Package org.openscience.cdk.tools.scaffold

Class NetworkNode<MoleculeType>

java.lang.Object

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

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

Type Parameters:

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

public class NetworkNode<MoleculeType>
extends ScaffoldNodeBase<MoleculeType>

The NetworkNodes are nodes from which a ScaffoldNetwork can be built. It is used to organise the IAtomContainers and enables a relationship between the different objects. A NetworkNode can have multiple children and parents. 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
NetworkNode(MoleculeType aMolecule)	Creates a NetworkNode

Method Summary

Modifier and Type	Method	Description
NetworkNode<MoleculeType>	addChild(MoleculeType aMolecule)	Adds a child to the network node, i.e. links it to a node on the level below.
void	addParent(NetworkNode<MoleculeType> aParent)	Add the parents node and add this node as child to the parent node if not already done.
int	getLevel()	Outputs the level on which the node is located in the graph structure.
List<NetworkNode<MoleculeType>>	getParents()	Get the parents of the node.
boolean	isOrphan()	Shows if the node has parents.
void	setParents(List<NetworkNode<MoleculeType>> aParents)	Set the parents of the 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

NetworkNode

public NetworkNode(MoleculeType aMolecule)

Creates a NetworkNode

Parameters:

aMolecule - molecule of the NetworkNode

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 NetworkNode<MoleculeType> addChild(MoleculeType aMolecule)
                                   throws NullPointerException

Adds a child to the network 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

addParent

public void addParent(NetworkNode<MoleculeType> aParent)
               throws NullPointerException

Add the parents node and add this node as child to the parent node if not already done.

Parameters:

aParent - parent that are added

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

getParents

public List<NetworkNode<MoleculeType>> getParents()

Get the parents of the node.

Returns:

parents node

setParents

public void setParents(List<NetworkNode<MoleculeType>> aParents)
                throws NullPointerException

Set the parents of the node.

Parameters:

aParents - parents that are set

Throws:

NullPointerException - if parameter is null