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.io	Input/Output for Logical Model.
org.colomoto.biolqm.io.antlr
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.maboss	The format used by MaBoSS - https://maboss.curie.fr/
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
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.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.subspace
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.inferinteraction	Infer interactions and their signs from a logical model.
org.colomoto.biolqm.tool.simulation	Some tools to run simulations on logical models.
org.colomoto.biolqm.tool.simulation.updater	Implementation of updating schemes: update the state of a model (i.e.
org.colomoto.biolqm.tool.stablestate	Identification of the stable states of a logical model.
org.colomoto.biolqm.tool.trapspaces

Uses of LogicalModel in org.colomoto.biolqm

Subinterfaces of LogicalModel in org.colomoto.biolqm

Modifier and Type	Interface and Description
interface	StatefulLogicalModel Extension of a logical model with the possibility to store initial states and oracles

Classes in org.colomoto.biolqm that implement LogicalModel

Modifier and Type	Class and Description
class	LogicalModelImpl Implementation of the LogicalModel interface.
class	StatefulLogicalModelImpl Extension of a logical model with the possibility to maintain a set of initial states and oracles. Implements the StatefulLogicalModel interface.

Methods in org.colomoto.biolqm that return LogicalModel

Modifier and Type	Method and Description
LogicalModel	LogicalModelImpl.clone()
LogicalModel	LogicalModel.clone() Make a copy of this model.
LogicalModel	LogicalModelImpl.getView(List<NodeInfo> neworder)
LogicalModel	LogicalModel.getView(List<NodeInfo> neworder) Get a logical model with the same nodes but a different order for the core components.
LogicalModel	LQMScriptLauncher.loadModel(String filename) Load a model guessing the format.
LogicalModel	LQMScriptLauncher.loadModel(String filename, String format) Load a model from a file.
static LogicalModel	LQMLauncher.loadModel(String filename, String format) Load a model from file.
LogicalModel	LQMScriptLauncher.modifyModel(LogicalModel model, String name) Construct a modified model.
LogicalModel	LQMScriptLauncher.modifyModel(LogicalModel model, String name, String parameters) Construct a modified model.

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.
LogicalModel	LQMScriptLauncher.modifyModel(LogicalModel model, String name) Construct a modified model.
LogicalModel	LQMScriptLauncher.modifyModel(LogicalModel model, String name, String parameters) Construct a modified model.
boolean	LQMScriptLauncher.saveModel(LogicalModel model, String filename, String format) Save a model to a file.
static boolean	LQMLauncher.saveModel(LogicalModel model, String filename, String format) Save a model to file

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

Constructor and Description
ConnectivityMatrix(LogicalModel model)
StatefulLogicalModelImpl(LogicalModel model, List<byte[]> states) Creates a stateful logical model based on an existing logical model

Uses of LogicalModel in org.colomoto.biolqm.io

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

Modifier and Type	Method and Description
LogicalModel	LogicalModelFormat.importFile(File f) Import a file in this format and build a logical model for it.
LogicalModel	AbstractFormat.importFile(File f)

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

Modifier and Type	Method and Description
void	AbstractFormat.export(LogicalModel model, OutputStream out)
void	LogicalModelFormat.export(LogicalModel model, OutputStreamProvider outputProvider) Export a logical model to this format.
void	AbstractFormat.export(LogicalModel model, OutputStreamProvider outputProvider)

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.

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
static LogicalModel	BNetImport.getModel(Reader reader) Entry point to parse a full model.
LogicalModel	BNetFormat.importFile(File f)

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

Modifier and Type	Method and Description
void	BNetFormat.export(LogicalModel model, OutputStream out)
void	BNetExport.export(LogicalModel model, OutputStream out) Export a logical model into logical functions.

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
static LogicalModel	BooleanNetImport.getModel(Reader reader) Entry point to parse a full model.
LogicalModel	BooleanNetFormat.importFile(File f)

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

Modifier and Type	Method and Description
void	BooleanNetFormat.export(LogicalModel model, OutputStream out)
void	BooleanNetExport.export(LogicalModel model, OutputStream out) Export a logical model into logical functions.

