A B C D E F G H I J K L M N O P Q R S T U V W X Y _

A

AbstractFormat - Class in org.colomoto.biolqm.io

Simple helper to fill in the boring parts of format declaration classes.

AbstractFormat(String, String) - Constructor for class org.colomoto.biolqm.io.AbstractFormat

AbstractFormat(String, String, boolean) - Constructor for class org.colomoto.biolqm.io.AbstractFormat

Deprecated.

AbstractFormat(String, String, MultivaluedSupport) - Constructor for class org.colomoto.biolqm.io.AbstractFormat

AbstractFormat(String, String[], String, MultivaluedSupport) - Constructor for class org.colomoto.biolqm.io.AbstractFormat

AbstractGINMLWriter - Class in org.colomoto.biolqm.io.ginml

Some common methods to write a GINML file.

AbstractGINMLWriter() - Constructor for class org.colomoto.biolqm.io.ginml.AbstractGINMLWriter

AbstractMultipleSuccessorUpdater - Class in org.colomoto.biolqm.tool.simulation.multiplesuccessor

Base class for updaters which yield multiple successors.

AbstractMultipleSuccessorUpdater(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.simulation.multiplesuccessor.AbstractMultipleSuccessorUpdater

AbstractPNEncoder - Class in org.colomoto.biolqm.io.petrinet

Export a regulatory graph to petri net (shared methods).

AbstractPNEncoder(LogicalModel) - Constructor for class org.colomoto.biolqm.io.petrinet.AbstractPNEncoder

AbstractRandomUpdater - Class in org.colomoto.biolqm.tool.simulation.random

Base class for random updaters.

AbstractRandomUpdater(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.simulation.random.AbstractRandomUpdater

AbstractTask<T> - Class in org.colomoto.common.task

Helper class implementing the boring part of a Task.

AbstractTask() - Constructor for class org.colomoto.common.task.AbstractTask

AbstractToolService<R,T extends ToolTask<R>> - Class in org.colomoto.biolqm.tool

Base class for the boring parts of tool declaration classes.

AbstractToolService(String, String) - Constructor for class org.colomoto.biolqm.tool.AbstractToolService

AbstractToolService(String, String, String, MultivaluedSupport) - Constructor for class org.colomoto.biolqm.tool.AbstractToolService

AbstractToolService(String, String[], String, String, MultivaluedSupport) - Constructor for class org.colomoto.biolqm.tool.AbstractToolService

AbstractToolTask<R> - Class in org.colomoto.biolqm.tool

AbstractToolTask(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.AbstractToolTask

add(int, int, int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

add(int, int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClassGroup

add(TrapSpace) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceList

add_fixed(int, int) - Method in interface org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolver

add_fixed(int, int) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverASP

add_fixed(int, int) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverBDD

add_fixed(int, int) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverFunctionASP

add_focus(int) - Method in interface org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolver

add_focus(int) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverASP

add_focus(int) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverBDD

add_focus(int) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverFunctionASP

add_variable(int, Formula, Formula) - Method in interface org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolver

add_variable(int, Formula, Formula) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverASP

add_variable(int, Formula, Formula) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverBDD

add_variable(int, Formula, Formula) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverFunctionASP

addActionListener(PanelChangedEventListener) - Method in class org.colomoto.biolqm.widgets.PriorityClassPanel

addAllSingleBuffers() - Method in class org.colomoto.biolqm.modifier.buffer.BufferingModifier

addAttr(String, String) - Method in class org.colomoto.common.xml.XMLWriter

add an attribute to the opened tag.

addComplexContent(String, boolean) - Method in class org.colomoto.common.xml.XMLWriter

Add a complex "text child", it will be enclosed into CDATA markers

addContent(String) - Method in class org.colomoto.common.xml.XMLWriter

Add a "text child"

addDelayBuffers() - Method in class org.colomoto.biolqm.modifier.buffer.BufferingModifier

addFormatedContent(String, boolean) - Method in class org.colomoto.common.xml.XMLWriter

Add a "text child", already formated: should _NOT_ be escaped

addGrp(int, ModelGrouping.RankedClassGroup) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

addMultipleBuffer(int, List<Integer>) - Method in class org.colomoto.biolqm.modifier.buffer.BufferingModifier

addPattern(byte[], boolean[]) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceList

addSingleBuffer(int, int) - Method in class org.colomoto.biolqm.modifier.buffer.BufferingModifier

addState(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.multiplesuccessor.MultipleSuccessorSimulation

Add a state to the result of this simulation.

addSuccessor(List<byte[]>, byte[]) - Method in class org.colomoto.biolqm.tool.simulation.multiplesuccessor.AbstractMultipleSuccessorUpdater

addTag(String) - Method in class org.colomoto.common.xml.XMLWriter

Add (i.e.

addTag(String, String[], String) - Method in class org.colomoto.common.xml.XMLWriter

Add (i.e.

addTag(String, String[]) - Method in class org.colomoto.common.xml.XMLWriter

Add (i.e.

addTag(String, String) - Method in class org.colomoto.common.xml.XMLWriter

Add (i.e.

addTransition(byte[], byte[]) - Method in class org.colomoto.biolqm.tool.simulation.multiplesuccessor.MultipleSuccessorSimulation

Add a transition

affectsNode(NodeInfo) - Method in class org.colomoto.biolqm.modifier.perturbation.FixedValuePerturbation

affectsNode(NodeInfo) - Method in class org.colomoto.biolqm.modifier.perturbation.InteractionPerturbation

affectsNode(NodeInfo) - Method in interface org.colomoto.biolqm.modifier.perturbation.LogicalModelPerturbation

Test if the perturbation affects the function of a specific node

affectsNode(NodeInfo) - Method in class org.colomoto.biolqm.modifier.perturbation.MultiplePerturbation

affectsNode(NodeInfo) - Method in class org.colomoto.biolqm.modifier.perturbation.RangePerturbation

ALIASES - Static variable in class org.colomoto.biolqm.tool.fixpoints.FixpointService

ALIASES - Static variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceService

altasp - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

and() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

and() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AndExprContext

AND - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

AND - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

AND() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AndExprContext

AND - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

AND - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

AND() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.AndExprContext

AND - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

AND - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

AND() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.AndExprContext

and() - Method in class org.colomoto.biolqm.io.antlr.MNetParser

and() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AndExprContext

AndContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BNetParser.AndContext

AndContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.MNetParser.AndContext

AndExprContext(BNetParser.ExprContext) - Constructor for class org.colomoto.biolqm.io.antlr.BNetParser.AndExprContext

AndExprContext(BooleanFunctionParser.ExprContext) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AndExprContext

AndExprContext(BooleanNetParser.ExprContext) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanNetParser.AndExprContext

AndExprContext(BoolsimParser.ExprContext) - Constructor for class org.colomoto.biolqm.io.antlr.BoolsimParser.AndExprContext

AndExprContext(MNetParser.ExprContext) - Constructor for class org.colomoto.biolqm.io.antlr.MNetParser.AndExprContext

APNNFormat - Class in org.colomoto.biolqm.io.petrinet

PNML is an xml-based format for Petri net models.

APNNFormat() - Constructor for class org.colomoto.biolqm.io.petrinet.APNNFormat

apply(LogicalModel) - Method in interface org.colomoto.biolqm.modifier.perturbation.LogicalModelPerturbation

Apply the perturbation.

args - Variable in class org.colomoto.biolqm.service.LQMServiceManager

array() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClassGroup

ask(MDDManager, NodeRelation, int, int) - Method in class org.colomoto.biolqm.tool.fixpoints.StableOperation

assign() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

assign() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.ModelContext

assign(int) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.ModelContext

assign() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

assign() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ModelContext

assign(int) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ModelContext

assign() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser

assign() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.ModelContext

assign(int) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.ModelContext

assign() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser

assign() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.ModelContext

assign(int) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.ModelContext

assign() - Method in class org.colomoto.biolqm.io.antlr.MNetParser

assign() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.ModelContext

assign(int) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.ModelContext

AssignContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BNetParser.AssignContext

AssignContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AssignContext

AssignContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanNetParser.AssignContext

AssignContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BoolsimParser.AssignContext

AssignContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.MNetParser.AssignContext

Assignment - Class in org.colomoto.biolqm.io.antlr

Assignment(int, FunctionNode) - Constructor for class org.colomoto.biolqm.io.antlr.Assignment

AsynchronousUpdater - Class in org.colomoto.biolqm.tool.simulation.multiplesuccessor

Updater for the asynchronous scheme: all possible changes are applied separately.

AsynchronousUpdater(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.simulation.multiplesuccessor.AsynchronousUpdater

Create a new asynchronous random.

AttractorService - Class in org.colomoto.biolqm.tool.attractor

Identification of synchronous attractors using a SAT solver, as proposed by E.

AttractorService() - Constructor for class org.colomoto.biolqm.tool.attractor.AttractorService

B

background(TaskListener) - Method in class org.colomoto.common.task.AbstractTask

background(TaskListener) - Method in interface org.colomoto.common.task.Task

Run the task in a separate thread.

BaseExporter - Class in org.colomoto.biolqm.io

Base class for model exporters.

BaseExporter(LogicalModel) - Constructor for class org.colomoto.biolqm.io.BaseExporter

BaseLoader - Class in org.colomoto.biolqm.io

Base class for model loader.

BaseLoader() - Constructor for class org.colomoto.biolqm.io.BaseLoader

BaseModifier - Class in org.colomoto.biolqm.modifier

BaseModifier() - Constructor for class org.colomoto.biolqm.modifier.BaseModifier

BaseService - Class in org.colomoto.biolqm.service

Common base class for all services, to store the associated metadata

BaseService(String, String, String, MultivaluedSupport) - Constructor for class org.colomoto.biolqm.service.BaseService

BaseService(String, String[], String, String, MultivaluedSupport) - Constructor for class org.colomoto.biolqm.service.BaseService

BaseUpdater - Class in org.colomoto.biolqm.tool.simulation

Base class for all updaters.

BaseUpdater(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.simulation.BaseUpdater

bdd - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

bddPaths(BDD) - Method in class org.colomoto.biolqm.tool.fixpoints.JBDDModel

biimps() - Method in class org.colomoto.biolqm.tool.fixpoints.JBDDModel

BlockSequentialUpdater - Class in org.colomoto.biolqm.tool.simulation.deterministic

Updater for a block-sequential scheme: there are groups of nodes updated in synchronous way, but the different groups are updated in sequential way, one after another.

BlockSequentialUpdater(ModelGrouping) - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.BlockSequentialUpdater

BlockSequentialUpdater(LogicalModel, int[][]) - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.BlockSequentialUpdater

BlockSequentialUpdater(LogicalModel, String) - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.BlockSequentialUpdater

BNetBaseListener - Class in org.colomoto.biolqm.io.antlr

This class provides an empty implementation of BNetListener, which can be extended to create a listener which only needs to handle a subset of the available methods.

BNetBaseListener() - Constructor for class org.colomoto.biolqm.io.antlr.BNetBaseListener

BNetExport - Class in org.colomoto.biolqm.io.bnet

Export logical model into a raw list of functions.

BNetExport(LogicalModel) - Constructor for class org.colomoto.biolqm.io.bnet.BNetExport

BNetFormat - Class in org.colomoto.biolqm.io.bnet

BNetFormat() - Constructor for class org.colomoto.biolqm.io.bnet.BNetFormat

BNetImport - Class in org.colomoto.biolqm.io.bnet

Simple import reading logical functions in a text file.

BNetImport() - Constructor for class org.colomoto.biolqm.io.bnet.BNetImport

BNetLexer - Class in org.colomoto.biolqm.io.antlr

BNetLexer(CharStream) - Constructor for class org.colomoto.biolqm.io.antlr.BNetLexer

BNetListener - Interface in org.colomoto.biolqm.io.antlr

This interface defines a complete listener for a parse tree produced by BNetParser.

BNetParser - Class in org.colomoto.biolqm.io.antlr

BNetParser(TokenStream) - Constructor for class org.colomoto.biolqm.io.antlr.BNetParser

BNetParser.AndContext - Class in org.colomoto.biolqm.io.antlr

BNetParser.AndExprContext - Class in org.colomoto.biolqm.io.antlr

BNetParser.AssignContext - Class in org.colomoto.biolqm.io.antlr

BNetParser.ExprContext - Class in org.colomoto.biolqm.io.antlr

BNetParser.HeaderContext - Class in org.colomoto.biolqm.io.antlr

BNetParser.ModelContext - Class in org.colomoto.biolqm.io.antlr

BNetParser.NotContext - Class in org.colomoto.biolqm.io.antlr

BNetParser.OrContext - Class in org.colomoto.biolqm.io.antlr

BNetParser.OrExprContext - Class in org.colomoto.biolqm.io.antlr

BNetParser.SimpleExprContext - Class in org.colomoto.biolqm.io.antlr

BNetParser.ValContext - Class in org.colomoto.biolqm.io.antlr

BNetParser.VarContext - Class in org.colomoto.biolqm.io.antlr

BooleanFunctionBaseListener - Class in org.colomoto.biolqm.io.antlr

This class provides an empty implementation of BooleanFunctionListener, which can be extended to create a listener which only needs to handle a subset of the available methods.

