org.ginsim.core.graph.regulatorygraph

Class RegulatoryGraphImpl

java.lang.Object

org.ginsim.core.graph.AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>

org.ginsim.core.graph.regulatorygraph.RegulatoryGraphImpl

All Implemented Interfaces:

Graph<RegulatoryNode,RegulatoryMultiEdge>, GraphModel<RegulatoryNode,RegulatoryMultiEdge>, GraphViewListener, RegulatoryGraph

public final class RegulatoryGraphImpl
extends AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>
implements RegulatoryGraph

Implementation of the RegulatoryGraph interface.

Author:

Aurelien Naldi

Field Summary

Fields

Modifier and Type	Field and Description
static String	GRAPH_ZIP_NAME

Fields inherited from class org.ginsim.core.graph.AbstractGraph

attributes, graphAnnotation, graphName, ZIP_PREFIX

Constructor Summary

Constructors

Constructor and Description
RegulatoryGraphImpl() Create a new Regulatory graph

Method Summary

Modifier and Type	Method and Description
RegulatoryMultiEdge	addEdge(RegulatoryNode source, RegulatoryNode target, RegulatoryEdgeSign sign) Add a signed edge
RegulatoryEdge	addNewEdge(String from, String to, byte minvalue, RegulatoryEdgeSign sign) add an edge from textual parameters (for the parser).
RegulatoryEdge	addNewEdge(String from, String to, byte minvalue, String sign) add an edge from textual parameters (for the parser).
RegulatoryNode	addNewNode(String id, String name, byte max) add a node from textual parameters (for the parser).
RegulatoryNode	addNode()
boolean	addNode(RegulatoryNode node) Add a node to this graph structure
static boolean	associationValid(RegulatoryGraph regGraph, DynamicGraph dynGraph) Test if an association between a regulatory graph and a state transition graph is valid: all what we can do is checking the node-order to see if they obviously differ (by size of node's name).
void	canApplyNewMaxValue(RegulatoryNode node, byte newMax, List l_fixable, List l_conflict)
void	changeNodeId(Object node, String newId)
protected List	doMerge(Graph<RegulatoryNode,RegulatoryMultiEdge> otherGraph) Specialized method that execute the merging of the given graph with the current one Must be override at specialized graph level
Map<String,String>	getAttributes() Retrieve graph-level attributes
String	getDisplayName(RegulatoryNode node) Retrieve the name to use when displaying a graph node.
protected GINMLWriter	getGINMLWriter()
protected String	getGraphZipName() Return the zip extension for the graph type
org.colomoto.mddlib.MDDManager	getMDDFactory() Construct a MDDFactory associated to the nodes of this graph
int[]	getMDDs(org.colomoto.mddlib.MDDManager factory) Construct MDD representation of the logical functions of the nodes of this graph.
org.colomoto.biolqm.LogicalModel	getModel() Get a ready-to-be-used model (list of nodes and functions, no graph structure)
org.colomoto.biolqm.LogicalModel	getModel(NodeOrderer orderer) Get a ready-to-be-used model (list of nodes and functions, no graph structure)
org.colomoto.biolqm.LogicalModel	getModel(NodeOrderer orderer, boolean withLayout) Get a ready-to-be-used model (list of nodes and functions, no graph structure)
List<org.colomoto.biolqm.NodeInfo>	getNodeInfos()
List<RegulatoryNode>	getNodeOrder() Return the node order
List<RegulatoryNode>	getNodeOrderForSimulation()
int	getNodeOrderSize() Return the size of the node order
Collection<RegulatoryNode>	getNodes() Return the Collection of the graph nodes
List<List<byte[]>>	getOracles() Accesses the oracles associated with the graph
List<byte[]>	getStates() Accesses the initial states associated with the graph
Graph	getSubgraph(Collection<RegulatoryNode> v_vertex, Collection<RegulatoryMultiEdge> v_edges) Specialized method that build the sub-graph corresponding to the given lists of vertices and edges The returned graph contains clones of the given graph objects structured as they are in the current graph
boolean	hasOracles() Checks whether the graph has oracles associated
boolean	idExists(String newId)
boolean	isStateful() Checks whether the graph has states associated
boolean	removeEdge(RegulatoryMultiEdge edge) Remove an edge from the graph.
boolean	removeNode(RegulatoryNode obj) Remove a node from the graph.
List<RegulatoryNode>	searchNodes(String regexp) Search the vertices with ID matching the given regular expression.
void	setAttribute(String name, String value)
void	setNodeOrder(List<RegulatoryNode> nodeOrder) Set a list of class dependent objects representing the order of node as defined by the model
void	setOracles(List<List<byte[]>> _oracles) Associates a set of oracles to the graph
void	setStates(List<byte[]> states) Associates a set of initial states to the graph