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
static LogicalModel	BoolSimImport.getModel(Reader reader) Entry point to parse a full model.
LogicalModel	BoolSimFormat.importFile(File f)

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

Modifier and Type	Method and Description
void	BoolSimFormat.export(LogicalModel model, OutputStream out)
void	BoolSimExport.export(LogicalModel model, OutputStream out) Export a logical model into logical functions.

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

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

Modifier and Type	Method and Description
void	CNetFormat.export(LogicalModel model, OutputStream out)
void	CNetExport.export(LogicalModel model, OutputStream out) Export a logical model into cnet truth tables.

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
static LogicalModel	BooleanFunctionImport.getModel(Reader reader) Entry point to parse a full model.
LogicalModel	BooleanFunctionFormat.importFile(File f)

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

Modifier and Type	Method and Description
void	BooleanFunctionFormat.export(LogicalModel model, OutputStream out)
void	BooleanFunctionExport.export(LogicalModel model, OutputStream out) Export a logical model into logical functions.

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
void	GINMLFormat.export(LogicalModel model, OutputStream out)

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
void	GNAFormat.export(LogicalModel model, OutputStream out)
void	GNAExport.export(LogicalModel model, OutputStream out) Export a logical model into logical functions.

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
void	MaBoSSFormat.export(LogicalModel model, OutputStreamProvider provider)

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.petrinet

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

Modifier and Type	Method and Description
void	PNFormat.export(LogicalModel model, OutputStreamProvider out)
void	PNFormat.export(LogicalModel model, PNConfig config, OutputStreamProvider out)

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
void	PintFormat.export(LogicalModel model, OutputStream out)
void	PintExport.export(LogicalModel model, OutputStream out) Export a logical model into automata network transitions

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.getModel()
LogicalModel	SBMLFormat.importFile(File f)

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

Modifier and Type	Method and Description
void	SBMLFormat.export(LogicalModel model, OutputStream out)

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

Constructor and Description
SBMLqualExport(LogicalModel model)

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.getModel(File file)
LogicalModel	TruthTableFormat.importFile(File f)

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

Modifier and Type	Method and Description
void	TruthTableFormat.export(LogicalModel model, OutputStream out)
void	TruthTableExport.export(LogicalModel model, OutputStream out) Exports a logical model into a truth table.

Uses of LogicalModel in org.colomoto.biolqm.modifier

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

Modifier and Type	Method and Description
LogicalModel	ModelModifier.getModifiedModel() Apply the modifier and retrieve the new model
LogicalModel	ModelModifierService.getModifiedModel(LogicalModel model, String parameters) Setup a modifier and directly retrieve the modified model.
LogicalModel	AbstractModelModifierService.getModifiedModel(LogicalModel model, String parameters)

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

Modifier and Type	Method and Description
LogicalModel	ModelModifierService.getModifiedModel(LogicalModel model, String parameters) Setup a modifier and directly retrieve the modified model.
LogicalModel	AbstractModelModifierService.getModifiedModel(LogicalModel model, String parameters)
ModelModifier	ModelModifierService.getModifier(LogicalModel model, String parameters) Setup a new modifier object.

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
static LogicalModel	Booleanizer.booleanize(LogicalModel ori)
LogicalModel	Booleanizer.getModel()
LogicalModel	ModelBooleanizerService.getModifiedModel(LogicalModel model)

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

Modifier and Type	Method and Description
static LogicalModel	Booleanizer.booleanize(LogicalModel ori)
LogicalModel	ModelBooleanizerService.getModifiedModel(LogicalModel model)
ModelModifier	ModelBooleanizerService.getModifier(LogicalModel model)
ModelModifier	ModelBooleanizerService.getModifier(LogicalModel model, String parameters)

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

Constructor and Description
Booleanizer(LogicalModel ori)

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
LogicalModel	LogicalModelPerturbation.apply(LogicalModel model) Apply the perturbation.
LogicalModel	AbstractPerturbation.apply(LogicalModel model)
LogicalModel	PerturbationModifier.getModifiedModel()

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

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

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

Constructor and Description
PerturbationModifier(LogicalModel model, LogicalModelPerturbation perturbation)

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.getModifiedModel()
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
ModelModifier	ModelReductionService.getModifier(LogicalModel model, ReductionSettings settings)
ModelModifier	ModelReductionService.getModifier(LogicalModel model, String parameters)
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)
ReductionModifier(LogicalModel model, ReductionSettings settings)

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	ModelReverser.getModifiedModel()
LogicalModel	ModelReverserService.getModifiedModel(LogicalModel model) Shorthand to retrieve a modified model without requiring a parameter String.

