Uses of Class
org.colomoto.biolqm.NodeInfo

Packages that use NodeInfo

Package	Description
org.colomoto.biolqm	Core for the bioLQM toolkit: Main data structures for Logical Models Service loader and manager Launcher and Command-Line Interface Script mode
org.colomoto.biolqm.helper.state
org.colomoto.biolqm.io.antlr	Parser implementations using the antlr parser generator.
org.colomoto.biolqm.io.petrinet	Petri net support.
org.colomoto.biolqm.io.sbml	SBML qual support.
org.colomoto.biolqm.modifier.booleanize	Construct Boolean versions of Multi-valued models
org.colomoto.biolqm.modifier.perturbation	Perturbation of logical models: local modifications of its logical functions.
org.colomoto.biolqm.tool.fixpoints	Identification of the stable states of a logical model.
org.colomoto.biolqm.tool.simulation.deterministic	Implementation of updating schemes: update the state of a model (i.e.
org.colomoto.biolqm.tool.simulation.random	Implementation of updating schemes: update the state of a model (i.e.
org.colomoto.biolqm.tool.trapspaces

Uses of NodeInfo in org.colomoto.biolqm

Methods in org.colomoto.biolqm that return NodeInfo

Modifier and Type	Method and Description
NodeInfo	NodeInfo.clone()
NodeInfo[]	NodeInfo.getBooleanizedGroup()
NodeInfo	LogicalModel.getComponent(String s_source) Retrieve a component by name.
NodeInfo	LogicalModelImpl.getComponent(String id)
NodeInfo	NodeInfoHolder.getNodeInfo() Get the internal NodeInfo.

Methods in org.colomoto.biolqm that return types with arguments of type NodeInfo

Modifier and Type	Method and Description
List<NodeInfo>	LogicalModel.getComponents() Get the list of core nodes in this model.
List<NodeInfo>	LogicalModelImpl.getComponents()
List<NodeInfo>	LogicalModel.getExtraComponents() Get the list of extra components in this model.
List<NodeInfo>	LogicalModelImpl.getExtraComponents()

Methods in org.colomoto.biolqm with parameters of type NodeInfo

Modifier and Type	Method and Description
ModelLayout	ModelLayout.copy(NodeInfo ni, ModelLayout.LayoutInfo source)
ModelLayout.LayoutInfo	ModelLayout.getInfo(NodeInfo ni)
ModelLayout	ModelLayout.set(NodeInfo ni, int x, int y, int width, int height)
void	NodeInfo.setBooleanizedGroup(NodeInfo[] booleanized_group)
ModelLayout.LayoutInfo	ModelLayout.setPosition(NodeInfo ni, int x, int y)

Method parameters in org.colomoto.biolqm with type arguments of type NodeInfo

Modifier and Type	Method and Description
LogicalModel	LogicalModel.getView(List<NodeInfo> neworder) Get a logical model with the same nodes but a different order for the core components.
LogicalModel	LogicalModelImpl.getView(List<NodeInfo> neworder)

Constructor parameters in org.colomoto.biolqm with type arguments of type NodeInfo

Constructor and Description
LogicalModelImpl(List<NodeInfo> nodeOrder, org.colomoto.mddlib.MDDManager ddmanager, int[] functions)
LogicalModelImpl(org.colomoto.mddlib.MDDManager ddmanager, List<NodeInfo> coreNodes, int[] coreFunctions, List<NodeInfo> extraNodes, int[] extraFunctions)
LogicalModelImpl(org.colomoto.mddlib.MDDManager ddmanager, List<NodeInfo> coreNodes, int[] coreFunctions, List<NodeInfo> extraNodes, int[] extraFunctions)

Uses of NodeInfo in org.colomoto.biolqm.helper.state

Methods in org.colomoto.biolqm.helper.state that return NodeInfo

Modifier and Type	Method and Description
NodeInfo[]	StateList.getComponents() Get the components defining this list of states.
NodeInfo[]	StateListProjection.getComponents()

Methods in org.colomoto.biolqm.helper.state with parameters of type NodeInfo

Modifier and Type	Method and Description
static int[]	StateListProjection.get_selection(NodeInfo[] components, Iterable<String> sel)

Uses of NodeInfo in org.colomoto.biolqm.io.antlr

Method parameters in org.colomoto.biolqm.io.antlr with type arguments of type NodeInfo

Modifier and Type	Method and Description
static LogicalModel	ExpressionStack.constructModel(org.colomoto.mddlib.logicalfunction.OperandFactory operandFactory, List<NodeInfo> nodes, Map<NodeInfo,org.colomoto.mddlib.logicalfunction.FunctionNode> var2function) Build a LogicalModel from a list of nodes and parsed functions.
static LogicalModel	ExpressionStack.constructModel(org.colomoto.mddlib.logicalfunction.OperandFactory operandFactory, List<NodeInfo> nodes, Map<NodeInfo,org.colomoto.mddlib.logicalfunction.FunctionNode> var2function) Build a LogicalModel from a list of nodes and parsed functions.
static LogicalModel	ExpressionStack.constructMVModel(org.colomoto.mddlib.logicalfunction.OperandFactory operandFactory, List<NodeInfo> nodes, Map<NodeInfo,List<Assignment>> var2assign)
static LogicalModel	ExpressionStack.constructMVModel(org.colomoto.mddlib.logicalfunction.OperandFactory operandFactory, List<NodeInfo> nodes, Map<NodeInfo,List<Assignment>> var2assign)

Uses of NodeInfo in org.colomoto.biolqm.io.petrinet

Fields in org.colomoto.biolqm.io.petrinet with type parameters of type NodeInfo

Modifier and Type	Field and Description
List<NodeInfo>	AbstractPNEncoder.nodeOrder

