Uses of Class
org.colomoto.common.task.AbstractTask

Packages that use AbstractTask

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.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

Uses of AbstractTask in org.colomoto.biolqm.io

Subclasses of AbstractTask in org.colomoto.biolqm.io

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

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

Subclasses of AbstractTask in org.colomoto.biolqm.io.bnet

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 AbstractTask in org.colomoto.biolqm.io.booleannet

Subclasses of AbstractTask in org.colomoto.biolqm.io.booleannet

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 AbstractTask in org.colomoto.biolqm.io.boolsim

Subclasses of AbstractTask in org.colomoto.biolqm.io.boolsim

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

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

Subclasses of AbstractTask in org.colomoto.biolqm.io.cnet

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

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

Subclasses of AbstractTask in org.colomoto.biolqm.io.functions

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 AbstractTask in org.colomoto.biolqm.io.gna

Subclasses of AbstractTask in org.colomoto.biolqm.io.gna

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

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

Subclasses of AbstractTask in org.colomoto.biolqm.io.implicanttables

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

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

Subclasses of AbstractTask in org.colomoto.biolqm.io.maboss

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

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

Subclasses of AbstractTask in org.colomoto.biolqm.io.mnet

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 AbstractTask in org.colomoto.biolqm.io.petrinet

Subclasses of AbstractTask in org.colomoto.biolqm.io.petrinet

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 AbstractTask in org.colomoto.biolqm.io.pint

Subclasses of AbstractTask in org.colomoto.biolqm.io.pint

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

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

Subclasses of AbstractTask in org.colomoto.biolqm.io.sbml

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 AbstractTask in org.colomoto.biolqm.io.truthtable

Subclasses of AbstractTask in org.colomoto.biolqm.io.truthtable

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 AbstractTask in org.colomoto.biolqm.modifier

Subclasses of AbstractTask in org.colomoto.biolqm.modifier

Modifier and Type	Class and Description
class	BaseModifier

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

Subclasses of AbstractTask in org.colomoto.biolqm.modifier.booleanize

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

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

Subclasses of AbstractTask in org.colomoto.biolqm.modifier.buffer

Modifier and Type	Class and Description
class	BufferingModifier

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

Subclasses of AbstractTask in org.colomoto.biolqm.modifier.perturbation

Modifier and Type	Class and Description
class	PerturbationModifier

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

Subclasses of AbstractTask in org.colomoto.biolqm.modifier.reduction

Modifier and Type	Class and Description
class	PatternReduction
class	ReductionModifier

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

Subclasses of AbstractTask in org.colomoto.biolqm.modifier.reverse

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

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

Subclasses of AbstractTask in org.colomoto.biolqm.modifier.sanitize

Modifier and Type	Class and Description
class	SanitizeModifier

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

Subclasses of AbstractTask in org.colomoto.biolqm.modifier.submodel

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 AbstractTask in org.colomoto.biolqm.modifier.subspace

Subclasses of AbstractTask in org.colomoto.biolqm.modifier.subspace

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

Uses of AbstractTask in org.colomoto.biolqm.tool

Subclasses of AbstractTask in org.colomoto.biolqm.tool

Modifier and Type	Class and Description
class	AbstractToolTask<R>

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

Subclasses of AbstractTask in org.colomoto.biolqm.tool.attractor

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

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

Subclasses of AbstractTask in org.colomoto.biolqm.tool.fixpoints

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

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

Subclasses of AbstractTask in org.colomoto.biolqm.tool.simulation.deterministic

Modifier and Type	Class and Description
class	TraceTask

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

Subclasses of AbstractTask in org.colomoto.biolqm.tool.simulation.random

Modifier and Type	Class and Description
class	RandomWalkTask

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

Subclasses of AbstractTask in org.colomoto.biolqm.tool.trapspaces

Modifier and Type	Class and Description
class	TrapSpaceTask