BooleanFunctionBaseListener() - Constructor for class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

BooleanFunctionExport - Class in org.colomoto.biolqm.io.functions

Export logical model into a raw list of functions.

BooleanFunctionExport(LogicalModel) - Constructor for class org.colomoto.biolqm.io.functions.BooleanFunctionExport

BooleanFunctionFormat - Class in org.colomoto.biolqm.io.functions

BooleanFunctionFormat() - Constructor for class org.colomoto.biolqm.io.functions.BooleanFunctionFormat

BooleanFunctionImport - Class in org.colomoto.biolqm.io.functions

Simple import reading logical functions in a text file.

BooleanFunctionImport() - Constructor for class org.colomoto.biolqm.io.functions.BooleanFunctionImport

BooleanFunctionLexer - Class in org.colomoto.biolqm.io.antlr

BooleanFunctionLexer(CharStream) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

BooleanFunctionListener - Interface in org.colomoto.biolqm.io.antlr

This interface defines a complete listener for a parse tree produced by BooleanFunctionParser.

BooleanFunctionParser - Class in org.colomoto.biolqm.io.antlr

BooleanFunctionParser(TokenStream) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

BooleanFunctionParser.AndExprContext - Class in org.colomoto.biolqm.io.antlr

BooleanFunctionParser.AssignContext - Class in org.colomoto.biolqm.io.antlr

BooleanFunctionParser.ExprContext - Class in org.colomoto.biolqm.io.antlr

BooleanFunctionParser.ModelContext - Class in org.colomoto.biolqm.io.antlr

BooleanFunctionParser.NotContext - Class in org.colomoto.biolqm.io.antlr

BooleanFunctionParser.OrExprContext - Class in org.colomoto.biolqm.io.antlr

BooleanFunctionParser.SimpleExprContext - Class in org.colomoto.biolqm.io.antlr

BooleanFunctionParser.ValContext - Class in org.colomoto.biolqm.io.antlr

BooleanFunctionParser.VarContext - Class in org.colomoto.biolqm.io.antlr

BooleanizeModifier - Class in org.colomoto.biolqm.modifier.booleanize

Construct a Boolean version of a multi-valued model.

BooleanizeModifier(LogicalModel) - Constructor for class org.colomoto.biolqm.modifier.booleanize.BooleanizeModifier

BooleanizeService - Class in org.colomoto.biolqm.modifier.booleanize

A service for model booleanization.

BooleanizeService() - Constructor for class org.colomoto.biolqm.modifier.booleanize.BooleanizeService

Public constructor which should only be used for service discovery.

BooleanNetBaseListener - Class in org.colomoto.biolqm.io.antlr

This class provides an empty implementation of BooleanNetListener, which can be extended to create a listener which only needs to handle a subset of the available methods.

BooleanNetBaseListener() - Constructor for class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

BooleanNetExport - Class in org.colomoto.biolqm.io.booleannet

Export logical model into a raw list of functions.

BooleanNetExport(LogicalModel) - Constructor for class org.colomoto.biolqm.io.booleannet.BooleanNetExport

BooleanNetFormat - Class in org.colomoto.biolqm.io.booleannet

BooleanNetFormat() - Constructor for class org.colomoto.biolqm.io.booleannet.BooleanNetFormat

BooleanNetImport - Class in org.colomoto.biolqm.io.booleannet

launch an antlr-generated parser, listen for events and feed them to an ExpressionStack

BooleanNetImport() - Constructor for class org.colomoto.biolqm.io.booleannet.BooleanNetImport

BooleanNetLexer - Class in org.colomoto.biolqm.io.antlr

BooleanNetLexer(CharStream) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanNetLexer

BooleanNetListener - Interface in org.colomoto.biolqm.io.antlr

This interface defines a complete listener for a parse tree produced by BooleanNetParser.

BooleanNetParser - Class in org.colomoto.biolqm.io.antlr

BooleanNetParser(TokenStream) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanNetParser

BooleanNetParser.AndExprContext - Class in org.colomoto.biolqm.io.antlr

BooleanNetParser.AssignContext - Class in org.colomoto.biolqm.io.antlr

BooleanNetParser.ExprContext - Class in org.colomoto.biolqm.io.antlr

BooleanNetParser.ModelContext - Class in org.colomoto.biolqm.io.antlr

BooleanNetParser.NotContext - Class in org.colomoto.biolqm.io.antlr

BooleanNetParser.OrExprContext - Class in org.colomoto.biolqm.io.antlr

BooleanNetParser.SimpleExprContext - Class in org.colomoto.biolqm.io.antlr

BooleanNetParser.ValContext - Class in org.colomoto.biolqm.io.antlr

BooleanNetParser.VarContext - Class in org.colomoto.biolqm.io.antlr

BoolsimBaseListener - Class in org.colomoto.biolqm.io.antlr

This class provides an empty implementation of BoolsimListener, which can be extended to create a listener which only needs to handle a subset of the available methods.

BoolsimBaseListener() - Constructor for class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

BoolSimExport - Class in org.colomoto.biolqm.io.boolsim

Export logical model into the boolsim format.

BoolSimExport(LogicalModel) - Constructor for class org.colomoto.biolqm.io.boolsim.BoolSimExport

BoolSimFormat - Class in org.colomoto.biolqm.io.boolsim

BoolSimFormat() - Constructor for class org.colomoto.biolqm.io.boolsim.BoolSimFormat

BoolSimImport - Class in org.colomoto.biolqm.io.boolsim

Import boolsim models.

BoolSimImport() - Constructor for class org.colomoto.biolqm.io.boolsim.BoolSimImport

BoolsimLexer - Class in org.colomoto.biolqm.io.antlr

BoolsimLexer(CharStream) - Constructor for class org.colomoto.biolqm.io.antlr.BoolsimLexer

BoolsimListener - Interface in org.colomoto.biolqm.io.antlr

This interface defines a complete listener for a parse tree produced by BoolsimParser.

BoolsimParser - Class in org.colomoto.biolqm.io.antlr

BoolsimParser(TokenStream) - Constructor for class org.colomoto.biolqm.io.antlr.BoolsimParser

BoolsimParser.AndExprContext - Class in org.colomoto.biolqm.io.antlr

BoolsimParser.AssignContext - Class in org.colomoto.biolqm.io.antlr

BoolsimParser.ExprContext - Class in org.colomoto.biolqm.io.antlr

BoolsimParser.ModelContext - Class in org.colomoto.biolqm.io.antlr

BoolsimParser.NotContext - Class in org.colomoto.biolqm.io.antlr

BoolsimParser.OpContext - Class in org.colomoto.biolqm.io.antlr

BoolsimParser.SimpleExprContext - Class in org.colomoto.biolqm.io.antlr

BoolsimParser.VarContext - Class in org.colomoto.biolqm.io.antlr

BufferingModifier - Class in org.colomoto.biolqm.modifier.buffer

BufferingModifier(LogicalModel) - Constructor for class org.colomoto.biolqm.modifier.buffer.BufferingModifier

BufferingService - Class in org.colomoto.biolqm.modifier.buffer

A service to add buffer components.

BufferingService() - Constructor for class org.colomoto.biolqm.modifier.buffer.BufferingService

Public constructor which should only be used for service discovery.

C

call() - Method in class org.colomoto.common.task.AbstractTask

cancel() - Method in class org.colomoto.common.task.AbstractTask

cancel() - Method in interface org.colomoto.common.task.Task

Mark the task as canceled.

canceled - Variable in class org.colomoto.common.task.AbstractTask

canExport() - Method in class org.colomoto.biolqm.io.AbstractFormat

canExport() - Method in interface org.colomoto.biolqm.io.LogicalModelFormat

Does this format supports export operation?

canLoad() - Method in class org.colomoto.biolqm.io.AbstractFormat

canLoad() - Method in interface org.colomoto.biolqm.io.LogicalModelFormat

Does this format supports loading models?

channelNames - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

channelNames - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

channelNames - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

channelNames - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

channelNames - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

channelNames - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

channelNames - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

clear() - Method in class org.colomoto.biolqm.io.antlr.ExpressionStack

cli() - Method in class org.colomoto.biolqm.tool.attractor.SATAttractorFinder

cli() - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointTask

cli() - Method in class org.colomoto.biolqm.tool.simulation.deterministic.TraceTask

cli() - Method in class org.colomoto.biolqm.tool.simulation.random.RandomWalkTask

cli() - Method in interface org.colomoto.biolqm.tool.ToolTask

cli() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

CLINGO - Static variable in class org.colomoto.biolqm.helper.clingo.ClingoLauncher

ClingoLauncher - Class in org.colomoto.biolqm.helper.clingo

ClingoLauncher(ClingoResultHandler, String) - Constructor for class org.colomoto.biolqm.helper.clingo.ClingoLauncher

ClingoResult - Class in org.colomoto.biolqm.helper.clingo

Parse and store individual results from a clingo run.

ClingoResult(String) - Constructor for class org.colomoto.biolqm.helper.clingo.ClingoResult

ClingoResultHandler - Interface in org.colomoto.biolqm.helper.clingo

clone() - Method in class org.colomoto.biolqm.helper.state.Range

clone() - Method in interface org.colomoto.biolqm.LogicalModel

Make a copy of this model.

clone(boolean) - Method in interface org.colomoto.biolqm.LogicalModel

clone() - Method in class org.colomoto.biolqm.LogicalModelImpl

clone(boolean) - Method in class org.colomoto.biolqm.LogicalModelImpl

clone() - Method in class org.colomoto.biolqm.NodeInfo

clone() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

clone() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

clone() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClassGroup

cloneWithModel(LogicalModel) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

close() - Method in interface org.colomoto.biolqm.io.StreamProvider

Close this collection of streams.

close() - Method in class org.colomoto.common.xml.XMLWriter

Close the writer: automatically closes all open tags and the underlying output stream.

closeTag() - Method in class org.colomoto.common.xml.XMLWriter

Close the currently opened tag.

CNetBaseListener - Class in org.colomoto.biolqm.io.antlr

This class provides an empty implementation of CNetListener, which can be extended to create a listener which only needs to handle a subset of the available methods.

CNetBaseListener() - Constructor for class org.colomoto.biolqm.io.antlr.CNetBaseListener

CNetExport - Class in org.colomoto.biolqm.io.cnet

Export logical model into cnet truth tables.

CNetExport(LogicalModel) - Constructor for class org.colomoto.biolqm.io.cnet.CNetExport

CNetFormat - Class in org.colomoto.biolqm.io.cnet

CNetFormat() - Constructor for class org.colomoto.biolqm.io.cnet.CNetFormat

CNetImport - Class in org.colomoto.biolqm.io.cnet

CNetImport() - Constructor for class org.colomoto.biolqm.io.cnet.CNetImport

CNetLexer - Class in org.colomoto.biolqm.io.antlr

CNetLexer(CharStream) - Constructor for class org.colomoto.biolqm.io.antlr.CNetLexer

CNetListener - Interface in org.colomoto.biolqm.io.antlr

This interface defines a complete listener for a parse tree produced by CNetParser.

CNetParser - Class in org.colomoto.biolqm.io.antlr

CNetParser(TokenStream) - Constructor for class org.colomoto.biolqm.io.antlr.CNetParser

CNetParser.CountContext - Class in org.colomoto.biolqm.io.antlr

CNetParser.CurvarContext - Class in org.colomoto.biolqm.io.antlr

CNetParser.LineContext - Class in org.colomoto.biolqm.io.antlr

CNetParser.ModelContext - Class in org.colomoto.biolqm.io.antlr

CNetParser.TableContext - Class in org.colomoto.biolqm.io.antlr

CNetParser.TtlineContext - Class in org.colomoto.biolqm.io.antlr

CNetParser.VaridContext - Class in org.colomoto.biolqm.io.antlr

collapse() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

collapseAll() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

columns - Variable in class org.colomoto.biolqm.helper.state.SimpleStateList

combine(Term) - Method in class org.colomoto.biolqm.helper.implicants.Term

COMMENT - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

COMMENT - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

COMMENT - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

COMMENT - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

COMMENT - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

COMMENT - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

COMMENT - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

COMMENT - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

COMMENT - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

COMMENT - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

COMMENT - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

COMMENT - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

COMMENT - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

COMMENT - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

compare(LogicalModel, LogicalModel) - Static method in class org.colomoto.biolqm.LogicalModelComparator

Compare two logical models.

