GuideTreeNode (biojava 5.2.0 API)

Type Parameters:

S - each Sequence in the tree is of type S

C - each element of a Sequence is a Compound of type C

All Superinterfaces:

TreeNode

All Known Implementing Classes:

GuideTree.Node
```
public interface GuideTreeNode<S extends Sequence<C>,C extends Compound>
extends TreeNode
```
Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.

Author:

Mark Chapman

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`GuideTreeNode<S,C>`	`getChild1()`	Returns the first child node of this node.
`GuideTreeNode<S,C>`	`getChild2()`	Returns the second child node of this node.
`double`	`getDistanceToParent()`	Returns the difference in height of this node and it's parent node.
`String`	`getName()`	Returns the name of this node.
`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.
`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 interface javax.swing.tree.TreeNode
children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

- Method Detail
  - getChild1
```
GuideTreeNode<S,C> getChild1()
```
    Returns the first child node of this node. For leaf nodes (sequences), this will be null.
    
    Returns:
    
    the first child node of this node
  - getChild2
```
GuideTreeNode<S,C> getChild2()
```
    Returns the second child node of this node. For leaf nodes (sequences), this will be null.
    
    Returns:
    
    the second child node of this node
  - getDistanceToParent
```
double getDistanceToParent()
```
    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.
    
    Returns:
    
    the difference in height of this node to it's parent node
  - getName
```
String getName()
```
    Returns the name of this node. For leaf nodes (sequences), this will likely be the accession ID.
    
    Returns:
    
    the name of this node
  - getProfile
```
Profile<S,C> getProfile()
```
    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 setProfile(Profile) has been called.
    
    Returns:
    
    the profile stored at this node
  - getProfileFuture
```
Future<ProfilePair<S,C>> getProfileFuture()
```
    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.
    
    Returns:
    
    the profile future stored at this node
  - setProfile
```
void setProfile(Profile<S,C> profile)
```
    Stores the given profile.
    
    Parameters:
    
    profile - new profile stored at this node
  - setProfileFuture
```
void setProfileFuture(Future<ProfilePair<S,C>> profileFuture)
```
    Stores the given profile future. This allows concurrent execution of alignment tasks.
    
    Parameters:
    
    profileFuture - new profile to be calculated and then stored at this node

Method Summary

Methods inherited from interface javax.swing.tree.TreeNode

Method Detail

getChild1

getChild2

getDistanceToParent

getName

getProfile

getProfileFuture

setProfile

setProfileFuture