org.biojava.nbio.alignment

Class GuideTree.Node

java.lang.Object

org.biojava.nbio.alignment.GuideTree.Node

All Implemented Interfaces:

javax.swing.tree.TreeNode, GuideTreeNode<S,C>

Enclosing class:

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

public class GuideTree.Node
extends java.lang.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 and Description
java.util.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(javax.swing.tree.TreeNode child)
java.lang.String	getName() Returns the name of this node.
GuideTreeNode<S,C>	getParent()
Profile<S,C>	getProfile() Returns the profile stored at this node.
java.util.concurrent.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(java.util.concurrent.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 Detail

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 java.lang.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 java.util.concurrent.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(java.util.concurrent.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 java.util.Enumeration<GuideTreeNode<S,C>> children()

Specified by:

children in interface javax.swing.tree.TreeNode

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface javax.swing.tree.TreeNode

getChildAt

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

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

getIndex

public int getIndex(javax.swing.tree.TreeNode child)

Specified by:

getIndex in interface javax.swing.tree.TreeNode

getParent

public GuideTreeNode<S,C> getParent()

Specified by:

getParent in interface javax.swing.tree.TreeNode

isLeaf

public boolean isLeaf()

Specified by:

isLeaf in interface javax.swing.tree.TreeNode