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

Modifier and Type	Method and Description
LogicalModel	ModelReverserService.getModifiedModel(LogicalModel model) Shorthand to retrieve a modified model without requiring a parameter String.
ModelModifier	ModelReverserService.getModifier(LogicalModel model) Shorthand to retrieve a modifier without requiring a parameter String.
ModelModifier	ModelReverserService.getModifier(LogicalModel model, String parameters)

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

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

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	SubSpaceRestriction.getModifiedModel()

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

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

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

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

Uses of LogicalModel in org.colomoto.biolqm.tool

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

Modifier and Type	Method and Description
R	LogicalModelTool.getResult(LogicalModel model) Get the analysis result.
R	AbstractTool.getResult(LogicalModel model)
R	LogicalModelTool.getResult(LogicalModel model, S settings) Get the analysis result with a custom setting.
R	LogicalModelTool.getResult(LogicalModel model, String... parameters) Get the analysis result.
R	AbstractTool.getResult(LogicalModel model, String... parameters)
R	LogicalModelTool.getResult(LogicalModel model, String parameters) Get the analysis result.
R	AbstractTool.getResult(LogicalModel model, String parameters)
void	LogicalModelTool.run(LogicalModel model, String... parameters) Run the tool on a logical 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
Object	AttractorTool.getResult(LogicalModel model, Object settings)
void	AttractorTool.run(LogicalModel model, String... parameters)

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.inferinteraction

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

Constructor and Description
InteractionSearcher(LogicalModel model)

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

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

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

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

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

Modifier and Type	Field and Description
protected LogicalModel	BaseUpdater.model

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

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

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

Constructor and Description
AbstractDeterministicUpdater(LogicalModel model)
AbstractMultipleSuccessorUpdater(LogicalModel model)
AbstractRandomUpdater(LogicalModel model)
AsynchronousUpdater(LogicalModel model) Create a new asynchronous updater.
BaseUpdater(LogicalModel model)
BlockSequentialUpdater(LogicalModel model, int[] o)
CompleteUpdater(LogicalModel model) Create a new full updater.
PriorityUpdater(LogicalModel model, PriorityClasses pcs)
RandomUpdaterWithRates(LogicalModel model) Create a new random updater
RandomUpdaterWithRates(LogicalModel model, double[] rates)
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
SynchronousUpdater(LogicalModel model) Create a new synchronous updater

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

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

Modifier and Type	Field and Description
protected LogicalModel	StructuralNodeOrderer.model

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

Modifier and Type	Method and Description
StableStateList	StableStateTool.getMDD(LogicalModel model)
Object	StableJBDD.getResult(LogicalModel model, Object settings)
StableStateList	StableStateTool.getResult(LogicalModel model, StableStateMethod settings)
void	StableStateTool.run(LogicalModel model, String... parameters)
void	StableJBDD.run(LogicalModel model, String... parameters)

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

Constructor and Description
JBDDModel(LogicalModel lm)
StableASP(LogicalModel model)
StableStateList(LogicalModel model)
StableStateSearcher(LogicalModel model) Create a new stable state searcher.
StructuralNodeOrderer(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
TrapSpaceList	TrapSpaceTool.getResult(LogicalModel model, TrapSpaceSettings settings)
Task<TrapSpaceList>	TrapSpaceTool.getTask(LogicalModel model, TrapSpaceSettings settings)
void	TrapSpaceTool.run(LogicalModel model, String... parameters)

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

Constructor and Description
TrapSpaceIdentifier(LogicalModel model, TrapSpaceSettings settings)
TrapSpaceList(TrapSpaceSettings settings, LogicalModel model)
TrapSpaceSolverASP(LogicalModel model, TrapSpaceSettings settings)
TrapSpaceSolverBDD(LogicalModel model, TrapSpaceSettings settings)