Uses of Interface
org.colomoto.biolqm.LogicalModel

Packages that use LogicalModel

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.inferinteraction	Infer interactions and their signs from a logical model.
org.colomoto.biolqm.io	Input/Output for Logical Model.
org.colomoto.biolqm.io.antlr	Parser implementations using the antlr parser generator.
org.colomoto.biolqm.io.bnet	The format used by boolnet and pyboolnet
org.colomoto.biolqm.io.booleannet	The format used by booleannet and related tools in Reka Albert's group
org.colomoto.biolqm.io.boolsim	The format used by boolsim/GenYsis.
org.colomoto.biolqm.io.cnet	The format used by boolnet and pyboolnet
org.colomoto.biolqm.io.functions	logical functions.
org.colomoto.biolqm.io.ginml	GINML support.
org.colomoto.biolqm.io.gna	GNA (non-xml) support.
org.colomoto.biolqm.io.implicanttables	Implicant table format.
org.colomoto.biolqm.io.maboss	The format used by MaBoSS - https://maboss.curie.fr/
org.colomoto.biolqm.io.mnet	A custom text format for multi-valued networks
org.colomoto.biolqm.io.petrinet	Petri net support.
org.colomoto.biolqm.io.pint	The format used by Pint - http://loicpauleve.name/pint
org.colomoto.biolqm.io.sbml	SBML qual support.
org.colomoto.biolqm.io.truthtable	TruthTable file reader.
org.colomoto.biolqm.modifier	Modifications of logical models.
org.colomoto.biolqm.modifier.booleanize	Construct Boolean versions of Multi-valued models
org.colomoto.biolqm.modifier.buffer	Expand a model using "buffer components".
org.colomoto.biolqm.modifier.perturbation	Perturbation of logical models: local modifications of its logical functions.
org.colomoto.biolqm.modifier.reduction	model modification: remove components from the core.
org.colomoto.biolqm.modifier.reverse	model modification: creates a new model capable of generating the reverse dynamics.
org.colomoto.biolqm.modifier.sanitize	Cleanups and sanity-checks, preserving the same model
org.colomoto.biolqm.modifier.submodel
org.colomoto.biolqm.modifier.subspace
org.colomoto.biolqm.service
org.colomoto.biolqm.tool	Tool definition, used to run actions from the command-line interface.
org.colomoto.biolqm.tool.attractor	Identification of the stable states of a logical model.
org.colomoto.biolqm.tool.fixpoints	Identification of the stable states of a logical model.
org.colomoto.biolqm.tool.simulation	Some tools to run simulations on logical models.
org.colomoto.biolqm.tool.simulation.deterministic	Implementation of updating schemes: update the state of a model (i.e.
org.colomoto.biolqm.tool.simulation.grouping
org.colomoto.biolqm.tool.simulation.multiplesuccessor	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 LogicalModel in org.colomoto.biolqm

Classes in org.colomoto.biolqm that implement LogicalModel

Modifier and Type	Class and Description
class	LogicalModelImpl Implementation of the LogicalModel interface.

Methods in org.colomoto.biolqm that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	LogicalModel.clone() Make a copy of this model.
LogicalModel	LogicalModelImpl.clone()
LogicalModel	LogicalModel.clone(boolean keepExtra)
LogicalModel	LogicalModelImpl.clone(boolean keepExtra)
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)

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

Modifier and Type	Method and Description
static boolean	LogicalModelComparator.compare(LogicalModel m1, LogicalModel m2) Compare two logical models.

Constructors in org.colomoto.biolqm with parameters of type LogicalModel

Constructor and Description
ConnectivityMatrix(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.helper.inferinteraction

Constructors in org.colomoto.biolqm.helper.inferinteraction with parameters of type LogicalModel

Constructor and Description
InteractionSearcher(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.io

Fields in org.colomoto.biolqm.io declared as LogicalModel

Modifier and Type	Field and Description
protected LogicalModel	BaseExporter.model

Methods in org.colomoto.biolqm.io that return LogicalModel

Modifier and Type	Method and Description
default LogicalModel	LogicalModelFormat.load(File source) Load a file in this format and build a logical model for it.
default LogicalModel	LogicalModelFormat.load(StreamProvider streams) Load a file in this format and build a logical model for it.
default LogicalModel	LogicalModelFormat.load(String filename) Load a file in this format and build a logical model for it.