CompleteUpdater - Class in org.colomoto.biolqm.tool.simulation.multiplesuccessor

Updater for the "complete" mode: include all asynchronous, synchronous and partially synchronous changes.

CompleteUpdater(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.simulation.multiplesuccessor.CompleteUpdater

Create a new full random.

component - Variable in class org.colomoto.biolqm.modifier.perturbation.FixedValuePerturbation

component - Variable in class org.colomoto.biolqm.modifier.perturbation.RangePerturbation

condition - Variable in class org.colomoto.biolqm.io.antlr.Assignment

ConnectivityMatrix - Class in org.colomoto.biolqm

Build and consult regulatory relations between variables in a Logical Model.

ConnectivityMatrix(LogicalModel) - Constructor for class org.colomoto.biolqm.ConnectivityMatrix

constructModel(OperandFactory, List<NodeInfo>, Map<NodeInfo, FunctionNode>) - Static method in class org.colomoto.biolqm.io.antlr.ExpressionStack

Build a LogicalModel from a list of nodes and parsed functions.

constructMVModel(OperandFactory, List<NodeInfo>, Map<NodeInfo, List<Assignment>>) - Static method in class org.colomoto.biolqm.io.antlr.ExpressionStack

contains(TrapSpace) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpace

copy(NodeInfo, ModelLayout.LayoutInfo) - Method in class org.colomoto.biolqm.ModelLayout

copyFrom(BNetParser.ExprContext) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.ExprContext

copyFrom(BooleanFunctionParser.ExprContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ExprContext

copyFrom(BooleanNetParser.ExprContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.ExprContext

copyFrom(BoolsimParser.ExprContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.ExprContext

copyFrom(MNetParser.ExprContext) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.ExprContext

count() - Method in class org.colomoto.biolqm.io.antlr.CNetParser

count() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.ModelContext

count() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TableContext

CountContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.CNetParser.CountContext

countValues(byte) - Method in class org.colomoto.biolqm.helper.implicants.Term

create(File) - Static method in interface org.colomoto.biolqm.io.StreamProvider

create(String) - Static method in interface org.colomoto.biolqm.io.StreamProvider

crop() - Method in class org.colomoto.biolqm.ModelLayout

crop(int) - Method in class org.colomoto.biolqm.ModelLayout

crop(int, int) - Method in class org.colomoto.biolqm.ModelLayout

curvar() - Method in class org.colomoto.biolqm.io.antlr.CNetParser

curvar() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TableContext

curvar() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser

curvar() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TableContext

CurvarContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.CNetParser.CurvarContext

CurvarContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.ITNETParser.CurvarContext

custom(MDDManager, NodeRelation, int, int) - Method in class org.colomoto.biolqm.tool.fixpoints.StableOperation

D

ddmanager - Variable in class org.colomoto.biolqm.io.petrinet.AbstractPNEncoder

decGroup(int, int, List<String>) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

decPriorities(int, int, List<String>) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

DEFAULT_DTD - Static variable in class org.colomoto.biolqm.io.ginml.AbstractGINMLWriter

DeterministicPriorityUpdater - Class in org.colomoto.biolqm.tool.simulation.deterministic

DeterministicPriorityUpdater(LogicalModel, int[][]) - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.DeterministicPriorityUpdater

DeterministicPriorityUpdater(LogicalModel, String) - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.DeterministicPriorityUpdater

DeterministicPriorityUpdater(ModelGrouping) - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.DeterministicPriorityUpdater

DeterministicSimulation - Class in org.colomoto.biolqm.tool.simulation.deterministic

A simple simulation engine for deterministic updaters (with a single successor).

DeterministicSimulation(DeterministicUpdater, byte[]) - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.DeterministicSimulation

DeterministicSimulation(DeterministicUpdater, byte[], int) - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.DeterministicSimulation

DeterministicSimulation(DeterministicUpdater, byte[], int, int) - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.DeterministicSimulation

DeterministicUpdater - Interface in org.colomoto.biolqm.tool.simulation.deterministic

Interface for deterministic updaters which always return the same single successor for a given state.

diag - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

document - Variable in class org.colomoto.biolqm.io.sbml.SBMLQualBundle

doExport(String, List<NodeInfo>, List[], byte[][], OutputStreamWriter) - Method in class org.colomoto.biolqm.io.petrinet.AbstractPNEncoder

doExport(String, List<NodeInfo>, List[], byte[][], OutputStreamWriter) - Method in class org.colomoto.biolqm.io.petrinet.PNEncoderAPNN

doExport(String, List<NodeInfo>, List[], byte[][], OutputStreamWriter) - Method in class org.colomoto.biolqm.io.petrinet.PNEncoderINA

doExport(String, List<NodeInfo>, List[], byte[][], OutputStreamWriter) - Method in class org.colomoto.biolqm.io.petrinet.PNEncoderPNML

done() - Method in class org.colomoto.biolqm.io.antlr.ExpressionStack

DontCare - Static variable in class org.colomoto.biolqm.helper.implicants.Term

DuplicateRemover - Class in org.colomoto.biolqm.modifier.reduction

DuplicateRemover() - Constructor for class org.colomoto.biolqm.modifier.reduction.DuplicateRemover

E

enqueue(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.multiplesuccessor.MultipleSuccessorSimulation

ensureFilled() - Method in class org.colomoto.biolqm.io.sbml.SBMLqualExport

enterAnd(BNetParser.AndContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Enter a parse tree produced by BNetParser.and().

enterAnd(BNetParser.AndContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Enter a parse tree produced by BNetParser.and().

enterAnd(MNetParser.AndContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Enter a parse tree produced by MNetParser.and().

enterAnd(MNetParser.AndContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Enter a parse tree produced by MNetParser.and().

enterAndExpr(BNetParser.AndExprContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Enter a parse tree produced by the andExpr labeled alternative in BNetParser.expr().

enterAndExpr(BNetParser.AndExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Enter a parse tree produced by the andExpr labeled alternative in BNetParser.expr().

enterAndExpr(BooleanFunctionParser.AndExprContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Enter a parse tree produced by the andExpr labeled alternative in BooleanFunctionParser.expr().

enterAndExpr(BooleanFunctionParser.AndExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Enter a parse tree produced by the andExpr labeled alternative in BooleanFunctionParser.expr().

enterAndExpr(BooleanNetParser.AndExprContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Enter a parse tree produced by the andExpr labeled alternative in BooleanNetParser.expr().

enterAndExpr(BooleanNetParser.AndExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Enter a parse tree produced by the andExpr labeled alternative in BooleanNetParser.expr().

enterAndExpr(BoolsimParser.AndExprContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

Enter a parse tree produced by the andExpr labeled alternative in BoolsimParser.expr().

enterAndExpr(BoolsimParser.AndExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BoolsimListener

Enter a parse tree produced by the andExpr labeled alternative in BoolsimParser.expr().

enterAndExpr(MNetParser.AndExprContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Enter a parse tree produced by the andExpr labeled alternative in MNetParser.expr().

enterAndExpr(MNetParser.AndExprContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Enter a parse tree produced by the andExpr labeled alternative in MNetParser.expr().

enterAssign(BNetParser.AssignContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Enter a parse tree produced by BNetParser.assign().

enterAssign(BNetParser.AssignContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Enter a parse tree produced by BNetParser.assign().

enterAssign(BooleanFunctionParser.AssignContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Enter a parse tree produced by BooleanFunctionParser.assign().

enterAssign(BooleanFunctionParser.AssignContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Enter a parse tree produced by BooleanFunctionParser.assign().

enterAssign(BooleanNetParser.AssignContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Enter a parse tree produced by BooleanNetParser.assign().

enterAssign(BooleanNetParser.AssignContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Enter a parse tree produced by BooleanNetParser.assign().

enterAssign(BoolsimParser.AssignContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

Enter a parse tree produced by BoolsimParser.assign().

enterAssign(BoolsimParser.AssignContext) - Method in interface org.colomoto.biolqm.io.antlr.BoolsimListener

Enter a parse tree produced by BoolsimParser.assign().

enterAssign(MNetParser.AssignContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Enter a parse tree produced by MNetParser.assign().

enterAssign(MNetParser.AssignContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Enter a parse tree produced by MNetParser.assign().

enterCount(CNetParser.CountContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

Enter a parse tree produced by CNetParser.count().

enterCount(CNetParser.CountContext) - Method in interface org.colomoto.biolqm.io.antlr.CNetListener

Enter a parse tree produced by CNetParser.count().

enterCurvar(CNetParser.CurvarContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

Enter a parse tree produced by CNetParser.curvar().

enterCurvar(CNetParser.CurvarContext) - Method in interface org.colomoto.biolqm.io.antlr.CNetListener

Enter a parse tree produced by CNetParser.curvar().

enterCurvar(ITNETParser.CurvarContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Enter a parse tree produced by ITNETParser.curvar().

enterCurvar(ITNETParser.CurvarContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Enter a parse tree produced by ITNETParser.curvar().

enterEveryRule(ParserRuleContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

enterEveryRule(ParserRuleContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

enterEveryRule(ParserRuleContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

enterEveryRule(ParserRuleContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

enterEveryRule(ParserRuleContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

enterEveryRule(ParserRuleContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

enterEveryRule(ParserRuleContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

enterHeader(BNetParser.HeaderContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Enter a parse tree produced by BNetParser.header().

enterHeader(BNetParser.HeaderContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Enter a parse tree produced by BNetParser.header().

enterLine(CNetParser.LineContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

Enter a parse tree produced by CNetParser.line().

enterLine(CNetParser.LineContext) - Method in interface org.colomoto.biolqm.io.antlr.CNetListener

Enter a parse tree produced by CNetParser.line().

enterLine(ITNETParser.LineContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Enter a parse tree produced by ITNETParser.line().

enterLine(ITNETParser.LineContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Enter a parse tree produced by ITNETParser.line().

enterMax(ITNETParser.MaxContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Enter a parse tree produced by ITNETParser.max().

enterMax(ITNETParser.MaxContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Enter a parse tree produced by ITNETParser.max().

enterModel(BNetParser.ModelContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Enter a parse tree produced by BNetParser.model().

enterModel(BNetParser.ModelContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Enter a parse tree produced by BNetParser.model().

enterModel(BooleanFunctionParser.ModelContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Enter a parse tree produced by BooleanFunctionParser.model().

enterModel(BooleanFunctionParser.ModelContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Enter a parse tree produced by BooleanFunctionParser.model().

enterModel(BooleanNetParser.ModelContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Enter a parse tree produced by BooleanNetParser.model().

enterModel(BooleanNetParser.ModelContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Enter a parse tree produced by BooleanNetParser.model().

enterModel(BoolsimParser.ModelContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

Enter a parse tree produced by BoolsimParser.model().

enterModel(BoolsimParser.ModelContext) - Method in interface org.colomoto.biolqm.io.antlr.BoolsimListener

Enter a parse tree produced by BoolsimParser.model().

enterModel(CNetParser.ModelContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

Enter a parse tree produced by CNetParser.model().

enterModel(CNetParser.ModelContext) - Method in interface org.colomoto.biolqm.io.antlr.CNetListener

Enter a parse tree produced by CNetParser.model().

enterModel(ITNETParser.ModelContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Enter a parse tree produced by ITNETParser.model().

enterModel(ITNETParser.ModelContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Enter a parse tree produced by ITNETParser.model().

enterModel(MNetParser.ModelContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Enter a parse tree produced by MNetParser.model().

enterModel(MNetParser.ModelContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Enter a parse tree produced by MNetParser.model().

enterNot(BNetParser.NotContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Enter a parse tree produced by BNetParser.not().

enterNot(BNetParser.NotContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Enter a parse tree produced by BNetParser.not().

enterNot(BooleanFunctionParser.NotContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Enter a parse tree produced by BooleanFunctionParser.not().

enterNot(BooleanFunctionParser.NotContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Enter a parse tree produced by BooleanFunctionParser.not().

enterNot(BooleanNetParser.NotContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Enter a parse tree produced by BooleanNetParser.not().

