,C>	getChildAt(int childIndex)
int	getChildCount()
double	getDistanceToParent()	Returns the difference in height of this node and it's parent node.
int	getIndex(TreeNode child)
String	getName()	Returns the name of this node.
GuideTreeNode<S,C>	getParent()
Profile<S,C>	getProfile()	Returns the profile stored at this node.
Future<ProfilePair<S,C>>	getProfileFuture()	Returns the profile future stored at this node, but does not force the calculation, yet.
boolean	isLeaf()
void	setProfile(Profile<S,C> profile)	Stores the given profile.
void	setProfileFuture(Future<ProfilePair<S,C>> profileFuture)	Stores the given profile future.

Methods inherited from class java.lang.Object

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

Method Details

getChild1

public GuideTreeNode<S,C> getChild1()

Description copied from interface: GuideTreeNode

Returns the first child node of this node. For leaf nodes (sequences), this will be null.

Specified by:

getChild1 in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

Returns:

the first child node of this node

getChild2

public GuideTreeNode<S,C> getChild2()

Description copied from interface: GuideTreeNode

Returns the second child node of this node. For leaf nodes (sequences), this will be null.

Specified by:

getChild2 in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

Returns:

the second child node of this node

getDistanceToParent

public double getDistanceToParent()

Description copied from interface: GuideTreeNode

Returns the difference in height of this node and it's parent node. A likely meaning of this distance is half the percent difference between this node and it's sibling node.

Specified by:

getDistanceToParent in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

Returns:

the difference in height of this node to it's parent node

getName

public String getName()

Description copied from interface: GuideTreeNode

Returns the name of this node. For leaf nodes (sequences), this will likely be the accession ID.

Specified by:

getName in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

Returns:

the name of this node

getProfile

public Profile<S,C> getProfile()

Description copied from interface: GuideTreeNode

Returns the profile stored at this node. If the node is a leaf, the profile is that of a single sequence. If not, this returns null until GuideTreeNode.setProfile(Profile) has been called.

Specified by:

getProfile in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

Returns:

the profile stored at this node

getProfileFuture

public Future<ProfilePair<S,C>> getProfileFuture()

Description copied from interface: GuideTreeNode

Returns the profile future stored at this node, but does not force the calculation, yet. This allows alignment tasks for the entire tree to be queued in a post-order traversal before concurrent execution.

Specified by:

getProfileFuture in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

Returns:

the profile future stored at this node

setProfile

public void setProfile(Profile<S,C> profile)

Description copied from interface: GuideTreeNode

Stores the given profile.

Specified by:

setProfile in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

Parameters:

profile - new profile stored at this node

setProfileFuture

public void setProfileFuture(Future<ProfilePair<S,C>> profileFuture)

Description copied from interface: GuideTreeNode

Stores the given profile future. This allows concurrent execution of alignment tasks.

Specified by:

setProfileFuture in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

Parameters:

profileFuture - new profile to be calculated and then stored at this node

children

public Enumeration<GuideTreeNode<S,C>> children()

Specified by:

children in interface TreeNode

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface TreeNode

getChildAt

public GuideTreeNode<S,C> getChildAt(int childIndex)

Specified by:

getChildAt in interface TreeNode

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

getIndex

public int getIndex(TreeNode child)

Specified by:

getIndex in interface TreeNode

getParent

public GuideTreeNode<S,C> getParent()

Specified by:

getParent in interface TreeNode

isLeaf

public boolean isLeaf()

Specified by:

isLeaf in interface TreeNode