Package org.openscience.cdk.tools.scaffold

Class TreeNode<MoleculeType>

java.lang.Object

org.openscience.cdk.tools.scaffold.ScaffoldNodeBase<MoleculeType>

org.openscience.cdk.tools.scaffold.TreeNode<MoleculeType>

Type Parameters:

MoleculeType - As MoleculeType, any data type can be defined. In our scenario, the node contains a CDK IAtomContainer.

public class TreeNode<MoleculeType>
extends ScaffoldNodeBase<MoleculeType>

The TreeNodes are nodes from which a ScaffoldTree can be built. It is used to organise the IAtomContainers and enables a relationship between the different objects. A TreeNode can have different children but only one parent. The parents are the smaller parent scaffolds.

Version:

1.0.0.0

Author:

Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de)

Field Summary

Fields inherited from class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase

children, molecule, nonVirtualOriginSmilesList, originSmilesList

Constructor Summary

Constructors

Constructor	Description
TreeNode(MoleculeType aMolecule)	Constructor

Method Summary

Modifier and Type	Method	Description
TreeNode<MoleculeType>	addChild(MoleculeType aMolecule)	Adds a child to the tree node, i.e. links it to a node on the level below.
int	getLevel()	Outputs the level on which the node is located in the graph structure.
TreeNode<MoleculeType>	getParent()	Get the parent node.
boolean	isOrphan()	Shows if the node has parents.
void	setParent(TreeNode<MoleculeType> aParent)	Set the parent node.

Methods inherited from class org.openscience.cdk.tools.scaffold.ScaffoldNodeBase

addNonVirtualOriginSmiles, addOriginSmiles, getChildren, getMolecule, getNonVirtualOriginCount, getNonVirtualOriginSmilesList, getOriginCount, getOriginSmilesList, hasNonVirtualOriginSmiles, isLeaf, setChildren, setMolecule, setNonVirtualOriginSmilesList, setOriginSmilesList

Methods inherited from class java.lang.Object

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

Constructor Details

TreeNode

public TreeNode(MoleculeType aMolecule)

Constructor

Parameters:

aMolecule - molecule of the TreeNode

Method Details

isOrphan

public boolean isOrphan()

Shows if the node has parents. Description copied from ScaffoldNodeBase.

Specified by:

isOrphan in class ScaffoldNodeBase<MoleculeType>

Returns:

Whether the node has parents

addChild

public TreeNode<MoleculeType> addChild(MoleculeType aMolecule)
                                throws NullPointerException

Adds a child to the tree node, i.e. links it to a node on the level below. Description copied from ScaffoldNodeBase.

Specified by:

addChild in class ScaffoldNodeBase<MoleculeType>

Parameters:

aMolecule - Molecule of the child

Returns:

Node of the child

Throws:

NullPointerException - if parameter is null

getLevel

public int getLevel()

Outputs the level on which the node is located in the graph structure. The level indicates the distance to the root (node without parents) and is determined by setting the level of the parent node + 1. The root itself has the level 0. The level is therefore dependent on the data structure and does not have to be set. Description copied from ScaffoldNodeBase.

Specified by:

getLevel in class ScaffoldNodeBase<MoleculeType>

Returns:

level of the node in the entire node collection

getParent

public TreeNode<MoleculeType> getParent()

Get the parent node.

Returns:

parent node

setParent

public void setParent(TreeNode<MoleculeType> aParent)
               throws NullPointerException

Set the parent node.

Parameters:

aParent - parent that are set

Throws:

NullPointerException - if parameter is null