enterNot(BooleanNetParser.NotContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Enter a parse tree produced by BooleanNetParser.not().

enterNot(BoolsimParser.NotContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

Enter a parse tree produced by BoolsimParser.not().

enterNot(BoolsimParser.NotContext) - Method in interface org.colomoto.biolqm.io.antlr.BoolsimListener

Enter a parse tree produced by BoolsimParser.not().

enterNot(MNetParser.NotContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Enter a parse tree produced by MNetParser.not().

enterNot(MNetParser.NotContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Enter a parse tree produced by MNetParser.not().

enterOp(BoolsimParser.OpContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

Enter a parse tree produced by BoolsimParser.op().

enterOp(BoolsimParser.OpContext) - Method in interface org.colomoto.biolqm.io.antlr.BoolsimListener

Enter a parse tree produced by BoolsimParser.op().

enterOr(BNetParser.OrContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Enter a parse tree produced by BNetParser.or().

enterOr(BNetParser.OrContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Enter a parse tree produced by BNetParser.or().

enterOr(MNetParser.OrContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Enter a parse tree produced by MNetParser.or().

enterOr(MNetParser.OrContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Enter a parse tree produced by MNetParser.or().

enterOrExpr(BNetParser.OrExprContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Enter a parse tree produced by the orExpr labeled alternative in BNetParser.expr().

enterOrExpr(BNetParser.OrExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Enter a parse tree produced by the orExpr labeled alternative in BNetParser.expr().

enterOrExpr(BooleanFunctionParser.OrExprContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Enter a parse tree produced by the orExpr labeled alternative in BooleanFunctionParser.expr().

enterOrExpr(BooleanFunctionParser.OrExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Enter a parse tree produced by the orExpr labeled alternative in BooleanFunctionParser.expr().

enterOrExpr(BooleanNetParser.OrExprContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Enter a parse tree produced by the orExpr labeled alternative in BooleanNetParser.expr().

enterOrExpr(BooleanNetParser.OrExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Enter a parse tree produced by the orExpr labeled alternative in BooleanNetParser.expr().

enterOrExpr(MNetParser.OrExprContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Enter a parse tree produced by the orExpr labeled alternative in MNetParser.expr().

enterOrExpr(MNetParser.OrExprContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Enter a parse tree produced by the orExpr labeled alternative in MNetParser.expr().

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AndContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AndExprContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AssignContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.HeaderContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.ModelContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.NotContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.OrContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.OrExprContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.SimpleExprContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.ValContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.VarContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AndExprContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AssignContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ModelContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.NotContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.OrExprContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.SimpleExprContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ValContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.VarContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.AndExprContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.AssignContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.ModelContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.NotContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.OrExprContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.SimpleExprContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.ValContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.VarContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.AndExprContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.AssignContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.ModelContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.NotContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.OpContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.SimpleExprContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.VarContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.CountContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.CurvarContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.LineContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.ModelContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TableContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TtlineContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.VaridContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.CurvarContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.LineContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.MaxContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.ModelContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TableContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TargetContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TtlineContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.VarContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AndContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AndExprContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AssignContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.ModelContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.NotContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.OrContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.OrExprContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.SimpleExprContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.ValContext

enterRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.VarContext

enterSimpleExpr(BNetParser.SimpleExprContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Enter a parse tree produced by the simpleExpr labeled alternative in BNetParser.expr().

enterSimpleExpr(BNetParser.SimpleExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Enter a parse tree produced by the simpleExpr labeled alternative in BNetParser.expr().

enterSimpleExpr(BooleanFunctionParser.SimpleExprContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Enter a parse tree produced by the simpleExpr labeled alternative in BooleanFunctionParser.expr().

enterSimpleExpr(BooleanFunctionParser.SimpleExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Enter a parse tree produced by the simpleExpr labeled alternative in BooleanFunctionParser.expr().

enterSimpleExpr(BooleanNetParser.SimpleExprContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Enter a parse tree produced by the simpleExpr labeled alternative in BooleanNetParser.expr().

enterSimpleExpr(BooleanNetParser.SimpleExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Enter a parse tree produced by the simpleExpr labeled alternative in BooleanNetParser.expr().

enterSimpleExpr(BoolsimParser.SimpleExprContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

Enter a parse tree produced by the simpleExpr labeled alternative in BoolsimParser.expr().

enterSimpleExpr(BoolsimParser.SimpleExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BoolsimListener

Enter a parse tree produced by the simpleExpr labeled alternative in BoolsimParser.expr().

enterSimpleExpr(MNetParser.SimpleExprContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Enter a parse tree produced by the simpleExpr labeled alternative in MNetParser.expr().

enterSimpleExpr(MNetParser.SimpleExprContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Enter a parse tree produced by the simpleExpr labeled alternative in MNetParser.expr().

enterTable(CNetParser.TableContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

Enter a parse tree produced by CNetParser.table().

enterTable(CNetParser.TableContext) - Method in interface org.colomoto.biolqm.io.antlr.CNetListener

Enter a parse tree produced by CNetParser.table().

enterTable(ITNETParser.TableContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Enter a parse tree produced by ITNETParser.table().

enterTable(ITNETParser.TableContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Enter a parse tree produced by ITNETParser.table().

enterTarget(ITNETParser.TargetContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Enter a parse tree produced by ITNETParser.target().

enterTarget(ITNETParser.TargetContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Enter a parse tree produced by ITNETParser.target().

enterTtline(CNetParser.TtlineContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

Enter a parse tree produced by CNetParser.ttline().

enterTtline(CNetParser.TtlineContext) - Method in interface org.colomoto.biolqm.io.antlr.CNetListener

Enter a parse tree produced by CNetParser.ttline().

enterTtline(ITNETParser.TtlineContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Enter a parse tree produced by ITNETParser.ttline().

enterTtline(ITNETParser.TtlineContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Enter a parse tree produced by ITNETParser.ttline().

enterVal(BNetParser.ValContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Enter a parse tree produced by BNetParser.val().

enterVal(BNetParser.ValContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Enter a parse tree produced by BNetParser.val().

enterVal(BooleanFunctionParser.ValContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Enter a parse tree produced by BooleanFunctionParser.val().

enterVal(BooleanFunctionParser.ValContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Enter a parse tree produced by BooleanFunctionParser.val().

enterVal(BooleanNetParser.ValContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Enter a parse tree produced by BooleanNetParser.val().

enterVal(BooleanNetParser.ValContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Enter a parse tree produced by BooleanNetParser.val().

enterVal(MNetParser.ValContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Enter a parse tree produced by MNetParser.val().

enterVal(MNetParser.ValContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Enter a parse tree produced by MNetParser.val().

enterVar(BNetParser.VarContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Enter a parse tree produced by BNetParser.var().

enterVar(BNetParser.VarContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Enter a parse tree produced by BNetParser.var().

enterVar(BooleanFunctionParser.VarContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Enter a parse tree produced by BooleanFunctionParser.var().

enterVar(BooleanFunctionParser.VarContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Enter a parse tree produced by BooleanFunctionParser.var().

enterVar(BooleanNetParser.VarContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Enter a parse tree produced by BooleanNetParser.var().

enterVar(BooleanNetParser.VarContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Enter a parse tree produced by BooleanNetParser.var().

enterVar(BoolsimParser.VarContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

Enter a parse tree produced by BoolsimParser.var().

enterVar(BoolsimParser.VarContext) - Method in interface org.colomoto.biolqm.io.antlr.BoolsimListener

Enter a parse tree produced by BoolsimParser.var().

enterVar(ITNETParser.VarContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Enter a parse tree produced by ITNETParser.var().

enterVar(ITNETParser.VarContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Enter a parse tree produced by ITNETParser.var().

enterVar(MNetParser.VarContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Enter a parse tree produced by MNetParser.var().

enterVar(MNetParser.VarContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Enter a parse tree produced by MNetParser.var().

enterVarid(CNetParser.VaridContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

Enter a parse tree produced by CNetParser.varid().

enterVarid(CNetParser.VaridContext) - Method in interface org.colomoto.biolqm.io.antlr.CNetListener

Enter a parse tree produced by CNetParser.varid().

equals(Formula) - Method in class org.colomoto.biolqm.helper.implicants.Formula

equals(Object) - Method in class org.colomoto.biolqm.helper.implicants.Term

equals(Object) - Method in class org.colomoto.biolqm.modifier.perturbation.FixedValuePerturbation

equals(Object) - Method in class org.colomoto.biolqm.modifier.perturbation.InteractionPerturbation

equals(Object) - Method in class org.colomoto.biolqm.modifier.perturbation.MultiplePerturbation

equals(Object) - Method in class org.colomoto.biolqm.modifier.perturbation.RangePerturbation

equals(Object) - Method in class org.colomoto.biolqm.NodeInfo

Compare the object to the given one.

equals(Object) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

equals(Object) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

Considers both classes with same ordered groups

equals(Object) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClassGroup

equals(Object) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpace

error(String) - Static method in class org.colomoto.biolqm.LQMLauncher

ErrorListener - Class in org.colomoto.biolqm.io.antlr

A simple error listener to be shared among antlr-based parsers

ErrorListener() - Constructor for class org.colomoto.biolqm.io.antlr.ErrorListener

exitAnd(BNetParser.AndContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Exit a parse tree produced by BNetParser.and().

exitAnd(BNetParser.AndContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Exit a parse tree produced by BNetParser.and().

exitAnd(MNetParser.AndContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Exit a parse tree produced by MNetParser.and().

exitAnd(MNetParser.AndContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Exit a parse tree produced by MNetParser.and().

exitAndExpr(BNetParser.AndExprContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Exit a parse tree produced by the andExpr labeled alternative in BNetParser.expr().

exitAndExpr(BNetParser.AndExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Exit a parse tree produced by the andExpr labeled alternative in BNetParser.expr().

exitAndExpr(BooleanFunctionParser.AndExprContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Exit a parse tree produced by the andExpr labeled alternative in BooleanFunctionParser.expr().

exitAndExpr(BooleanFunctionParser.AndExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Exit a parse tree produced by the andExpr labeled alternative in BooleanFunctionParser.expr().

exitAndExpr(BooleanNetParser.AndExprContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Exit a parse tree produced by the andExpr labeled alternative in BooleanNetParser.expr().

exitAndExpr(BooleanNetParser.AndExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Exit a parse tree produced by the andExpr labeled alternative in BooleanNetParser.expr().

exitAndExpr(BoolsimParser.AndExprContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

Exit a parse tree produced by the andExpr labeled alternative in BoolsimParser.expr().

exitAndExpr(BoolsimParser.AndExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BoolsimListener

Exit a parse tree produced by the andExpr labeled alternative in BoolsimParser.expr().

exitAndExpr(MNetParser.AndExprContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Exit a parse tree produced by the andExpr labeled alternative in MNetParser.expr().

exitAndExpr(MNetParser.AndExprContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Exit a parse tree produced by the andExpr labeled alternative in MNetParser.expr().

exitAssign(BNetParser.AssignContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Exit a parse tree produced by BNetParser.assign().

exitAssign(BNetParser.AssignContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Exit a parse tree produced by BNetParser.assign().

exitAssign(BooleanFunctionParser.AssignContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Exit a parse tree produced by BooleanFunctionParser.assign().

exitAssign(BooleanFunctionParser.AssignContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Exit a parse tree produced by BooleanFunctionParser.assign().

exitAssign(BooleanNetParser.AssignContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Exit a parse tree produced by BooleanNetParser.assign().

exitAssign(BooleanNetParser.AssignContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Exit a parse tree produced by BooleanNetParser.assign().

exitAssign(BoolsimParser.AssignContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

Exit a parse tree produced by BoolsimParser.assign().

exitAssign(BoolsimParser.AssignContext) - Method in interface org.colomoto.biolqm.io.antlr.BoolsimListener

Exit a parse tree produced by BoolsimParser.assign().

exitAssign(MNetParser.AssignContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Exit a parse tree produced by MNetParser.assign().

exitAssign(MNetParser.AssignContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Exit a parse tree produced by MNetParser.assign().

exitCount(CNetParser.CountContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

Exit a parse tree produced by CNetParser.count().

exitCount(CNetParser.CountContext) - Method in interface org.colomoto.biolqm.io.antlr.CNetListener

Exit a parse tree produced by CNetParser.count().

exitCurvar(CNetParser.CurvarContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

