Uses of Interface
org.colomoto.common.task.Task

Packages that use Task

Package	Description
org.colomoto.biolqm.io	Input/Output for Logical Model.
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.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.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
org.colomoto.common.task	Task interface and tools: callables which can run in background.

Uses of Task in org.colomoto.biolqm.io

Subinterfaces of Task in org.colomoto.biolqm.io

Modifier and Type	Interface and Description
interface	ModelExporter Model exporters are tasks dedicated to exporting a model in a specific format.
interface	ModelLoader Model loaders are tasks dedicated to loading a model from a specific format.

Classes in org.colomoto.biolqm.io that implement Task

Modifier and Type	Class and Description
class	BaseExporter Base class for model exporters.
class	BaseLoader Base class for model loader.

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

Classes in org.colomoto.biolqm.io.bnet that implement Task

Modifier and Type	Class and Description
class	BNetExport Export logical model into a raw list of functions.
class	BNetImport Simple import reading logical functions in a text file.

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

Classes in org.colomoto.biolqm.io.booleannet that implement Task

Modifier and Type	Class and Description
class	BooleanNetExport Export logical model into a raw list of functions.
class	BooleanNetImport launch an antlr-generated parser, listen for events and feed them to an ExpressionStack

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

Classes in org.colomoto.biolqm.io.boolsim that implement Task

Modifier and Type	Class and Description
class	BoolSimExport Export logical model into the boolsim format.
class	BoolSimImport Import boolsim models.

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

Classes in org.colomoto.biolqm.io.cnet that implement Task

Modifier and Type	Class and Description
class	CNetExport Export logical model into cnet truth tables.
class	CNetImport

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

Classes in org.colomoto.biolqm.io.functions that implement Task

Modifier and Type	Class and Description
class	BooleanFunctionExport Export logical model into a raw list of functions.
class	BooleanFunctionImport Simple import reading logical functions in a text file.

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

Classes in org.colomoto.biolqm.io.gna that implement Task

Modifier and Type	Class and Description
class	GNAExport Exports a logical model into the non-xml GNA format.

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

Classes in org.colomoto.biolqm.io.implicanttables that implement Task

Modifier and Type	Class and Description
class	ImplicantTableExport Export logical model into lists of implicant tables.
class	ImplicantTableImport

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

Classes in org.colomoto.biolqm.io.maboss that implement Task

Modifier and Type	Class and Description
class	MaBoSSEncoder Export a Boolean(ized) LogicalModel into MaBoSS format

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

Classes in org.colomoto.biolqm.io.mnet that implement Task

Modifier and Type	Class and Description
class	MNetExport Export logical model into a list of multi-valued functions.
class	MNetImport Simple import reading multi-valued logical functions from a text file.

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

Classes in org.colomoto.biolqm.io.petrinet that implement Task

Modifier and Type	Class and Description
class	AbstractPNEncoder Export a regulatory graph to petri net (shared methods).
class	PNEncoderAPNN Export a regulatory graph to petri net (APNN format).
class	PNEncoderINA Export a regulatory graph to Petri net (INA format).
class	PNEncoderPNML Export a regulatory graph to Petri net (PNML format).

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

Classes in org.colomoto.biolqm.io.pint that implement Task

Modifier and Type	Class and Description
class	PintExport Export logical model into the Pint format.

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

Classes in org.colomoto.biolqm.io.sbml that implement Task

Modifier and Type	Class and Description
class	SBMLqualExport SBML export using JSBML and the "qual" extension.
class	SBMLqualImport Crude SBML import using JSBML and the qual extension.

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

Classes in org.colomoto.biolqm.io.truthtable that implement Task

Modifier and Type	Class and Description
class	TruthTableExport Exports a logical model into the Truth Table format.
class	TruthTableImport Imports a file in the Truth Table format into a LogicalModel.

Uses of Task in org.colomoto.biolqm.modifier

Subinterfaces of Task in org.colomoto.biolqm.modifier

Modifier and Type	Interface and Description
interface	ModelModifier Model Modifiers are tasks dedicated to the construction of modified logical models.

Classes in org.colomoto.biolqm.modifier that implement Task

Modifier and Type	Class and Description
class	BaseModifier

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

Classes in org.colomoto.biolqm.modifier.booleanize that implement Task

Modifier and Type	Class and Description
class	BooleanizeModifier Construct a Boolean version of a multi-valued model.

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

Classes in org.colomoto.biolqm.modifier.buffer that implement Task

Modifier and Type	Class and Description
class	BufferingModifier

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

Classes in org.colomoto.biolqm.modifier.perturbation that implement Task

Modifier and Type	Class and Description
class	PerturbationModifier

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

Classes in org.colomoto.biolqm.modifier.reduction that implement Task

Modifier and Type	Class and Description
class	PatternReduction
class	ReductionModifier

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

Classes in org.colomoto.biolqm.modifier.reverse that implement Task

Modifier and Type	Class and Description
class	ReverseModifier Wrap ReverseOperation to properly create a new model capable of generating the reverse dynamics.

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

Classes in org.colomoto.biolqm.modifier.sanitize that implement Task

Modifier and Type	Class and Description
class	SanitizeModifier

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

Classes in org.colomoto.biolqm.modifier.submodel that implement Task

Modifier and Type	Class and Description
class	SubmodelModifier Given a list of component names, this modifier will extract a sub-model containing: - the given list of components, - all dependent components of these nodes (involved in the logical functions) as input components (if they are not fixed values).

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

Classes in org.colomoto.biolqm.modifier.subspace that implement Task

Modifier and Type	Class and Description
class	SubSpaceModifier Model Modifier to restrict a model into a subspace.

Uses of Task in org.colomoto.biolqm.service

Subinterfaces of Task in org.colomoto.biolqm.service

Modifier and Type	Interface and Description
interface	ModelTask Model Tasks are tasks which return a model.

Uses of Task in org.colomoto.biolqm.tool

Subinterfaces of Task in org.colomoto.biolqm.tool

Modifier and Type	Interface and Description
interface	ToolTask<R>

Classes in org.colomoto.biolqm.tool that implement Task

Modifier and Type	Class and Description
class	AbstractToolTask<R>

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

Classes in org.colomoto.biolqm.tool.attractor that implement Task

Modifier and Type	Class and Description
class	SATAttractorFinder Identification of synchronous attractors using a SAT solver, as proposed by E.

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

Classes in org.colomoto.biolqm.tool.fixpoints that implement Task

Modifier and Type	Class and Description
class	FixpointSearcher Perform a stable state search for a given model.
class	FixpointTask

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

Classes in org.colomoto.biolqm.tool.simulation.deterministic that implement Task

Modifier and Type	Class and Description
class	TraceTask

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

Classes in org.colomoto.biolqm.tool.simulation.random that implement Task

Modifier and Type	Class and Description
class	RandomWalkTask

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

Classes in org.colomoto.biolqm.tool.trapspaces that implement Task

Modifier and Type	Class and Description
class	TrapSpaceTask

Uses of Task in org.colomoto.common.task

Classes in org.colomoto.common.task that implement Task

Modifier and Type	Class and Description
class	AbstractTask<T> Helper class implementing the boring part of a Task.

Methods in org.colomoto.common.task with parameters of type Task

Modifier and Type	Method and Description
void	TaskListener.taskUpdated(Task task) Notifies a task update (finished or canceled)