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

Interface Graph<S extends Node>

All Known Implementing Classes:

AbstractGraph, ADF, SDRF

public interface Graph<S extends Node>

A directed, acyclic graph that can be used to store Nodes that are linked together. Edges are implicit.

Author:

Tony Burdett

Method Summary

Methods

Modifier and Type	Method and Description
void	addNode(S node) Store a node in the Graph.
void	checkForCycles(Node node, Node childNode) Assertain whether this graph contains any cycles.
Collection<? extends S>	getAllNodes() Lookup all nodes in the SDRF graph
<T extends S> T	getNode(String nodeName, Class<T> nodeType) Lookup a node by name and class type in the SDRF graph.
S	getNode(String nodeName, String nodeType) Lookup a node by name and type in the SDRF graph.
int	getNodeCount() Returns the total number of nodes stored by this SDRF graph.
<T extends S> Collection<T>	getNodes(Class<T> nodeType) Lookup all nodes of the given class type in the SDRF graph.
Collection<? extends S>	getNodes(String nodeType) Lookup all nodes of the given type (by SDRF spec name) in the SDRF graph.
Collection<? extends S>	getRootNodes() Lookup all 'root' nodes in the SDRF graph.
void	removeNode(S node) Remove a node that was previously stored in the Graph.
void	resolveGraphStructure(S node) Update this node being stored with appropriate references to it's parents and update any child node references that are already present in the graph.
void	updateNode(S node) Updates an node in the SDRF graph, on the assumption that its position in the graph, or its children, have been altered.

Method Detail

addNode

void addNode(S node)
             throws ParseException

Store a node in the Graph. This node will be added to the internal graph representation of nodes represented by the graph object. In this way, this graph object represents the data encoded by the spreadsheet rather than directly representing the spreadsheet data structure.

Parameters:

node - the node to store

Throws:

ParseException - if the node being stored would violate the principle that the graph is acyclic

removeNode

void removeNode(S node)

Remove a node that was previously stored in the Graph. This node will be taken out of the internal graph representation of nodes represented by this object.

Note: this method also removes any references elsewhere in the graph to this Node, from parent and child nodes. You should relink your graph around the removed node once you have taken it out: but be warned, this may compromise the structure of the graph.

Parameters:

node - the node to remove

updateNode

void updateNode(S node)
                throws ParseException

Updates an node in the SDRF graph, on the assumption that its position in the graph, or its children, have been altered. Whenever you add or remove children or parents of a node, you should call this method to ensure the SDRF graph stays accurate

Parameters:

node - the node that needs updating

Throws:

ParseException - if the node being stored would violate the principle that the graph is acyclic

getNode

<T extends S> T getNode(String nodeName,
                      Class<T> nodeType)

Lookup a node by name and class type in the SDRF graph. This will return the node if it exists, or null if not.

Type Parameters:

T - the generic node type to lookup

Parameters:

nodeName - the node name

nodeType - the class type of the node

Returns:

the node, if it exists, or null otherwise

getNode

S getNode(String nodeName,
        String nodeType)

Lookup a node by name and type in the SDRF graph. This will return the node if it exists, or null if not.

Parameters:

nodeName - the node name

nodeType - the tag that describes the node in the SDRF spec

Returns:

the node, if it exists, or null otherwise

getNodes

<T extends S> Collection<T> getNodes(Class<T> nodeType)

Lookup all nodes of the given class type in the SDRF graph. This will return a collection of the nodes of this type, which will be empty if there are none.

Type Parameters:

T - the generic node type to lookup

Parameters:

nodeType - the class type of the node

Returns:

the node, if it exists, or null otherwise

getNodes

Collection<? extends S> getNodes(String nodeType)

Lookup all nodes of the given type (by SDRF spec name) in the SDRF graph. This will return a collection of the nodes of this type, which will be empty if there are none.

Parameters:

nodeType - the class type of the node

Returns:

the node, if it exists, or null otherwise

getRootNodes

Collection<? extends S> getRootNodes()

Lookup all 'root' nodes in the SDRF graph. A root node is the node in the graph declared at the far left hand side of the SDRF spreadsheet; the nodes which all others are children of. Normally, this is likely to be a "Source" node, but the SDRF specification allows for any nodes to be present here. Use this method to return the full collection.

This method is essentially a convenience method around getNodes(Class), substituting the class parameter for the known root node type.

Returns:

the collection of root nodes in the SDRF graph

getAllNodes

Collection<? extends S> getAllNodes()

Lookup all nodes in the SDRF graph

Returns:

all nodes in the SDRF

getNodeCount

int getNodeCount()

Returns the total number of nodes stored by this SDRF graph.

Returns:

the number of nodes in this SDRF

resolveGraphStructure

void resolveGraphStructure(S node)
                           throws ParseException

Update this node being stored with appropriate references to it's parents and update any child node references that are already present in the graph.

Parameters:

node - the node being stored

Throws:

ParseException - if the node being stored would violate the principle that the graph is acyclic

checkForCycles

void checkForCycles(Node node,
                  Node childNode)
                    throws ParseException

Assertain whether this graph contains any cycles. This graph interface is designed to store DAGs and as such any detected cycles should result in a ParseException being thrown

Parameters:

node - the node to check

childNode - the child node that should be added

Throws:

ParseException - if a cycle is detected