Methods inherited from class org.ginsim.core.graph.AbstractGraph

addEdge, addViewListener, containsEdge, containsNode, copyView, damage, doSave, fireGraphChange, fireMetaChange, getAnnotation, getCachedEdgeAttributeReader, getCachedNodeAttributeReader, getDimension, getEdge, getEdgeAttributeReader, getEdges, getExistingNode, getGraphName, getIncomingEdges, getNodeAttributeReader, getNodeByName, getNodeCount, getOutgoingEdges, getShortestPath, getStronglyConnectedComponents, getStyleManager, isEmpty, merge, refresh, repaint, save, save, setGraphName

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.ginsim.core.graph.Graph

addViewListener, copyView, fireGraphChange, getDimension, getEdgeAttributeReader, getNodeAttributeReader, getStyleManager, save, save

Methods inherited from interface org.ginsim.core.graph.GraphModel

addEdge, containsEdge, containsNode, getAnnotation, getEdge, getEdges, getExistingNode, getGraphName, getIncomingEdges, getNodeByName, getNodeCount, getOutgoingEdges, getShortestPath, getStronglyConnectedComponents, merge, setGraphName

Field Detail

GRAPH_ZIP_NAME

public static final String GRAPH_ZIP_NAME

See Also:

Constant Field Values

Constructor Detail

RegulatoryGraphImpl

public RegulatoryGraphImpl()

Create a new Regulatory graph

Method Detail

getNodeOrder

public List<RegulatoryNode> getNodeOrder()

Description copied from interface: RegulatoryGraph

Return the node order

Specified by:

getNodeOrder in interface RegulatoryGraph

Returns:

the node order as a list of RegulatoryNode

getNodeInfos

public List<org.colomoto.biolqm.NodeInfo> getNodeInfos()

Specified by:

getNodeInfos in interface RegulatoryGraph

getNodeOrderSize

public int getNodeOrderSize()

Description copied from class: AbstractGraph

Return the size of the node order

Specified by:

getNodeOrderSize in interface GraphModel<RegulatoryNode,RegulatoryMultiEdge>

Specified by:

getNodeOrderSize in class AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>

Returns:

the size of the node order

setNodeOrder

public void setNodeOrder(List<RegulatoryNode> nodeOrder)

Description copied from interface: RegulatoryGraph

Set a list of class dependent objects representing the order of node as defined by the model

Specified by:

setNodeOrder in interface RegulatoryGraph

Parameters:

nodeOrder - the list of objects representing the order of node as defined by the model

addNode

public RegulatoryNode addNode()

Specified by:

addNode in interface RegulatoryGraph

Returns:

addNode

public boolean addNode(RegulatoryNode node)

Description copied from class: AbstractGraph

Add a node to this graph structure

Specified by:

addNode in interface GraphModel<RegulatoryNode,RegulatoryMultiEdge>

Overrides:

addNode in class AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>

Returns:

the created node

addEdge

public RegulatoryMultiEdge addEdge(RegulatoryNode source,
                                   RegulatoryNode target,
                                   RegulatoryEdgeSign sign)

Description copied from interface: RegulatoryGraph

Add a signed edge

Specified by:

addEdge in interface RegulatoryGraph

Returns:

getDisplayName

public String getDisplayName(RegulatoryNode node)

Description copied from interface: Graph

Retrieve the name to use when displaying a graph node.