Exit a parse tree produced by CNetParser.curvar().

exitCurvar(CNetParser.CurvarContext) - Method in interface org.colomoto.biolqm.io.antlr.CNetListener

Exit a parse tree produced by CNetParser.curvar().

exitCurvar(ITNETParser.CurvarContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Exit a parse tree produced by ITNETParser.curvar().

exitCurvar(ITNETParser.CurvarContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Exit a parse tree produced by ITNETParser.curvar().

exitEveryRule(ParserRuleContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

exitEveryRule(ParserRuleContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

exitEveryRule(ParserRuleContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

exitEveryRule(ParserRuleContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

exitEveryRule(ParserRuleContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

exitEveryRule(ParserRuleContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

exitEveryRule(ParserRuleContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

exitHeader(BNetParser.HeaderContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Exit a parse tree produced by BNetParser.header().

exitHeader(BNetParser.HeaderContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Exit a parse tree produced by BNetParser.header().

exitLine(CNetParser.LineContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

Exit a parse tree produced by CNetParser.line().

exitLine(CNetParser.LineContext) - Method in interface org.colomoto.biolqm.io.antlr.CNetListener

Exit a parse tree produced by CNetParser.line().

exitLine(ITNETParser.LineContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Exit a parse tree produced by ITNETParser.line().

exitLine(ITNETParser.LineContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Exit a parse tree produced by ITNETParser.line().

exitMax(ITNETParser.MaxContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Exit a parse tree produced by ITNETParser.max().

exitMax(ITNETParser.MaxContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Exit a parse tree produced by ITNETParser.max().

exitModel(BNetParser.ModelContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Exit a parse tree produced by BNetParser.model().

exitModel(BNetParser.ModelContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Exit a parse tree produced by BNetParser.model().

exitModel(BooleanFunctionParser.ModelContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Exit a parse tree produced by BooleanFunctionParser.model().

exitModel(BooleanFunctionParser.ModelContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Exit a parse tree produced by BooleanFunctionParser.model().

exitModel(BooleanNetParser.ModelContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Exit a parse tree produced by BooleanNetParser.model().

exitModel(BooleanNetParser.ModelContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Exit a parse tree produced by BooleanNetParser.model().

exitModel(BoolsimParser.ModelContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

Exit a parse tree produced by BoolsimParser.model().

exitModel(BoolsimParser.ModelContext) - Method in interface org.colomoto.biolqm.io.antlr.BoolsimListener

Exit a parse tree produced by BoolsimParser.model().

exitModel(CNetParser.ModelContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

Exit a parse tree produced by CNetParser.model().

exitModel(CNetParser.ModelContext) - Method in interface org.colomoto.biolqm.io.antlr.CNetListener

Exit a parse tree produced by CNetParser.model().

exitModel(ITNETParser.ModelContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Exit a parse tree produced by ITNETParser.model().

exitModel(ITNETParser.ModelContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Exit a parse tree produced by ITNETParser.model().

exitModel(MNetParser.ModelContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Exit a parse tree produced by MNetParser.model().

exitModel(MNetParser.ModelContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Exit a parse tree produced by MNetParser.model().

exitNot(BNetParser.NotContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Exit a parse tree produced by BNetParser.not().

exitNot(BNetParser.NotContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Exit a parse tree produced by BNetParser.not().

exitNot(BooleanFunctionParser.NotContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Exit a parse tree produced by BooleanFunctionParser.not().

exitNot(BooleanFunctionParser.NotContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Exit a parse tree produced by BooleanFunctionParser.not().

exitNot(BooleanNetParser.NotContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Exit a parse tree produced by BooleanNetParser.not().

exitNot(BooleanNetParser.NotContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Exit a parse tree produced by BooleanNetParser.not().

exitNot(BoolsimParser.NotContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

Exit a parse tree produced by BoolsimParser.not().

exitNot(BoolsimParser.NotContext) - Method in interface org.colomoto.biolqm.io.antlr.BoolsimListener

Exit a parse tree produced by BoolsimParser.not().

exitNot(MNetParser.NotContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Exit a parse tree produced by MNetParser.not().

exitNot(MNetParser.NotContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Exit a parse tree produced by MNetParser.not().

exitOp(BoolsimParser.OpContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

Exit a parse tree produced by BoolsimParser.op().

exitOp(BoolsimParser.OpContext) - Method in interface org.colomoto.biolqm.io.antlr.BoolsimListener

Exit a parse tree produced by BoolsimParser.op().

exitOr(BNetParser.OrContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Exit a parse tree produced by BNetParser.or().

exitOr(BNetParser.OrContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Exit a parse tree produced by BNetParser.or().

exitOr(MNetParser.OrContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Exit a parse tree produced by MNetParser.or().

exitOr(MNetParser.OrContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Exit a parse tree produced by MNetParser.or().

exitOrExpr(BNetParser.OrExprContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Exit a parse tree produced by the orExpr labeled alternative in BNetParser.expr().

exitOrExpr(BNetParser.OrExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Exit a parse tree produced by the orExpr labeled alternative in BNetParser.expr().

exitOrExpr(BooleanFunctionParser.OrExprContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Exit a parse tree produced by the orExpr labeled alternative in BooleanFunctionParser.expr().

exitOrExpr(BooleanFunctionParser.OrExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Exit a parse tree produced by the orExpr labeled alternative in BooleanFunctionParser.expr().

exitOrExpr(BooleanNetParser.OrExprContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Exit a parse tree produced by the orExpr labeled alternative in BooleanNetParser.expr().

exitOrExpr(BooleanNetParser.OrExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Exit a parse tree produced by the orExpr labeled alternative in BooleanNetParser.expr().

exitOrExpr(MNetParser.OrExprContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Exit a parse tree produced by the orExpr labeled alternative in MNetParser.expr().

exitOrExpr(MNetParser.OrExprContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Exit a parse tree produced by the orExpr labeled alternative in MNetParser.expr().

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AndContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AndExprContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AssignContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.HeaderContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.ModelContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.NotContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.OrContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.OrExprContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.SimpleExprContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.ValContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.VarContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AndExprContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AssignContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ModelContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.NotContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.OrExprContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.SimpleExprContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ValContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.VarContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.AndExprContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.AssignContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.ModelContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.NotContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.OrExprContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.SimpleExprContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.ValContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.VarContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.AndExprContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.AssignContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.ModelContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.NotContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.OpContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.SimpleExprContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.VarContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.CountContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.CurvarContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.LineContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.ModelContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TableContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TtlineContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.VaridContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.CurvarContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.LineContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.MaxContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.ModelContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TableContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TargetContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TtlineContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.VarContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AndContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AndExprContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AssignContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.ModelContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.NotContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.OrContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.OrExprContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.SimpleExprContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.ValContext

exitRule(ParseTreeListener) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.VarContext

exitSimpleExpr(BNetParser.SimpleExprContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Exit a parse tree produced by the simpleExpr labeled alternative in BNetParser.expr().

exitSimpleExpr(BNetParser.SimpleExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Exit a parse tree produced by the simpleExpr labeled alternative in BNetParser.expr().

exitSimpleExpr(BooleanFunctionParser.SimpleExprContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Exit a parse tree produced by the simpleExpr labeled alternative in BooleanFunctionParser.expr().

exitSimpleExpr(BooleanFunctionParser.SimpleExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Exit a parse tree produced by the simpleExpr labeled alternative in BooleanFunctionParser.expr().

exitSimpleExpr(BooleanNetParser.SimpleExprContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Exit a parse tree produced by the simpleExpr labeled alternative in BooleanNetParser.expr().

exitSimpleExpr(BooleanNetParser.SimpleExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Exit a parse tree produced by the simpleExpr labeled alternative in BooleanNetParser.expr().

exitSimpleExpr(BoolsimParser.SimpleExprContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

Exit a parse tree produced by the simpleExpr labeled alternative in BoolsimParser.expr().

exitSimpleExpr(BoolsimParser.SimpleExprContext) - Method in interface org.colomoto.biolqm.io.antlr.BoolsimListener

Exit a parse tree produced by the simpleExpr labeled alternative in BoolsimParser.expr().

exitSimpleExpr(MNetParser.SimpleExprContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Exit a parse tree produced by the simpleExpr labeled alternative in MNetParser.expr().

exitSimpleExpr(MNetParser.SimpleExprContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Exit a parse tree produced by the simpleExpr labeled alternative in MNetParser.expr().

exitTable(CNetParser.TableContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

Exit a parse tree produced by CNetParser.table().

exitTable(CNetParser.TableContext) - Method in interface org.colomoto.biolqm.io.antlr.CNetListener

Exit a parse tree produced by CNetParser.table().

exitTable(ITNETParser.TableContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Exit a parse tree produced by ITNETParser.table().

exitTable(ITNETParser.TableContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Exit a parse tree produced by ITNETParser.table().

exitTarget(ITNETParser.TargetContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Exit a parse tree produced by ITNETParser.target().

exitTarget(ITNETParser.TargetContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Exit a parse tree produced by ITNETParser.target().

exitTtline(CNetParser.TtlineContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

Exit a parse tree produced by CNetParser.ttline().

exitTtline(CNetParser.TtlineContext) - Method in interface org.colomoto.biolqm.io.antlr.CNetListener

Exit a parse tree produced by CNetParser.ttline().

exitTtline(ITNETParser.TtlineContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Exit a parse tree produced by ITNETParser.ttline().

exitTtline(ITNETParser.TtlineContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Exit a parse tree produced by ITNETParser.ttline().

exitVal(BNetParser.ValContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Exit a parse tree produced by BNetParser.val().

exitVal(BNetParser.ValContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Exit a parse tree produced by BNetParser.val().

exitVal(BooleanFunctionParser.ValContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Exit a parse tree produced by BooleanFunctionParser.val().

exitVal(BooleanFunctionParser.ValContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Exit a parse tree produced by BooleanFunctionParser.val().

exitVal(BooleanNetParser.ValContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Exit a parse tree produced by BooleanNetParser.val().

exitVal(BooleanNetParser.ValContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Exit a parse tree produced by BooleanNetParser.val().

exitVal(MNetParser.ValContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Exit a parse tree produced by MNetParser.val().

exitVal(MNetParser.ValContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Exit a parse tree produced by MNetParser.val().

exitVar(BNetParser.VarContext) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

Exit a parse tree produced by BNetParser.var().

exitVar(BNetParser.VarContext) - Method in interface org.colomoto.biolqm.io.antlr.BNetListener

Exit a parse tree produced by BNetParser.var().

exitVar(BooleanFunctionParser.VarContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

Exit a parse tree produced by BooleanFunctionParser.var().

exitVar(BooleanFunctionParser.VarContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanFunctionListener

Exit a parse tree produced by BooleanFunctionParser.var().

exitVar(BooleanNetParser.VarContext) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

Exit a parse tree produced by BooleanNetParser.var().

exitVar(BooleanNetParser.VarContext) - Method in interface org.colomoto.biolqm.io.antlr.BooleanNetListener

Exit a parse tree produced by BooleanNetParser.var().

exitVar(BoolsimParser.VarContext) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

Exit a parse tree produced by BoolsimParser.var().

exitVar(BoolsimParser.VarContext) - Method in interface org.colomoto.biolqm.io.antlr.BoolsimListener

Exit a parse tree produced by BoolsimParser.var().

exitVar(ITNETParser.VarContext) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

Exit a parse tree produced by ITNETParser.var().

exitVar(ITNETParser.VarContext) - Method in interface org.colomoto.biolqm.io.antlr.ITNETListener

Exit a parse tree produced by ITNETParser.var().

exitVar(MNetParser.VarContext) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

Exit a parse tree produced by MNetParser.var().

exitVar(MNetParser.VarContext) - Method in interface org.colomoto.biolqm.io.antlr.MNetListener

Exit a parse tree produced by MNetParser.var().

exitVarid(CNetParser.VaridContext) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

Exit a parse tree produced by CNetParser.varid().

exitVarid(CNetParser.VaridContext) - Method in interface org.colomoto.biolqm.io.antlr.CNetListener

Exit a parse tree produced by CNetParser.varid().