Methods in org.colomoto.biolqm.io with parameters of type LogicalModel

Modifier and Type	Method and Description
default void	LogicalModelFormat.export(LogicalModel model, File destination) Export a logical model to this format.
default void	LogicalModelFormat.export(LogicalModel model, StreamProvider streams) Export a logical model to this format.
default void	LogicalModelFormat.export(LogicalModel model, String filename) Export a logical model to this format.
default ModelExporter	LogicalModelFormat.getExporter(LogicalModel model) Get a new model exporter to this format.

Constructors in org.colomoto.biolqm.io with parameters of type LogicalModel

Constructor and Description
BaseExporter(LogicalModel model)

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

Methods in org.colomoto.biolqm.io.antlr that return LogicalModel

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.constructMVModel(org.colomoto.mddlib.logicalfunction.OperandFactory operandFactory, List<NodeInfo> nodes, Map<NodeInfo,List<Assignment>> var2assign)

Uses of LogicalModel in org.colomoto.biolqm.io.bnet

Methods in org.colomoto.biolqm.io.bnet that return LogicalModel

Modifier and Type	Method and Description
protected LogicalModel	BNetImport.performTask()

Methods in org.colomoto.biolqm.io.bnet with parameters of type LogicalModel

Modifier and Type	Method and Description
BNetExport	BNetFormat.getExporter(LogicalModel model)

Constructors in org.colomoto.biolqm.io.bnet with parameters of type LogicalModel

Constructor and Description
BNetExport(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.io.booleannet

Methods in org.colomoto.biolqm.io.booleannet that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	BooleanNetImport.performTask()

Methods in org.colomoto.biolqm.io.booleannet with parameters of type LogicalModel

Modifier and Type	Method and Description
BooleanNetExport	BooleanNetFormat.getExporter(LogicalModel model)

Constructors in org.colomoto.biolqm.io.booleannet with parameters of type LogicalModel

Constructor and Description
BooleanNetExport(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.io.boolsim

Methods in org.colomoto.biolqm.io.boolsim that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	BoolSimImport.performTask()

Methods in org.colomoto.biolqm.io.boolsim with parameters of type LogicalModel

Modifier and Type	Method and Description
BoolSimExport	BoolSimFormat.getExporter(LogicalModel model)

Constructors in org.colomoto.biolqm.io.boolsim with parameters of type LogicalModel

Constructor and Description
BoolSimExport(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.io.cnet

Methods in org.colomoto.biolqm.io.cnet that return LogicalModel

Modifier and Type	Method and Description
protected LogicalModel	CNetImport.performTask()

Methods in org.colomoto.biolqm.io.cnet with parameters of type LogicalModel

Modifier and Type	Method and Description
CNetExport	CNetFormat.getExporter(LogicalModel model)

Constructors in org.colomoto.biolqm.io.cnet with parameters of type LogicalModel

Constructor and Description
CNetExport(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.io.functions

Methods in org.colomoto.biolqm.io.functions that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	BooleanFunctionImport.performTask()

Methods in org.colomoto.biolqm.io.functions with parameters of type LogicalModel

Modifier and Type	Method and Description
BooleanFunctionExport	BooleanFunctionFormat.getExporter(LogicalModel model)

Constructors in org.colomoto.biolqm.io.functions with parameters of type LogicalModel

Constructor and Description
BooleanFunctionExport(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.io.ginml

Methods in org.colomoto.biolqm.io.ginml with parameters of type LogicalModel

Modifier and Type	Method and Description
org.colomoto.biolqm.io.ginml.GINMLExporter	GINMLFormat.getExporter(LogicalModel model)

Constructors in org.colomoto.biolqm.io.ginml with parameters of type LogicalModel

Constructor and Description
LogicalModel2GINML(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.io.gna

Methods in org.colomoto.biolqm.io.gna with parameters of type LogicalModel

Modifier and Type	Method and Description
GNAExport	GNAFormat.getExporter(LogicalModel model)

Constructors in org.colomoto.biolqm.io.gna with parameters of type LogicalModel

Constructor and Description
GNAExport(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.io.implicanttables

Methods in org.colomoto.biolqm.io.implicanttables that return LogicalModel

Modifier and Type	Method and Description
protected LogicalModel	ImplicantTableImport.performTask()

Methods in org.colomoto.biolqm.io.implicanttables with parameters of type LogicalModel