Specified by:

getDisplayName in interface Graph<RegulatoryNode,RegulatoryMultiEdge>

Overrides:

getDisplayName in class AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>

Returns:

getAttributes

public Map<String,String> getAttributes()

Description copied from interface: Graph

Retrieve graph-level attributes

Specified by:

getAttributes in interface Graph<RegulatoryNode,RegulatoryMultiEdge>

Overrides:

getAttributes in class AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>

Returns:

a map of attribute values, it can be empty but should not be null

setAttribute

public void setAttribute(String name,
                         String value)

Specified by:

setAttribute in interface Graph<RegulatoryNode,RegulatoryMultiEdge>

Overrides:

setAttribute in class AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>

getGraphZipName

protected String getGraphZipName()

Description copied from class: AbstractGraph

Return the zip extension for the graph type

Overrides:

getGraphZipName in class AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>

Returns:

the zip extension for the graph type

getGINMLWriter

protected GINMLWriter getGINMLWriter()

Overrides:

getGINMLWriter in class AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>

idExists

public boolean idExists(String newId)

Specified by:

idExists in interface RegulatoryGraph

Returns:

True if a node of the graph has the given ID

changeNodeId

public void changeNodeId(Object node,
                         String newId)
                  throws GsException

Specified by:

changeNodeId in interface RegulatoryGraph

Throws:

GsException

removeEdge

public boolean removeEdge(RegulatoryMultiEdge edge)

Description copied from class: AbstractGraph

Remove an edge from the graph.

Specified by:

removeEdge in interface GraphModel<RegulatoryNode,RegulatoryMultiEdge>

Overrides:

removeEdge in class AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>

Returns:

true if the edge was effectively removed

removeNode

public boolean removeNode(RegulatoryNode obj)

Description copied from class: AbstractGraph

Remove a node from the graph.

Specified by:

removeNode in interface GraphModel<RegulatoryNode,RegulatoryMultiEdge>

Overrides:

removeNode in class AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>

Returns:

true if the node was effectively removed

addNewNode

public RegulatoryNode addNewNode(String id,
                                 String name,
                                 byte max)

Description copied from interface: RegulatoryGraph

add a node from textual parameters (for the parser).

Specified by:

addNewNode in interface RegulatoryGraph

Returns:

the new node.

addNewEdge

public RegulatoryEdge addNewEdge(String from,
                                 String to,
                                 byte minvalue,
                                 String sign)
                          throws GsException

Description copied from interface: RegulatoryGraph

add an edge from textual parameters (for the parser).

Specified by:

addNewEdge in interface RegulatoryGraph

Returns:

the new edge

Throws:

GsException

addNewEdge

public RegulatoryEdge addNewEdge(String from,
                                 String to,
                                 byte minvalue,
                                 RegulatoryEdgeSign sign)
                          throws GsException

Description copied from interface: RegulatoryGraph

add an edge from textual parameters (for the parser).

Specified by:

addNewEdge in interface RegulatoryGraph

Returns:

the new edge.

Throws:

GsException

canApplyNewMaxValue

public void canApplyNewMaxValue(RegulatoryNode node,
                                byte newMax,
                                List l_fixable,
                                List l_conflict)

Specified by:

canApplyNewMaxValue in interface RegulatoryGraph

doMerge

protected List doMerge(Graph<RegulatoryNode,RegulatoryMultiEdge> otherGraph)

Description copied from class: AbstractGraph

Specialized method that execute the merging of the given graph with the current one Must be override at specialized graph level

Specified by:

doMerge in class AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>

Returns:

getSubgraph

public Graph getSubgraph(Collection<RegulatoryNode> v_vertex,
                         Collection<RegulatoryMultiEdge> v_edges)

Description copied from class: AbstractGraph

Specialized method that build the sub-graph corresponding to the given lists of vertices and edges The returned graph contains clones of the given graph objects structured as they are in the current graph

Specified by:

getSubgraph in interface GraphModel<RegulatoryNode,RegulatoryMultiEdge>

Specified by:

getSubgraph in class AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>

Parameters:

v_vertex - the list of node to include in the desired sub-graph

v_edges - the list of edges to include in the sub-graph

Returns:

a Graph containing clones of initial vertices and edges structured as they are in the current graph

associationValid

public static boolean associationValid(RegulatoryGraph regGraph,
                                       DynamicGraph dynGraph)

Test if an association between a regulatory graph and a state transition graph is valid: all what we can do is checking the node-order to see if they obviously differ (by size of node's name). if this function returns true, it's _NOT_ a garanty that both graphs are compatibles, for exemple the state transition graph could have higher max value for one of the node.

Parameters:

regGraph -

dynGraph -

Returns:

true if the two graph can be associated

getMDDFactory

public org.colomoto.mddlib.MDDManager getMDDFactory()

Description copied from interface: RegulatoryGraph

Construct a MDDFactory associated to the nodes of this graph

Specified by:

getMDDFactory in interface RegulatoryGraph

Returns:

a new MDDFactory.

getMDDs

public int[] getMDDs(org.colomoto.mddlib.MDDManager factory)

Description copied from interface: RegulatoryGraph

Construct MDD representation of the logical functions of the nodes of this graph.

Specified by:

getMDDs in interface RegulatoryGraph

Parameters:

factory - a MDDFactory associated with the nodes of this graph

Returns:

an array containing references to the MDD roots in the factory

getNodeOrderForSimulation

public List<RegulatoryNode> getNodeOrderForSimulation()

Specified by:

getNodeOrderForSimulation in interface RegulatoryGraph

Returns:

getModel

public org.colomoto.biolqm.LogicalModel getModel()

Description copied from interface: RegulatoryGraph

Get a ready-to-be-used model (list of nodes and functions, no graph structure)

Specified by:

getModel in interface RegulatoryGraph

Returns:

a model matching this RegulatoryGraph

getModel

public org.colomoto.biolqm.LogicalModel getModel(NodeOrderer orderer)

Description copied from interface: RegulatoryGraph

Get a ready-to-be-used model (list of nodes and functions, no graph structure)

Specified by:

getModel in interface RegulatoryGraph

Parameters:

orderer - helper providing the desired node order

Returns:

a model matching this RegulatoryGraph

getModel

public org.colomoto.biolqm.LogicalModel getModel(NodeOrderer orderer,
                                                 boolean withLayout)

Description copied from interface: RegulatoryGraph

Get a ready-to-be-used model (list of nodes and functions, no graph structure)

Specified by:

getModel in interface RegulatoryGraph

Parameters:

orderer - helper providing the desired node order

withLayout - flag to add layout information

Returns:

a model matching this RegulatoryGraph

searchNodes

public List<RegulatoryNode> searchNodes(String regexp)

Description copied from class: AbstractGraph

Search the vertices with ID matching the given regular expression. Other kind of graph could overwrite this method.

Specified by:

searchNodes in interface GraphModel<RegulatoryNode,RegulatoryMultiEdge>

Overrides:

searchNodes in class AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>

Parameters:

regexp - the regular expression node ID must match to be selected

Returns:

a List of vertices

getNodes

public Collection<RegulatoryNode> getNodes()

Description copied from interface: GraphModel

Return the Collection of the graph nodes

Specified by:

getNodes in interface GraphModel<RegulatoryNode,RegulatoryMultiEdge>

Overrides:

getNodes in class AbstractGraph<RegulatoryNode,RegulatoryMultiEdge>

Returns:

a Collection of the graph vertices.

getStates

public List<byte[]> getStates()

Description copied from interface: RegulatoryGraph

Accesses the initial states associated with the graph

Specified by:

getStates in interface RegulatoryGraph

Returns:

a list of states

setStates

public void setStates(List<byte[]> states)

Description copied from interface: RegulatoryGraph

Associates a set of initial states to the graph

Specified by:

setStates in interface RegulatoryGraph

Parameters:

states - the list of states

isStateful

public boolean isStateful()

Description copied from interface: RegulatoryGraph

Checks whether the graph has states associated

Specified by:

isStateful in interface RegulatoryGraph

Returns:

true if the graph maintains a set of initial states

getOracles

public List<List<byte[]>> getOracles()

Description copied from interface: RegulatoryGraph

Accesses the oracles associated with the graph

Specified by:

getOracles in interface RegulatoryGraph

Returns:

a list of oracles

setOracles

public void setOracles(List<List<byte[]>> _oracles)

Description copied from interface: RegulatoryGraph

Associates a set of oracles to the graph

Specified by:

setOracles in interface RegulatoryGraph

Parameters:

_oracles - the list of oracles

hasOracles

public boolean hasOracles()

Description copied from interface: RegulatoryGraph

Checks whether the graph has oracles associated

Specified by:

hasOracles in interface RegulatoryGraph

Returns:

true if the graph has oracles defined