expand(boolean) - Method in class org.colomoto.biolqm.io.implicanttables.ImplicantTableExport

expand() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

export() - Method in class org.colomoto.biolqm.io.BaseExporter

export() - Method in class org.colomoto.biolqm.io.bnet.BNetExport

export() - Method in class org.colomoto.biolqm.io.booleannet.BooleanNetExport

export() - Method in class org.colomoto.biolqm.io.boolsim.BoolSimExport

export() - Method in class org.colomoto.biolqm.io.cnet.CNetExport

export() - Method in class org.colomoto.biolqm.io.functions.BooleanFunctionExport

export(OutputStream) - Method in class org.colomoto.biolqm.io.ginml.AbstractGINMLWriter

Start the GINML export.

export() - Method in class org.colomoto.biolqm.io.gna.GNAExport

export() - Method in class org.colomoto.biolqm.io.implicanttables.ImplicantTableExport

export(LogicalModel, StreamProvider) - Method in interface org.colomoto.biolqm.io.LogicalModelFormat

Export a logical model to this format.

export(LogicalModel, File) - Method in interface org.colomoto.biolqm.io.LogicalModelFormat

Export a logical model to this format.

export(LogicalModel, String) - Method in interface org.colomoto.biolqm.io.LogicalModelFormat

Export a logical model to this format.

export() - Method in class org.colomoto.biolqm.io.maboss.MaBoSSEncoder

export() - Method in class org.colomoto.biolqm.io.mnet.MNetExport

export() - Method in class org.colomoto.biolqm.io.petrinet.AbstractPNEncoder

export() - Method in class org.colomoto.biolqm.io.pint.PintExport

export() - Method in class org.colomoto.biolqm.io.sbml.SBMLqualExport

export() - Method in class org.colomoto.biolqm.io.truthtable.TruthTableExport

expr() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AndExprContext

expr(int) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AndExprContext

expr() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AssignContext

expr() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

expr() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.OrExprContext

expr(int) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.OrExprContext

expr() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.SimpleExprContext

expr() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AndExprContext

expr(int) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AndExprContext

expr() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AssignContext

expr() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

expr() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.OrExprContext

expr(int) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.OrExprContext

expr() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.SimpleExprContext

expr() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.AndExprContext

expr(int) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.AndExprContext

expr() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.AssignContext

expr() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser

expr() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.OrExprContext

expr(int) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.OrExprContext

expr() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.SimpleExprContext

expr() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.AndExprContext

expr(int) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.AndExprContext

expr() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.AssignContext

expr() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser

expr() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AndExprContext

expr(int) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AndExprContext

expr() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AssignContext

expr() - Method in class org.colomoto.biolqm.io.antlr.MNetParser

expr() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.OrExprContext

expr(int) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.OrExprContext

expr() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.SimpleExprContext

ExprContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BNetParser.ExprContext

ExprContext() - Constructor for class org.colomoto.biolqm.io.antlr.BNetParser.ExprContext

ExprContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ExprContext

ExprContext() - Constructor for class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ExprContext

ExprContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanNetParser.ExprContext

ExprContext() - Constructor for class org.colomoto.biolqm.io.antlr.BooleanNetParser.ExprContext

ExprContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BoolsimParser.ExprContext

ExprContext() - Constructor for class org.colomoto.biolqm.io.antlr.BoolsimParser.ExprContext

ExprContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.MNetParser.ExprContext

ExprContext() - Constructor for class org.colomoto.biolqm.io.antlr.MNetParser.ExprContext

ExpressionStack - Class in org.colomoto.biolqm.io.antlr

Stack to reconstruct a parsed logical expression.

ExpressionStack(OperandFactory) - Constructor for class org.colomoto.biolqm.io.antlr.ExpressionStack

ExtensionLoader - Class in org.colomoto.biolqm.service

Helper class to support extensions.

ExtensionLoader() - Constructor for class org.colomoto.biolqm.service.ExtensionLoader

extra - Variable in class org.colomoto.biolqm.tool.fixpoints.FixpointTask

extractIDs(List<NodeInfo>) - Static method in class org.colomoto.biolqm.tool.fixpoints.FixpointList

F

fileWriter(String) - Static method in class org.colomoto.biolqm.service.LQMServiceManager

Open a file for writing.

fillExtraValues(byte[], byte[]) - Method in interface org.colomoto.biolqm.LogicalModel

Compute the value of all extra components for a given state.

fillExtraValues(byte[], byte[]) - Method in class org.colomoto.biolqm.LogicalModelImpl

fillState(byte[], int) - Method in interface org.colomoto.biolqm.helper.state.StateList

Retrieve a full state instead of a single value.

fillState(byte[], int) - Method in class org.colomoto.biolqm.helper.state.StateListProjection

fillState(byte[], int) - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointList

fillState(byte[], int) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceList

findNextRequiredNegation(int, byte[]) - Method in class org.colomoto.biolqm.helper.implicants.Term

FixedComponentRemover - Class in org.colomoto.biolqm.modifier.reduction

Detect fixed components and propagate their fixed value to their targets

FixedComponentRemover() - Constructor for class org.colomoto.biolqm.modifier.reduction.FixedComponentRemover

FixedValuePerturbation - Class in org.colomoto.biolqm.modifier.perturbation

Simple perturbation to fix the value of a component.

FixedValuePerturbation(NodeInfo) - Constructor for class org.colomoto.biolqm.modifier.perturbation.FixedValuePerturbation

Create a simple KO perturbation.

FixedValuePerturbation(NodeInfo, int) - Constructor for class org.colomoto.biolqm.modifier.perturbation.FixedValuePerturbation

Create a simple perturbation to fix the value of a component.

FixpointList - Class in org.colomoto.biolqm.tool.fixpoints

FixpointList(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.fixpoints.FixpointList

FixpointList(List<NodeInfo>) - Constructor for class org.colomoto.biolqm.tool.fixpoints.FixpointList

FixpointList(List<NodeInfo>, List<NodeInfo>, MDDManager, int[]) - Constructor for class org.colomoto.biolqm.tool.fixpoints.FixpointList

FixpointMethod - Enum in org.colomoto.biolqm.tool.fixpoints

FixpointSearcher - Class in org.colomoto.biolqm.tool.fixpoints

Perform a stable state search for a given model.

FixpointSearcher(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.fixpoints.FixpointSearcher

Create a new stable state searcher.

FixpointService - Class in org.colomoto.biolqm.tool.fixpoints

FixpointService() - Constructor for class org.colomoto.biolqm.tool.fixpoints.FixpointService

FixpointTask - Class in org.colomoto.biolqm.tool.fixpoints

FixpointTask(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.fixpoints.FixpointTask

flag - Variable in enum org.colomoto.biolqm.service.MultivaluedSupport

focusComponents - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

forcePattern - Variable in class org.colomoto.biolqm.modifier.reduction.ReductionModifier

Formula - Class in org.colomoto.biolqm.helper.implicants

Formula(List<Term>) - Constructor for class org.colomoto.biolqm.helper.implicants.Formula

Formula(List<Term>, int[]) - Constructor for class org.colomoto.biolqm.helper.implicants.Formula

FREE - Static variable in interface org.colomoto.biolqm.helper.state.StateList

FUNC_DUAL - Static variable in class org.colomoto.biolqm.helper.inferinteraction.InteractionSearcher

FUNC_NEGATIVE - Static variable in class org.colomoto.biolqm.helper.inferinteraction.InteractionSearcher

FUNC_NON - Static variable in class org.colomoto.biolqm.helper.inferinteraction.InteractionSearcher

FUNC_POSITIVE - Static variable in class org.colomoto.biolqm.helper.inferinteraction.InteractionSearcher

functions - Variable in class org.colomoto.biolqm.io.petrinet.AbstractPNEncoder

G

get(String) - Method in class org.colomoto.biolqm.helper.clingo.ClingoResult

get(int, int) - Method in interface org.colomoto.biolqm.helper.state.StateList

Retrieve a specific value

get(int, int) - Method in class org.colomoto.biolqm.helper.state.StateListProjection

get(int) - Method in class org.colomoto.biolqm.modifier.buffer.BufferingModifier

get(Class<T>) - Static method in class org.colomoto.biolqm.service.LQMServiceManager

Retrieve any service by class

get(int, int) - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointList

get() - Method in class org.colomoto.biolqm.tool.fixpoints.StableASP

get(int, int) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceList

get_selection(NodeInfo[], Iterable<String>) - Static method in class org.colomoto.biolqm.helper.state.StateListProjection

getAliases() - Method in class org.colomoto.biolqm.service.BaseService

getAliases() - Method in interface org.colomoto.biolqm.service.Service

getATN() - Method in class org.colomoto.biolqm.io.antlr.BNetLexer

getATN() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

getATN() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

getATN() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

getATN() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

getATN() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser

getATN() - Method in class org.colomoto.biolqm.io.antlr.BoolsimLexer

getATN() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser

getATN() - Method in class org.colomoto.biolqm.io.antlr.CNetLexer

getATN() - Method in class org.colomoto.biolqm.io.antlr.CNetParser

getATN() - Method in class org.colomoto.biolqm.io.antlr.ITNETLexer

getATN() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser

getATN() - Method in class org.colomoto.biolqm.io.antlr.MNetLexer

getATN() - Method in class org.colomoto.biolqm.io.antlr.MNetParser

getBDD(LogicalModel) - Static method in class org.colomoto.biolqm.tool.fixpoints.JBDDModel

getBooleanizedGroup() - Method in class org.colomoto.biolqm.NodeInfo

getBooleanizedMap() - Method in interface org.colomoto.biolqm.LogicalModel

Get the Boolean - multi-valued mapping information for booleanized models.

getBooleanizedMap() - Method in class org.colomoto.biolqm.LogicalModelImpl

getBuffer() - Method in class org.colomoto.common.xml.XMLWriter

If toBuffer has previously been called, stop saving to buffer.

getChannelNames() - Method in class org.colomoto.biolqm.io.antlr.BNetLexer

getChannelNames() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

getChannelNames() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

getChannelNames() - Method in class org.colomoto.biolqm.io.antlr.BoolsimLexer

getChannelNames() - Method in class org.colomoto.biolqm.io.antlr.CNetLexer

getChannelNames() - Method in class org.colomoto.biolqm.io.antlr.ITNETLexer

getChannelNames() - Method in class org.colomoto.biolqm.io.antlr.MNetLexer

getClass(int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

getClassLoader() - Static method in class org.colomoto.biolqm.service.ExtensionLoader

Retrieve a class loader covering the extensions.

getClassVars(int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

getComponent(String) - Method in interface org.colomoto.biolqm.LogicalModel

Retrieve a component by name.

getComponent(String) - Method in class org.colomoto.biolqm.LogicalModelImpl

getComponentIndex(String) - Method in interface org.colomoto.biolqm.LogicalModel

Retrieve a component by name.

getComponentIndex(String) - Method in class org.colomoto.biolqm.LogicalModelImpl

getComponents() - Method in interface org.colomoto.biolqm.helper.state.StateList

Get the components defining this list of states.

getComponents() - Method in class org.colomoto.biolqm.helper.state.StateListProjection

getComponents() - Method in interface org.colomoto.biolqm.LogicalModel

Get the list of core nodes in this model.

getComponents() - Method in class org.colomoto.biolqm.LogicalModelImpl

getComponents() - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointList

getComponents() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceList

getCoreTargets(int, boolean) - Method in class org.colomoto.biolqm.ConnectivityMatrix

Get the list of components regulated by a given core component.

getDescription() - Method in class org.colomoto.biolqm.service.BaseService

getDescription() - Method in interface org.colomoto.biolqm.service.Service

Provide a brief description of parameters for the help message

getDeterministicBlocks() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

getDeterministicUpdater(LogicalModel, String) - Static method in class org.colomoto.biolqm.tool.simulation.UpdaterFactory

getDisplayName() - Method in class org.colomoto.biolqm.NodeInfo

getEmptySuccessors() - Static method in class org.colomoto.biolqm.tool.simulation.multiplesuccessor.AbstractMultipleSuccessorUpdater

getErrors() - Method in class org.colomoto.biolqm.io.antlr.ErrorListener

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.bnet.BNetFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.booleannet.BooleanNetFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.boolsim.BoolSimFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.cnet.CNetFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.functions.BooleanFunctionFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.ginml.GINMLFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.gna.GNAFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.implicanttables.ImplicantTableFormat

getExporter(LogicalModel) - Method in interface org.colomoto.biolqm.io.LogicalModelFormat

Get a new model exporter to this format.