Modifier and Type	Method and Description
ImplicantTableExport	ImplicantTableFormat.getExporter(LogicalModel model)

Constructors in org.colomoto.biolqm.io.implicanttables with parameters of type LogicalModel

Constructor and Description
ImplicantTableExport(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.io.maboss

Methods in org.colomoto.biolqm.io.maboss with parameters of type LogicalModel

Modifier and Type	Method and Description
MaBoSSEncoder	MaBoSSFormat.getExporter(LogicalModel model)

Constructors in org.colomoto.biolqm.io.maboss with parameters of type LogicalModel

Constructor and Description
MaBoSSEncoder(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.io.mnet

Methods in org.colomoto.biolqm.io.mnet that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	MNetImport.performTask()

Methods in org.colomoto.biolqm.io.mnet with parameters of type LogicalModel

Modifier and Type	Method and Description
MNetExport	MNetFormat.getExporter(LogicalModel model)

Constructors in org.colomoto.biolqm.io.mnet with parameters of type LogicalModel

Constructor and Description
MNetExport(LogicalModel model)

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

Methods in org.colomoto.biolqm.io.petrinet with parameters of type LogicalModel

Modifier and Type	Method and Description
PNEncoderAPNN	APNNFormat.getExporter(LogicalModel model)
abstract AbstractPNEncoder	PetriNetFormat.getExporter(LogicalModel model)
PNEncoderINA	INAFormat.getExporter(LogicalModel model)
PNEncoderPNML	PNMLFormat.getExporter(LogicalModel model)

Constructors in org.colomoto.biolqm.io.petrinet with parameters of type LogicalModel

Constructor and Description
AbstractPNEncoder(LogicalModel model)
PNEncoderAPNN(LogicalModel model)
PNEncoderINA(LogicalModel model)
PNEncoderPNML(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.io.pint

Methods in org.colomoto.biolqm.io.pint with parameters of type LogicalModel

Modifier and Type	Method and Description
PintExport	PintFormat.getExporter(LogicalModel model)

Constructors in org.colomoto.biolqm.io.pint with parameters of type LogicalModel

Constructor and Description
PintExport(LogicalModel model)

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

Methods in org.colomoto.biolqm.io.sbml that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	SBMLqualImport.performTask()

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

Modifier and Type	Method and Description
SBMLqualExport	SBMLFormat.getExporter(LogicalModel model)

Constructors in org.colomoto.biolqm.io.sbml with parameters of type LogicalModel

Constructor and Description
SBMLqualExport(LogicalModel model)
SBMLqualExport(LogicalModel model, boolean addLayout)

Uses of LogicalModel in org.colomoto.biolqm.io.truthtable

Methods in org.colomoto.biolqm.io.truthtable that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	TruthTableImport.performTask()

Methods in org.colomoto.biolqm.io.truthtable with parameters of type LogicalModel

Modifier and Type	Method and Description
TruthTableExport	TruthTableFormat.getExporter(LogicalModel model)

Constructors in org.colomoto.biolqm.io.truthtable with parameters of type LogicalModel

Constructor and Description
TruthTableExport(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.modifier

Methods in org.colomoto.biolqm.modifier that return LogicalModel

Modifier and Type	Method and Description
default LogicalModel	ModelModifierService.modify(LogicalModel model) Apply a modifier with the default parameters.
default LogicalModel	ModelModifierService.modify(LogicalModel model, String parameters) Setup a modifier and directly retrieve the modified model.

Methods in org.colomoto.biolqm.modifier with parameters of type LogicalModel

Modifier and Type	Method and Description
ModelModifier	ModelModifierService.getModifier(LogicalModel model) Get a new modifier object.
default ModelModifier	ModelModifierService.getModifier(LogicalModel model, String parameters) Setup a new modifier object.
default LogicalModel	ModelModifierService.modify(LogicalModel model) Apply a modifier with the default parameters.
default LogicalModel	ModelModifierService.modify(LogicalModel model, String parameters) Setup a modifier and directly retrieve the modified model.

