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

Class AbstractGraph<S extends Node>

java.lang.Object

uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractGraph<S>

All Implemented Interfaces:

Graph<S>

Direct Known Subclasses:

ADF, SDRF

public abstract class AbstractGraph<S extends Node>
extends Object
implements Graph<S>

An abstract top-level implementation of a MAGE-TAB graph. This takes care of all the basic functionality of storing, removing and querying for nodes and checking graph integrity.

Author:

Tony Burdett

Constructor Summary

Constructors

Constructor and Description
AbstractGraph()

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
protected org.slf4j.Logger	getLog()
<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(Node 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.

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractGraph

public AbstractGraph()

Method Detail

getLog

protected org.slf4j.Logger getLog()

addNode

public void addNode(S node)
             throws ParseException

Description copied from interface: Graph

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.

Specified by:

addNode in interface Graph<S extends Node>

Parameters:

node - the node to store

Throws:

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

removeNode

public void removeNode(Node node)

Description copied from interface: Graph

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.

Specified by:

removeNode in interface Graph<S extends Node>

Parameters:

node - the node to remove

updateNode

public void updateNode(S node)
                throws ParseException

Description copied from interface: Graph

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

Specified by:

updateNode in interface Graph<S extends Node>

Parameters:

node - the node that needs updating

Throws:

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

getNode

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

Description copied from interface: Graph

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

Specified by:

getNode in interface Graph<S extends Node>

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

public S getNode(String nodeName,
        String nodeType)

Description copied from interface: Graph

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

Specified by:

getNode in interface Graph<S extends Node>

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

getAllNodes

public Collection<? extends S> getAllNodes()

Description copied from interface: Graph

Lookup all nodes in the SDRF graph

Specified by:

getAllNodes in interface Graph<S extends Node>

Returns:

all nodes in the SDRF

getNodes

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

Description copied from interface: Graph

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.

Specified by:

getNodes in interface Graph<S extends Node>

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

public Collection<? extends S> getNodes(String nodeType)

Description copied from interface: Graph

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.

Specified by:

getNodes in interface Graph<S extends Node>

Parameters:

nodeType - the class type of the node

Returns:

the node, if it exists, or null otherwise

getRootNodes

public Collection<? extends S> getRootNodes()

Description copied from interface: Graph

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 Graph.getNodes(Class), substituting the class parameter for the known root node type.

Specified by:

getRootNodes in interface Graph<S extends Node>

Returns:

the collection of root nodes in the SDRF graph

getNodeCount

public int getNodeCount()

Description copied from interface: Graph

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

Specified by:

getNodeCount in interface Graph<S extends Node>

Returns:

the number of nodes in this SDRF

resolveGraphStructure

public void resolveGraphStructure(S node)
                           throws ParseException

Description copied from interface: Graph

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.

Specified by:

resolveGraphStructure in interface Graph<S extends Node>

Parameters:

node - the node being stored

Throws:

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

checkForCycles

public void checkForCycles(Node node,
                  Node childNode)
                    throws ParseException

Description copied from interface: Graph

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

Specified by:

checkForCycles in interface Graph<S extends Node>

Parameters:

node - the node to check

childNode - the child node that should be added

Throws:

ParseException - if a cycle is detected