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.maboss.MaBoSSFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.mnet.MNetFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.petrinet.APNNFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.petrinet.INAFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.petrinet.PetriNetFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.petrinet.PNMLFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.pint.PintFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.sbml.SBMLFormat

getExporter(LogicalModel) - Method in class org.colomoto.biolqm.io.truthtable.TruthTableFormat

getExtraComponents() - Method in interface org.colomoto.biolqm.LogicalModel

Get the list of extra components in this model.

getExtraComponents() - Method in class org.colomoto.biolqm.LogicalModelImpl

getExtraData() - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointList

getExtraLogicalFunctions() - Method in interface org.colomoto.biolqm.LogicalModel

Get the logical function of extra components in this model.

getExtraLogicalFunctions() - Method in class org.colomoto.biolqm.LogicalModelImpl

getExtraValue(int, byte[]) - Method in interface org.colomoto.biolqm.LogicalModel

Compute the value of an extra component for a given state.

getExtraValue(int, byte[]) - Method in class org.colomoto.biolqm.LogicalModelImpl

getFile() - Method in interface org.colomoto.biolqm.io.StreamProvider

Deprecated.

getFile() - Method in class org.colomoto.biolqm.io.StreamProviderFileImpl

getFormat(String) - Static method in class org.colomoto.biolqm.LQMLauncher

getFormat(String) - Static method in class org.colomoto.biolqm.service.LQMServiceManager

Get the format declaration for a given ID.

getFormats() - Static method in class org.colomoto.biolqm.service.LQMServiceManager

Get the available formats.

getGrammarFileName() - Method in class org.colomoto.biolqm.io.antlr.BNetLexer

getGrammarFileName() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

getGrammarFileName() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

getGrammarFileName() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

getGrammarFileName() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

getGrammarFileName() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser

getGrammarFileName() - Method in class org.colomoto.biolqm.io.antlr.BoolsimLexer

getGrammarFileName() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser

getGrammarFileName() - Method in class org.colomoto.biolqm.io.antlr.CNetLexer

getGrammarFileName() - Method in class org.colomoto.biolqm.io.antlr.CNetParser

getGrammarFileName() - Method in class org.colomoto.biolqm.io.antlr.ITNETLexer

getGrammarFileName() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser

getGrammarFileName() - Method in class org.colomoto.biolqm.io.antlr.MNetLexer

getGrammarFileName() - Method in class org.colomoto.biolqm.io.antlr.MNetParser

getGroupValues(int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

getID() - Method in class org.colomoto.biolqm.service.BaseService

getID() - Method in interface org.colomoto.biolqm.service.Service

get the ID of the service.

getInclusionDiagram() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceList

getIndexForName(String) - Method in class org.colomoto.biolqm.io.sbml.SBMLqualImport

Retrieve the model component corresponding to a SBML ID.

getInfo(NodeInfo) - Method in class org.colomoto.biolqm.ModelLayout

getInitialstate() - Method in class org.colomoto.biolqm.io.petrinet.AbstractPNEncoder

getLayout() - Method in interface org.colomoto.biolqm.LogicalModel

Retrieve the associated layout information.

getLayout() - Method in class org.colomoto.biolqm.LogicalModelImpl

getLoader() - Method in class org.colomoto.biolqm.io.bnet.BNetFormat

getLoader() - Method in class org.colomoto.biolqm.io.booleannet.BooleanNetFormat

getLoader() - Method in class org.colomoto.biolqm.io.boolsim.BoolSimFormat

getLoader() - Method in class org.colomoto.biolqm.io.cnet.CNetFormat

getLoader() - Method in class org.colomoto.biolqm.io.functions.BooleanFunctionFormat

getLoader() - Method in class org.colomoto.biolqm.io.implicanttables.ImplicantTableFormat

getLoader() - Method in interface org.colomoto.biolqm.io.LogicalModelFormat

Get a new model loader from this format.

getLoader() - Method in class org.colomoto.biolqm.io.mnet.MNetFormat

getLoader() - Method in class org.colomoto.biolqm.io.sbml.SBMLFormat

getLoader() - Method in class org.colomoto.biolqm.io.truthtable.TruthTableFormat

getLogicalFunctions() - Method in interface org.colomoto.biolqm.LogicalModel

Get the logical function of core components in this model.

getLogicalFunctions() - Method in class org.colomoto.biolqm.LogicalModelImpl

getMax() - Method in class org.colomoto.biolqm.NodeInfo

getMDD(LogicalModel) - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointTask

getMDD(LogicalModel, boolean) - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointTask

getMDDManager() - Method in interface org.colomoto.biolqm.LogicalModel

Get the MDD factory holding logical functions for this model.

getMDDManager() - Method in class org.colomoto.biolqm.LogicalModelImpl

getMDDManager() - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointSearcher

Convenience method to retrieve the MDDManager in which the result is stored.

getModel() - Method in class org.colomoto.biolqm.modifier.reduction.ModelReducer

Get a logical model for the modified functions.

getModel(boolean) - Method in class org.colomoto.biolqm.modifier.reduction.ModelReducer

getModel(boolean, boolean) - Method in class org.colomoto.biolqm.modifier.reduction.ModelReducer

getModel() - Method in class org.colomoto.biolqm.tool.simulation.BaseUpdater

getModel() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

getModel() - Method in interface org.colomoto.biolqm.tool.simulation.LogicalModelUpdater

getModel() - Method in class org.colomoto.biolqm.tool.simulation.random.RandomUpdaterWrapper

getModeNames() - Method in class org.colomoto.biolqm.io.antlr.BNetLexer

getModeNames() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

getModeNames() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

getModeNames() - Method in class org.colomoto.biolqm.io.antlr.BoolsimLexer

getModeNames() - Method in class org.colomoto.biolqm.io.antlr.CNetLexer

getModeNames() - Method in class org.colomoto.biolqm.io.antlr.ITNETLexer

getModeNames() - Method in class org.colomoto.biolqm.io.antlr.MNetLexer

getModifier(LogicalModel) - Method in class org.colomoto.biolqm.modifier.booleanize.BooleanizeService

getModifier(LogicalModel) - Method in class org.colomoto.biolqm.modifier.buffer.BufferingService

getModifier(LogicalModel, String) - Method in interface org.colomoto.biolqm.modifier.ModelModifierService

Setup a new modifier object.

getModifier(LogicalModel) - Method in interface org.colomoto.biolqm.modifier.ModelModifierService

Get a new modifier object.

getModifier(LogicalModel) - Method in class org.colomoto.biolqm.modifier.perturbation.PerturbationService

getModifier(LogicalModel) - Method in class org.colomoto.biolqm.modifier.reduction.ReductionService

getModifier(LogicalModel) - Method in class org.colomoto.biolqm.modifier.reverse.ReverseService

getModifier(LogicalModel) - Method in class org.colomoto.biolqm.modifier.sanitize.SanitizeService

getModifier(LogicalModel) - Method in class org.colomoto.biolqm.modifier.submodel.SubmodelService

getModifier(LogicalModel) - Method in class org.colomoto.biolqm.modifier.subspace.SubSpaceService

getModifier(String) - Static method in class org.colomoto.biolqm.service.LQMServiceManager

Get the service for a given ID.

getModifiers() - Static method in class org.colomoto.biolqm.service.LQMServiceManager

Get the available model modifier services.

getMultipleSuccessorUpdater(LogicalModel, String) - Static method in class org.colomoto.biolqm.tool.simulation.UpdaterFactory

getMultivaluedSupport() - Method in class org.colomoto.biolqm.service.BaseService

getMultivaluedSupport() - Method in interface org.colomoto.biolqm.service.Service

Precise type of support for multivalued models.

getName() - Method in class org.colomoto.biolqm.NodeInfo

getName() - Method in class org.colomoto.biolqm.service.BaseService

getName() - Method in interface org.colomoto.biolqm.service.Service

Get a longer name for the service.

getNodeID() - Method in class org.colomoto.biolqm.NodeInfo

getNodeInfo() - Method in interface org.colomoto.biolqm.NodeInfoHolder

Get the internal NodeInfo.

getNodes() - Method in class org.colomoto.biolqm.io.ginml.AbstractGINMLWriter

get the names of the nodes to save in GINML.

getNodes() - Method in class org.colomoto.biolqm.io.ginml.LogicalModel2GINML

getNodes() - Method in class org.colomoto.biolqm.tool.simulation.deterministic.DeterministicSimulation

getNodes() - Method in class org.colomoto.biolqm.tool.simulation.random.RandomWalkSimulation

getNumVars() - Method in class org.colomoto.biolqm.helper.implicants.Term

getNVars() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceList

getPaths() - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointSearcher

Get the path (variable assignment) corresponding to stable states.

getPrimes(int, int) - Method in class org.colomoto.biolqm.helper.implicants.MDD2PrimeImplicants

Extract the prime implicants from a MDD-represented function.

getProcessBuilder(String...) - Method in class org.colomoto.biolqm.helper.HelperTool

getProgram() - Method in class org.colomoto.biolqm.tool.fixpoints.StableASP

getQualBundle() - Method in class org.colomoto.biolqm.io.sbml.SBMLqualImport

getRandomUpdater(LogicalModel, String) - Static method in class org.colomoto.biolqm.tool.simulation.UpdaterFactory

getRegulatorEffects(int, boolean) - Method in class org.colomoto.biolqm.ConnectivityMatrix

Get sign information about the regulators of a node.

getRegulatorList() - Method in class org.colomoto.biolqm.helper.implicants.ImplicantSearcher

getRegulatorList() - Method in class org.colomoto.biolqm.helper.implicants.RestrictedPathSearcher

getRegulators(int, boolean) - Method in class org.colomoto.biolqm.ConnectivityMatrix

Get the list of core components regulating a given component.

getRegulators() - Method in class org.colomoto.biolqm.helper.implicants.ImplicantSearcher

getRegulators() - Method in class org.colomoto.biolqm.helper.implicants.RestrictedPathSearcher

Retrieve the list of regulators on which this searcher is restricted.

getResult() - Method in class org.colomoto.common.task.AbstractTask

getResult() - Method in interface org.colomoto.common.task.Task

Retrieve the result of the task.

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AndContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AssignContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.ExprContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.HeaderContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.ModelContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.NotContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.OrContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.ValContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.VarContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AssignContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ExprContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ModelContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.NotContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ValContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.VarContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.AssignContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.ExprContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.ModelContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.NotContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.ValContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.VarContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.AssignContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.ExprContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.ModelContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.NotContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.OpContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.VarContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.CountContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.CurvarContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.LineContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.ModelContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TableContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TtlineContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.VaridContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.CurvarContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.LineContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.MaxContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.ModelContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TableContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TargetContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TtlineContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.VarContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AndContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AssignContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.ExprContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.ModelContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.NotContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.OrContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.ValContext

getRuleIndex() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.VarContext

getRuleNames() - Method in class org.colomoto.biolqm.io.antlr.BNetLexer

getRuleNames() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

getRuleNames() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

getRuleNames() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

getRuleNames() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

getRuleNames() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser

getRuleNames() - Method in class org.colomoto.biolqm.io.antlr.BoolsimLexer

getRuleNames() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser

getRuleNames() - Method in class org.colomoto.biolqm.io.antlr.CNetLexer

getRuleNames() - Method in class org.colomoto.biolqm.io.antlr.CNetParser

getRuleNames() - Method in class org.colomoto.biolqm.io.antlr.ITNETLexer

getRuleNames() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser

getRuleNames() - Method in class org.colomoto.biolqm.io.antlr.MNetLexer

getRuleNames() - Method in class org.colomoto.biolqm.io.antlr.MNetParser

getSBMLBundle() - Method in class org.colomoto.biolqm.io.sbml.SBMLqualExport

getSBMLDocument() - Method in class org.colomoto.biolqm.io.sbml.SBMLqualExport

getSerializedATN() - Method in class org.colomoto.biolqm.io.antlr.BNetLexer

getSerializedATN() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

getSerializedATN() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

getSerializedATN() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

getSerializedATN() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

getSerializedATN() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser

getSerializedATN() - Method in class org.colomoto.biolqm.io.antlr.BoolsimLexer

getSerializedATN() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser

getSerializedATN() - Method in class org.colomoto.biolqm.io.antlr.CNetLexer

getSerializedATN() - Method in class org.colomoto.biolqm.io.antlr.CNetParser

getSerializedATN() - Method in class org.colomoto.biolqm.io.antlr.ITNETLexer

getSerializedATN() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser

getSerializedATN() - Method in class org.colomoto.biolqm.io.antlr.MNetLexer

getSerializedATN() - Method in class org.colomoto.biolqm.io.antlr.MNetParser

getSimulation() - Method in class org.colomoto.biolqm.tool.simulation.deterministic.TraceTask

getSimulation() - Method in class org.colomoto.biolqm.tool.simulation.random.RandomWalkTask

getSingleSuccessors(byte[]) - Static method in class org.colomoto.biolqm.tool.simulation.multiplesuccessor.AbstractMultipleSuccessorUpdater

getSpecies(NodeInfo) - Method in class org.colomoto.biolqm.io.sbml.SBMLqualExport

getStable(MDDManager, int, int, MDDVariable) - Method in class org.colomoto.biolqm.tool.fixpoints.StableOperation