Method parameters in org.colomoto.biolqm.io.petrinet with type arguments of type NodeInfo

Modifier and Type	Method and Description
protected void	PNEncoderPNML.doExport(String netName, List<NodeInfo> v_no, List[] t_transition, byte[][] t_markup, OutputStreamWriter fout)
protected void	PNEncoderINA.doExport(String netName, List<NodeInfo> nodes, List[] t_transition, byte[][] t_markup, OutputStreamWriter out)
protected abstract void	AbstractPNEncoder.doExport(String netName, List<NodeInfo> nodes, List[] t_transition, byte[][] t_markup, OutputStreamWriter out)
protected void	PNEncoderAPNN.doExport(String netName, List<NodeInfo> v_no, List[] t_transition, byte[][] t_markup, OutputStreamWriter out)

Uses of NodeInfo in org.colomoto.biolqm.io.sbml

Methods in org.colomoto.biolqm.io.sbml with parameters of type NodeInfo

Modifier and Type	Method and Description
org.sbml.jsbml.ext.qual.QualitativeSpecies	SBMLqualExport.getSpecies(NodeInfo ni)

Uses of NodeInfo in org.colomoto.biolqm.modifier.booleanize

Method parameters in org.colomoto.biolqm.modifier.booleanize with type arguments of type NodeInfo

Modifier and Type	Method and Description
static void	BooleanizeModifier.preventForbiddenStates(org.colomoto.mddlib.MDDManager newDDM, List<NodeInfo> components, int[] functions) Ensure that a booleanized model has no transition leading to forbidden states.

Uses of NodeInfo in org.colomoto.biolqm.modifier.perturbation

Fields in org.colomoto.biolqm.modifier.perturbation declared as NodeInfo

Modifier and Type	Field and Description
NodeInfo	RangePerturbation.component
NodeInfo	FixedValuePerturbation.component
NodeInfo	InteractionPerturbation.regulator
NodeInfo	InteractionPerturbation.target

Methods in org.colomoto.biolqm.modifier.perturbation with parameters of type NodeInfo

Modifier and Type	Method and Description
boolean	MultiplePerturbation.affectsNode(NodeInfo node)
boolean	RangePerturbation.affectsNode(NodeInfo node)
boolean	FixedValuePerturbation.affectsNode(NodeInfo node)
boolean	InteractionPerturbation.affectsNode(NodeInfo node)
boolean	LogicalModelPerturbation.affectsNode(NodeInfo node) Test if the perturbation affects the function of a specific node

Method parameters in org.colomoto.biolqm.modifier.perturbation with type arguments of type NodeInfo

Modifier and Type	Method and Description
void	MultiplePerturbation.restrictValues(byte[] state, List<NodeInfo> nodeOrder)
void	RangePerturbation.restrictValues(byte[] state, List<NodeInfo> nodeOrder)
void	FixedValuePerturbation.restrictValues(byte[] state, List<NodeInfo> nodeOrder)
void	InteractionPerturbation.restrictValues(byte[] state, List<NodeInfo> nodeOrder)
void	LogicalModelPerturbation.restrictValues(byte[] state, List<NodeInfo> components) Apply the perturbation(s) directly to a state, i.e., restricts the values of the state in the valid range of the perturbation(s).

Constructors in org.colomoto.biolqm.modifier.perturbation with parameters of type NodeInfo

Constructor and Description
FixedValuePerturbation(NodeInfo target) Create a simple KO perturbation.
FixedValuePerturbation(NodeInfo target, int value) Create a simple perturbation to fix the value of a component.
InteractionPerturbation(NodeInfo regulator, NodeInfo target, int regValue)
RangePerturbation(NodeInfo target, int min, int max) Create a range restriction.

Uses of NodeInfo in org.colomoto.biolqm.tool.fixpoints

Methods in org.colomoto.biolqm.tool.fixpoints that return NodeInfo

Modifier and Type	Method and Description
static NodeInfo[]	FixpointList.extractIDs(List<NodeInfo> list)
NodeInfo[]	FixpointList.getComponents()

Method parameters in org.colomoto.biolqm.tool.fixpoints with type arguments of type NodeInfo

Modifier and Type	Method and Description
static NodeInfo[]	FixpointList.extractIDs(List<NodeInfo> list)

Constructor parameters in org.colomoto.biolqm.tool.fixpoints with type arguments of type NodeInfo

Constructor and Description
FixpointList(List<NodeInfo> nodes)
FixpointList(List<NodeInfo> nodes, List<NodeInfo> extraNodes, org.colomoto.mddlib.MDDManager ddmanager, int[] extraFunctions)
FixpointList(List<NodeInfo> nodes, List<NodeInfo> extraNodes, org.colomoto.mddlib.MDDManager ddmanager, int[] extraFunctions)

Uses of NodeInfo in org.colomoto.biolqm.tool.simulation.deterministic

Methods in org.colomoto.biolqm.tool.simulation.deterministic that return types with arguments of type NodeInfo

Modifier and Type	Method and Description
List<NodeInfo>	DeterministicSimulation.getNodes()

Uses of NodeInfo in org.colomoto.biolqm.tool.simulation.random

Methods in org.colomoto.biolqm.tool.simulation.random that return types with arguments of type NodeInfo

Modifier and Type	Method and Description
List<NodeInfo>	RandomWalkSimulation.getNodes()

Uses of NodeInfo in org.colomoto.biolqm.tool.trapspaces

Fields in org.colomoto.biolqm.tool.trapspaces declared as NodeInfo

Modifier and Type	Field and Description
NodeInfo[]	TrapSpaceList.nodes

Methods in org.colomoto.biolqm.tool.trapspaces that return NodeInfo

Modifier and Type	Method and Description
NodeInfo[]	TrapSpaceList.getComponents()