org.ginsim.core.graph.regulatorygraph

Interface RegulatoryGraph

All Superinterfaces:

Graph<RegulatoryNode,RegulatoryMultiEdge>, GraphModel<RegulatoryNode,RegulatoryMultiEdge>

All Known Implementing Classes:

RegulatoryGraphImpl

public interface RegulatoryGraph
extends Graph<RegulatoryNode,RegulatoryMultiEdge>

The regulatory graph

Author:

Aurelien Naldi

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()
void	canApplyNewMaxValue(RegulatoryNode node, byte newMax, List l_fixable, List l_conflict)
void	changeNodeId(Object node, String newId)
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()
List<List<byte[]>>	getOracles() Accesses the oracles associated with the graph
List<byte[]>	getStates() Accesses the initial states associated with the graph
boolean	hasOracles() Checks whether the graph has oracles associated
boolean	idExists(String newId)
boolean	isStateful() Checks whether the graph has states associated
void	setNodeOrder(List<RegulatoryNode> list) Set a list of class dependent objects representing the order of node as defined by the model
void	setOracles(List<List<byte[]>> list) Associates a set of oracles to the graph
void	setStates(List<byte[]> list) Associates a set of initial states to the graph

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

addViewListener, copyView, fireGraphChange, getAttributes, getDimension, getDisplayName, getEdgeAttributeReader, getNodeAttributeReader, getStyleManager, save, save, setAttribute

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

addEdge, addNode, containsEdge, containsNode, getAnnotation, getEdge, getEdges, getExistingNode, getGraphName, getIncomingEdges, getNodeByName, getNodeCount, getNodeOrderSize, getNodes, getOutgoingEdges, getShortestPath, getStronglyConnectedComponents, getSubgraph, merge, removeEdge, removeNode, searchNodes, setGraphName

Method Detail

getNodeOrder

List<RegulatoryNode> getNodeOrder()

Return the node order

Returns:

the node order as a list of RegulatoryNode

getNodeInfos

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

addNewNode

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

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

Parameters:

id -

name -

max -

Returns:

the new node.

addNode

RegulatoryNode addNode()

Returns:

idExists

boolean idExists(String newId)

Parameters:

newId -

Returns:

True if a node of the graph has the given ID

addNewEdge

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

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

Parameters:

from -

to -

minvalue -

sign -

Returns:

the new edge.

Throws:

GsException

addNewEdge

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

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

Parameters:

from -

to -

minvalue -

sign -

Returns:

the new edge

Throws:

GsException

addEdge

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

Add a signed edge

Parameters:

source -

target -

sign -

Returns:

getMDDs

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

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

Parameters:

factory - a MDDFactory associated with the nodes of this graph

Returns:

an array containing references to the MDD roots in the factory

getMDDFactory

org.colomoto.mddlib.MDDManager getMDDFactory()

Construct a MDDFactory associated to the nodes of this graph

Returns:

a new MDDFactory.

changeNodeId

void changeNodeId(Object node,
                  String newId)
           throws GsException

Parameters:

node -

newId -

Throws:

GsException

getNodeOrderForSimulation

List<RegulatoryNode> getNodeOrderForSimulation()

Returns:

setNodeOrder

void setNodeOrder(List<RegulatoryNode> list)

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

Parameters:

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

canApplyNewMaxValue

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

Parameters:

node -

newMax -

l_fixable -

l_conflict -

getModel

org.colomoto.biolqm.LogicalModel getModel()

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

Returns:

a model matching this RegulatoryGraph

getModel

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

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

Parameters:

orderer - helper providing the desired node order

Returns:

a model matching this RegulatoryGraph

getModel

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

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

Parameters:

orderer - helper providing the desired node order

withLayout - flag to add layout information

Returns:

a model matching this RegulatoryGraph

isStateful

boolean isStateful()

Checks whether the graph has states associated

Returns:

true if the graph maintains a set of initial states

hasOracles

boolean hasOracles()

Checks whether the graph has oracles associated

Returns:

true if the graph has oracles defined

getStates

List<byte[]> getStates()

Accesses the initial states associated with the graph

Returns:

a list of states

getOracles

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

Accesses the oracles associated with the graph

Returns:

a list of oracles

setStates

void setStates(List<byte[]> list)

Associates a set of initial states to the graph

Parameters:

list - the list of states

setOracles

void setOracles(List<List<byte[]>> list)

Associates a set of oracles to the graph

Parameters:

list - the list of oracles