Build the stability condition for a node, and merge it with the existing condition.

getStatus() - Method in class org.colomoto.common.task.AbstractTask

getStatus() - Method in interface org.colomoto.common.task.Task

Retrieve the status of the task.

getStringRepresentation() - Method in class org.colomoto.biolqm.modifier.perturbation.FixedValuePerturbation

getStringRepresentation() - Method in class org.colomoto.biolqm.modifier.perturbation.InteractionPerturbation

getStringRepresentation() - Method in interface org.colomoto.biolqm.modifier.perturbation.LogicalModelPerturbation

getStringRepresentation() - Method in class org.colomoto.biolqm.modifier.perturbation.MultiplePerturbation

getStringRepresentation() - Method in class org.colomoto.biolqm.modifier.perturbation.RangePerturbation

getSuccessor(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.deterministic.BlockSequentialUpdater

getSuccessor(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.deterministic.DeterministicPriorityUpdater

getSuccessor(byte[]) - Method in interface org.colomoto.biolqm.tool.simulation.deterministic.DeterministicUpdater

Get the unique successor of a state.

getSuccessor(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.deterministic.SequentialUpdater

getSuccessor(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.deterministic.SynchronousUpdater

getSuccessors(List<byte[]>) - Static method in class org.colomoto.biolqm.tool.simulation.multiplesuccessor.AbstractMultipleSuccessorUpdater

getSuccessors(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.multiplesuccessor.AsynchronousUpdater

getSuccessors(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.multiplesuccessor.CompleteUpdater

getSuccessors(byte[]) - Method in interface org.colomoto.biolqm.tool.simulation.multiplesuccessor.MultipleSuccessorsUpdater

Get all successors for a given state.

getSuccessors(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.multiplesuccessor.PriorityUpdater

getTargetValue(int, byte[]) - Method in interface org.colomoto.biolqm.LogicalModel

Compute the target value of a core component for a given state.

getTargetValue(int, byte[]) - Method in class org.colomoto.biolqm.LogicalModelImpl

getTask(LogicalModel) - Method in class org.colomoto.biolqm.tool.attractor.AttractorService

getTask(LogicalModel) - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointService

getTask(LogicalModel) - Method in interface org.colomoto.biolqm.tool.ModelToolService

Construct a default setting object.

getTask(LogicalModel, String) - Method in interface org.colomoto.biolqm.tool.ModelToolService

Construct a parsed setting object.

getTask(LogicalModel, String...) - Method in interface org.colomoto.biolqm.tool.ModelToolService

Construct a default setting object.

getTask(LogicalModel) - Method in class org.colomoto.biolqm.tool.simulation.deterministic.TraceService

getTask(LogicalModel) - Method in class org.colomoto.biolqm.tool.simulation.random.RandomWalkService

getTask(LogicalModel) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceService

getTerms() - Method in class org.colomoto.biolqm.helper.implicants.Formula

getTokenNames() - Method in class org.colomoto.biolqm.io.antlr.BNetLexer

Deprecated.

getTokenNames() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

Deprecated.

getTokenNames() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

Deprecated.

getTokenNames() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

Deprecated.

getTokenNames() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

Deprecated.

getTokenNames() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser

Deprecated.

getTokenNames() - Method in class org.colomoto.biolqm.io.antlr.BoolsimLexer

Deprecated.

getTokenNames() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser

Deprecated.

getTokenNames() - Method in class org.colomoto.biolqm.io.antlr.CNetLexer

Deprecated.

getTokenNames() - Method in class org.colomoto.biolqm.io.antlr.CNetParser

Deprecated.

getTokenNames() - Method in class org.colomoto.biolqm.io.antlr.ITNETLexer

Deprecated.

getTokenNames() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser

Deprecated.

getTokenNames() - Method in class org.colomoto.biolqm.io.antlr.MNetLexer

Deprecated.

getTokenNames() - Method in class org.colomoto.biolqm.io.antlr.MNetParser

Deprecated.

getTool(String) - Static method in class org.colomoto.biolqm.service.LQMServiceManager

Get the tool declaration for a given ID.

getTools() - Static method in class org.colomoto.biolqm.service.LQMServiceManager

Get the available tools.

getVars(LogicalModel) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

getVars(LogicalModel) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClassGroup

getVarsValue(int) - Method in class org.colomoto.biolqm.helper.implicants.Term

getView(List<NodeInfo>) - Method in interface org.colomoto.biolqm.LogicalModel

Get a logical model with the same nodes but a different order for the core components.

getView(List<NodeInfo>) - Method in class org.colomoto.biolqm.LogicalModelImpl

getVocabulary() - Method in class org.colomoto.biolqm.io.antlr.BNetLexer

getVocabulary() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

getVocabulary() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

getVocabulary() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

getVocabulary() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

getVocabulary() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser

getVocabulary() - Method in class org.colomoto.biolqm.io.antlr.BoolsimLexer

getVocabulary() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser

getVocabulary() - Method in class org.colomoto.biolqm.io.antlr.CNetLexer

getVocabulary() - Method in class org.colomoto.biolqm.io.antlr.CNetParser

getVocabulary() - Method in class org.colomoto.biolqm.io.antlr.ITNETLexer

getVocabulary() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser

getVocabulary() - Method in class org.colomoto.biolqm.io.antlr.MNetLexer

getVocabulary() - Method in class org.colomoto.biolqm.io.antlr.MNetParser

GINMLFormat - Class in org.colomoto.biolqm.io.ginml

Format description for GINML files.

GINMLFormat() - Constructor for class org.colomoto.biolqm.io.ginml.GINMLFormat

globalAsyncFunctions() - Method in class org.colomoto.biolqm.tool.fixpoints.JBDDModel

globalAsynchronousFunction() - Method in class org.colomoto.biolqm.tool.fixpoints.JBDDModel

globalFunctions() - Method in class org.colomoto.biolqm.tool.fixpoints.JBDDModel

globalStable() - Method in class org.colomoto.biolqm.tool.fixpoints.JBDDModel

globalSynchronousFunction() - Method in class org.colomoto.biolqm.tool.fixpoints.JBDDModel

GNAExport - Class in org.colomoto.biolqm.io.gna

Exports a logical model into the non-xml GNA format.

GNAExport(LogicalModel) - Constructor for class org.colomoto.biolqm.io.gna.GNAExport

GNAFormat - Class in org.colomoto.biolqm.io.gna

Format description for GNA (non-xml) files.

GNAFormat() - Constructor for class org.colomoto.biolqm.io.gna.GNAFormat

groupCollapse(int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

groupExpand(int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

H

handle(ClingoResult) - Method in interface org.colomoto.biolqm.helper.clingo.ClingoResultHandler

handle(ClingoResult) - Method in class org.colomoto.biolqm.tool.fixpoints.StableASP

handle(ClingoResult) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverASP

handle(ClingoResult) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverFunctionASP

handleDuplicates - Variable in class org.colomoto.biolqm.modifier.reduction.ReductionModifier

handleFixed - Variable in class org.colomoto.biolqm.modifier.reduction.ReductionModifier

handleOutputs - Variable in class org.colomoto.biolqm.modifier.reduction.ReductionModifier

hasErrors() - Method in class org.colomoto.biolqm.io.antlr.ErrorListener

hasExtraComponents() - Method in interface org.colomoto.biolqm.LogicalModel

Check if the model has extra component(s).

hasExtraComponents() - Method in class org.colomoto.biolqm.LogicalModelImpl

hashCode() - Method in class org.colomoto.biolqm.helper.implicants.Term

hashCode() - Method in class org.colomoto.biolqm.NodeInfo

hashCode() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpace

hasLayout() - Method in interface org.colomoto.biolqm.LogicalModel

Check if this model has associated layout information.

hasLayout() - Method in class org.colomoto.biolqm.LogicalModelImpl

hasNext() - Method in class org.colomoto.biolqm.helper.state.PatternStateIterator

hasReduction() - Method in class org.colomoto.biolqm.modifier.reduction.ReductionModifier

header() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

header() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.ModelContext

HeaderContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BNetParser.HeaderContext

height - Variable in class org.colomoto.biolqm.ModelLayout.LayoutInfo

help() - Static method in class org.colomoto.biolqm.LQMLauncher

HELP_LINE - Static variable in class org.colomoto.biolqm.tool.fixpoints.FixpointService

HELP_LINE - Static variable in class org.colomoto.biolqm.tool.simulation.deterministic.TraceService

HELP_LINE - Static variable in class org.colomoto.biolqm.tool.simulation.random.RandomWalkService

HELP_LINE - Static variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceService

HELP_MESSAGE - Static variable in class org.colomoto.biolqm.tool.fixpoints.FixpointService

HELP_MESSAGE - Static variable in class org.colomoto.biolqm.tool.simulation.deterministic.TraceService

HELP_MESSAGE - Static variable in class org.colomoto.biolqm.tool.simulation.random.RandomWalkService

HELP_MESSAGE - Static variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceService

HelperTool - Class in org.colomoto.biolqm.helper

Locate and call external tools.

HelperTool(String) - Constructor for class org.colomoto.biolqm.helper.HelperTool

I

ID - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

ID - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

ID() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.VarContext

ID - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

ID - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

ID() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.VarContext

ID - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

ID - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

ID() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.VarContext

ID - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

ID - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

ID() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.VarContext

ID - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

ID - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

ID() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.VarContext

ID - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

ID - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

ID() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.VarContext

ID - Static variable in class org.colomoto.biolqm.io.bnet.BNetFormat

ID - Static variable in class org.colomoto.biolqm.io.booleannet.BooleanNetFormat

ID - Static variable in class org.colomoto.biolqm.io.boolsim.BoolSimFormat

ID - Static variable in class org.colomoto.biolqm.io.cnet.CNetFormat

ID - Static variable in class org.colomoto.biolqm.io.functions.BooleanFunctionFormat

ID - Static variable in class org.colomoto.biolqm.io.implicanttables.ImplicantTableFormat

ID - Static variable in class org.colomoto.biolqm.io.mnet.MNetFormat

ID - Static variable in class org.colomoto.biolqm.modifier.booleanize.BooleanizeService

The identifier used to retrieve this service by name

ID - Static variable in class org.colomoto.biolqm.modifier.buffer.BufferingService

The identifier used to retrieve this service by name

ID - Static variable in class org.colomoto.biolqm.modifier.perturbation.PerturbationService

The identifier used to retrieve this service by name

ID - Static variable in class org.colomoto.biolqm.modifier.reduction.ReductionService

The identifier used to retrieve this service by name

ID - Static variable in class org.colomoto.biolqm.modifier.reverse.ReverseService

The identifier used to retrieve this service by name

ID - Static variable in class org.colomoto.biolqm.modifier.sanitize.SanitizeService

The identifier used to retrieve this service by name

ID - Static variable in class org.colomoto.biolqm.modifier.submodel.SubmodelService

The identifier used to retrieve this service by name

ID - Static variable in class org.colomoto.biolqm.modifier.subspace.SubSpaceService

The identifier used to retrieve this service by name

ident(String) - Method in class org.colomoto.biolqm.io.antlr.ExpressionStack

ident(String, int) - Method in class org.colomoto.biolqm.io.antlr.ExpressionStack

ImplicantSearcher - Class in org.colomoto.biolqm.helper.implicants

Restrict the paths given by a PathSearcher to the list of actual regulators

ImplicantSearcher(MDDManager, int) - Constructor for class org.colomoto.biolqm.helper.implicants.ImplicantSearcher

ImplicantTableExport - Class in org.colomoto.biolqm.io.implicanttables

Export logical model into lists of implicant tables.

ImplicantTableExport(LogicalModel) - Constructor for class org.colomoto.biolqm.io.implicanttables.ImplicantTableExport

ImplicantTableFormat - Class in org.colomoto.biolqm.io.implicanttables

ImplicantTableFormat() - Constructor for class org.colomoto.biolqm.io.implicanttables.ImplicantTableFormat

ImplicantTableImport - Class in org.colomoto.biolqm.io.implicanttables

ImplicantTableImport() - