uk.ac.ebi.arrayexpress2.magetab.datamodel.graph

Interface Node

All Known Subinterfaces:

ADFNode, SDRFNode

All Known Implementing Classes:

AbstractADFNode, AbstractNode, AbstractSDRFNode, ArrayDataMatrixNode, ArrayDataNode, ArrayDesignNode, AssayNode, CompositeElementNode, DerivedArrayDataMatrixNode, DerivedArrayDataNode, ExtractNode, FeatureNode, HybridizationNode, ImageNode, LabeledExtractNode, NormalizationNode, ProtocolApplicationNode, ReporterNode, SampleNode, ScanNode, SourceNode, UnresolvedPlaceholderNode

public interface Node

A node in a MAGETAB graph data structure (either ADF or SDRF). Nodes have defined types, depending on the header in the specification, and can have a subset of attributes. These attributes vary according to the type. This interface provides methods for setting the node type (i.e. the header value - this may be qualified with subtypes in some cases by including [] or () values), the node name (the actual value entered into a cell) and the set of child nodes in the graph, as encoded in the MAGE-TAB spreadsheet.

Author:

Tony Burdett

Method Summary

Methods

Modifier and Type	Method and Description
void	addChildNode(Node childNode) Adds the child node to this Node.
void	addChildNode(String tag, String value) Adds a child node to this Node.
void	addParentNode(Node parentNode) Adds a parent node to this node
void	addParentNode(String tag, String value) Adds a parent node to this Node.
Set<Node>	getChildNodes() Returns the set of nodes that are children of this node.
String	getNodeName() Get the value associated to this node in the spreadsheet.
String	getNodeType() Get the type of this node in the graph.
Set<Node>	getParentNodes() Returns the set of nodes that are parents of this node.
void	removeChildNode(Node childNode) Removes the reference to the child from this node
void	removeParentNode(Node parentNode) Removes the reference to the parent from this node
void	setNodeName(String name) Set the value associated to this node in the spreadsheet.
boolean	updateChildNode(Node nodeToUpdate) Updates a child node equal to the supplied node with a new object reference.
boolean	updateParentNode(Node nodeToUpdate) Updates a parent node equal to the supplied node with a new object reference.

Method Detail

getNodeType

String getNodeType()

Get the type of this node in the graph.

Returns:

the standardised header string for this node

setNodeName

void setNodeName(String name)

Set the value associated to this node in the spreadsheet. In other words, the particular entry in the current row under the given type.

Parameters:

name - the value for this node name entry

getNodeName

String getNodeName()

Get the value associated to this node in the spreadsheet. In other words, the particular entry in the current row under the given type.

Returns:

the value for this node name entry

addChildNode

void addChildNode(Node childNode)

Adds the child node to this Node.

Parameters:

childNode - the node to add

removeChildNode

void removeChildNode(Node childNode)

Removes the reference to the child from this node

Parameters:

childNode - the node to remove

addChildNode

void addChildNode(String tag,
                String value)

Adds a child node to this Node. The child node will be a placeholder until all references are correctly resolved, but this placeholder will be equal to the actual node.

Parameters:

tag - the type (or column header, or tag) of the node to add

value - the value (or node name) of the node to add

updateChildNode

boolean updateChildNode(Node nodeToUpdate)

Updates a child node equal to the supplied node with a new object reference. Use this whenever temporary nodes (usually of type UnresolvedPlaceholderNode) have been stored, and are subsequently updated with a correct type.

This method capitalises on the fact that nodes with the same type and name parameter are equal, even if the actual object references are different. Invoking this method updates the node to the new reference.

Parameters:

nodeToUpdate - the new object reference to use

Returns:

true if the node was replaced, false otherwise

getChildNodes

Set<Node> getChildNodes()

Returns the set of nodes that are children of this node.

Returns:

the nodes that are directly linked downstream of this node

addParentNode

void addParentNode(Node parentNode)

Adds a parent node to this node

Parameters:

parentNode - the parent node to add

removeParentNode

void removeParentNode(Node parentNode)

Removes the reference to the parent from this node

Parameters:

parentNode - the node to remove

addParentNode

void addParentNode(String tag,
                 String value)

Adds a parent node to this Node. The parent node will be a placeholder until all references are correctly resolved, but this placeholder will be equal to the actual node.

Parameters:

tag - the type (or column header, or tag) of the node to add

value - the value (or node name) of the node to add

updateParentNode

boolean updateParentNode(Node nodeToUpdate)

Updates a parent node equal to the supplied node with a new object reference. Use this whenever temporary nodes (usually of type UnresolvedPlaceholderNode) have been stored, and are subsequently updated with a correct type.

This method capitalises on the fact that nodes with the same type and name parameter are equal, even if the actual object references are different. Invoking this method updates the node to the new reference.

Parameters:

nodeToUpdate - the new object reference to use

Returns:

true if the node was replaced, false otherwise

getParentNodes

Set<Node> getParentNodes()

Returns the set of nodes that are parents of this node.

Returns:

the parents of this node