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

Methods in org.colomoto.biolqm.modifier.booleanize that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	BooleanizeModifier.performTask()

Methods in org.colomoto.biolqm.modifier.booleanize with parameters of type LogicalModel

Modifier and Type	Method and Description
ModelModifier	BooleanizeService.getModifier(LogicalModel model)

Constructors in org.colomoto.biolqm.modifier.booleanize with parameters of type LogicalModel

Constructor and Description
BooleanizeModifier(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.modifier.buffer

Methods in org.colomoto.biolqm.modifier.buffer that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	BufferingModifier.performTask()

Methods in org.colomoto.biolqm.modifier.buffer with parameters of type LogicalModel

Modifier and Type	Method and Description
ModelModifier	BufferingService.getModifier(LogicalModel model)

Constructors in org.colomoto.biolqm.modifier.buffer with parameters of type LogicalModel

Constructor and Description
BufferingModifier(LogicalModel model)

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

Methods in org.colomoto.biolqm.modifier.perturbation that return LogicalModel

Modifier and Type	Method and Description
default LogicalModel	LogicalModelPerturbation.apply(LogicalModel model) Apply the perturbation.
LogicalModel	PerturbationModifier.performTask()

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

Modifier and Type	Method and Description
default LogicalModel	LogicalModelPerturbation.apply(LogicalModel model) Apply the perturbation.
ModelModifier	PerturbationService.getModifier(LogicalModel model)
void	MultiplePerturbation.update(LogicalModel model)
void	RangePerturbation.update(LogicalModel model)
void	FixedValuePerturbation.update(LogicalModel model)
void	InteractionPerturbation.update(LogicalModel model)
void	LogicalModelPerturbation.update(LogicalModel model) Apply the perturbation to a model directly (do not create a modified model).

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

Constructor and Description
PerturbationModifier(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.modifier.reduction

Methods in org.colomoto.biolqm.modifier.reduction that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	ModelReducer.getModel() Get a logical model for the modified functions.
LogicalModel	ModelReducer.getModel(boolean includeExtra)
LogicalModel	ModelReducer.getModel(boolean preserveFixedInputs, boolean includeExtra)
LogicalModel	ReductionModifier.performTask()
LogicalModel	PatternReduction.performTask()
static LogicalModel	FixedComponentRemover.reduceFixed(LogicalModel model, boolean removeFixed)
static LogicalModel	DuplicateRemover.removeDuplicateComponents(LogicalModel model)

Methods in org.colomoto.biolqm.modifier.reduction with parameters of type LogicalModel

Modifier and Type	Method and Description
ReductionModifier	ReductionService.getModifier(LogicalModel model)
static LogicalModel	FixedComponentRemover.reduceFixed(LogicalModel model, boolean removeFixed)
static LogicalModel	DuplicateRemover.removeDuplicateComponents(LogicalModel model)

Constructors in org.colomoto.biolqm.modifier.reduction with parameters of type LogicalModel

Constructor and Description
ModelReducer(LogicalModel model)
PatternReduction(LogicalModel model, StatePattern pattern)
ReductionModifier(LogicalModel model)
ReductionModifier(LogicalModel model, String parameters)

Uses of LogicalModel in org.colomoto.biolqm.modifier.reverse

Methods in org.colomoto.biolqm.modifier.reverse that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	ReverseModifier.performTask()

Methods in org.colomoto.biolqm.modifier.reverse with parameters of type LogicalModel

Modifier and Type	Method and Description
ModelModifier	ReverseService.getModifier(LogicalModel model)

Constructors in org.colomoto.biolqm.modifier.reverse with parameters of type LogicalModel

Constructor and Description
ReverseModifier(LogicalModel model) Prepare a Model modifier for model reversal.

Uses of LogicalModel in org.colomoto.biolqm.modifier.sanitize

Methods in org.colomoto.biolqm.modifier.sanitize that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	SanitizeModifier.performTask()

Methods in org.colomoto.biolqm.modifier.sanitize with parameters of type LogicalModel

Modifier and Type	Method and Description
ModelModifier	SanitizeService.getModifier(LogicalModel model)

Constructors in org.colomoto.biolqm.modifier.sanitize with parameters of type LogicalModel

Constructor and Description
SanitizeModifier(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.modifier.submodel

Methods in org.colomoto.biolqm.modifier.submodel that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	SubmodelModifier.performTask()

Methods in org.colomoto.biolqm.modifier.submodel with parameters of type LogicalModel

Modifier and Type	Method and Description
ModelModifier	SubmodelService.getModifier(LogicalModel model)

Constructors in org.colomoto.biolqm.modifier.submodel with parameters of type LogicalModel

Constructor and Description
SubmodelModifier(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.modifier.subspace

Methods in org.colomoto.biolqm.modifier.subspace that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	SubSpaceModifier.performTask()

Methods in org.colomoto.biolqm.modifier.subspace with parameters of type LogicalModel

Modifier and Type	Method and Description
ModelModifier	SubSpaceService.getModifier(LogicalModel model)

Constructors in org.colomoto.biolqm.modifier.subspace with parameters of type LogicalModel

Constructor and Description
SubSpaceModifier(LogicalModel model)
SubSpaceModifier(LogicalModel model, byte[] pattern)

Uses of LogicalModel in org.colomoto.biolqm.service

Methods in org.colomoto.biolqm.service that return LogicalModel

Modifier and Type	Method and Description
static LogicalModel	LQMServiceManager.load(String filename) Load a model guessing the format.
static LogicalModel	LQMServiceManager.load(String filename, String format) Load a model from file.
static LogicalModel	LQMServiceManager.modify(LogicalModel model, String name) Construct a modified model.
static LogicalModel	LQMServiceManager.modify(LogicalModel model, String name, String parameters) Construct a modified model.

Methods in org.colomoto.biolqm.service with parameters of type LogicalModel

Modifier and Type	Method and Description
static LogicalModel	LQMServiceManager.modify(LogicalModel model, String name) Construct a modified model.
static LogicalModel	LQMServiceManager.modify(LogicalModel model, String name, String parameters) Construct a modified model.
static boolean	LQMServiceManager.save(LogicalModel model, String filename, String format) Save a model to file

Uses of LogicalModel in org.colomoto.biolqm.tool

Fields in org.colomoto.biolqm.tool declared as LogicalModel

Modifier and Type	Field and Description
LogicalModel	AbstractToolTask.model

Methods in org.colomoto.biolqm.tool with parameters of type LogicalModel

Modifier and Type	Method and Description
T	ModelToolService.getTask(LogicalModel model) Construct a default setting object.
default T	ModelToolService.getTask(LogicalModel model, String... parameters) Construct a default setting object.
default T	ModelToolService.getTask(LogicalModel model, String parameters) Construct a parsed setting object.

Constructors in org.colomoto.biolqm.tool with parameters of type LogicalModel

Constructor and Description
AbstractToolTask(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.tool.attractor

Methods in org.colomoto.biolqm.tool.attractor with parameters of type LogicalModel

Modifier and Type	Method and Description
SATAttractorFinder	AttractorService.getTask(LogicalModel model)

Constructors in org.colomoto.biolqm.tool.attractor with parameters of type LogicalModel

Constructor and Description
SATAttractorFinder(LogicalModel model)

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

Fields in org.colomoto.biolqm.tool.fixpoints declared as LogicalModel

Modifier and Type	Field and Description
protected LogicalModel	StructuralNodeOrderer.model

Methods in org.colomoto.biolqm.tool.fixpoints with parameters of type LogicalModel

Modifier and Type	Method and Description
static FixpointList	JBDDModel.getBDD(LogicalModel model)
FixpointList	FixpointTask.getMDD(LogicalModel model)
FixpointList	FixpointTask.getMDD(LogicalModel model, boolean pattern)
FixpointTask	FixpointService.getTask(LogicalModel model)

Constructors in org.colomoto.biolqm.tool.fixpoints with parameters of type LogicalModel

Constructor and Description
FixpointList(LogicalModel model)
FixpointSearcher(LogicalModel model) Create a new stable state searcher.
FixpointTask(LogicalModel model)
JBDDModel(LogicalModel lm)
StableASP(LogicalModel model)
StructuralNodeOrderer(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.tool.simulation

Fields in org.colomoto.biolqm.tool.simulation declared as LogicalModel

Modifier and Type	Field and Description
protected LogicalModel	BaseUpdater.model

Methods in org.colomoto.biolqm.tool.simulation that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	BaseUpdater.getModel()
LogicalModel	LogicalModelUpdater.getModel()

Methods in org.colomoto.biolqm.tool.simulation with parameters of type LogicalModel

Modifier and Type	Method and Description
static DeterministicUpdater	UpdaterFactory.getDeterministicUpdater(LogicalModel model, String s)
static MultipleSuccessorsUpdater	UpdaterFactory.getMultipleSuccessorUpdater(LogicalModel model, String s)
static RandomUpdater	UpdaterFactory.getRandomUpdater(LogicalModel model, String s)
static byte[]	InitialStateFactory.parseInitialState(LogicalModel model, String s)

Constructors in org.colomoto.biolqm.tool.simulation with parameters of type LogicalModel

Constructor and Description
BaseUpdater(LogicalModel model)

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

Methods in org.colomoto.biolqm.tool.simulation.deterministic with parameters of type LogicalModel

Modifier and Type	Method and Description
TraceTask	TraceService.getTask(LogicalModel model)

Constructors in org.colomoto.biolqm.tool.simulation.deterministic with parameters of type LogicalModel

Constructor and Description
BlockSequentialUpdater(LogicalModel model, int[][] blocks)
BlockSequentialUpdater(LogicalModel model, String config)
DeterministicPriorityUpdater(LogicalModel model, int[][] blocks)
DeterministicPriorityUpdater(LogicalModel model, String config)
SequentialUpdater(LogicalModel model) Create a new sequential updater, using the default order
SequentialUpdater(LogicalModel model, int[] order) Create a new sequential updater, using a custom order
SequentialUpdater(LogicalModel model, String s_order) Create a new sequential updater, using a custom order
SynchronousUpdater(LogicalModel model) Create a new synchronous updater
TraceTask(LogicalModel model)

Uses of LogicalModel in org.colomoto.biolqm.tool.simulation.grouping

Fields in org.colomoto.biolqm.tool.simulation.grouping declared as LogicalModel

Modifier and Type	Field and Description
protected LogicalModel	ModelGrouping.model

Methods in org.colomoto.biolqm.tool.simulation.grouping that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	ModelGrouping.getModel()

Methods in org.colomoto.biolqm.tool.simulation.grouping with parameters of type LogicalModel

Modifier and Type	Method and Description
ModelGrouping	ModelGrouping.cloneWithModel(LogicalModel modifiedModel)
List<List<String>>	ModelGrouping.RankedClass.getVars(LogicalModel m)
List<String>	ModelGrouping.RankedClassGroup.getVars(LogicalModel m)

Constructors in org.colomoto.biolqm.tool.simulation.grouping with parameters of type LogicalModel

Constructor and Description
ModelGrouping(LogicalModel m)
ModelGrouping(LogicalModel m, String textFormat)
RankedClass(LogicalModel m, String textFormat)
RankedClassGroup(LogicalModel m, String textFormat)

Uses of LogicalModel in org.colomoto.biolqm.tool.simulation.multiplesuccessor

Constructors in org.colomoto.biolqm.tool.simulation.multiplesuccessor with parameters of type LogicalModel

Constructor and Description
AbstractMultipleSuccessorUpdater(LogicalModel model)
AsynchronousUpdater(LogicalModel model) Create a new asynchronous random.
CompleteUpdater(LogicalModel model) Create a new full random.
PriorityUpdater(LogicalModel model, String setup)

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

Methods in org.colomoto.biolqm.tool.simulation.random that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	RandomUpdaterWrapper.getModel()

Methods in org.colomoto.biolqm.tool.simulation.random with parameters of type LogicalModel

Modifier and Type	Method and Description
RandomWalkTask	RandomWalkService.getTask(LogicalModel model)

Constructors in org.colomoto.biolqm.tool.simulation.random with parameters of type LogicalModel

Constructor and Description
AbstractRandomUpdater(LogicalModel model)
RandomUpdaterWithRates(LogicalModel model) Create a new random random
RandomUpdaterWithRates(LogicalModel model, double[] rates)
RandomWalkTask(LogicalModel model)

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

Methods in org.colomoto.biolqm.tool.trapspaces with parameters of type LogicalModel

Modifier and Type	Method and Description
TrapSpaceTask	TrapSpaceService.getTask(LogicalModel model)

Constructors in org.colomoto.biolqm.tool.trapspaces with parameters of type LogicalModel

Constructor and Description
TrapSpaceList(TrapSpaceTask settings, LogicalModel model)
TrapSpaceSolverASP(LogicalModel model, TrapSpaceTask settings)
TrapSpaceSolverBDD(LogicalModel model, TrapSpaceTask settings)
TrapSpaceSolverFunctionASP(LogicalModel model, TrapSpaceTask settings)
TrapSpaceTask(LogicalModel model)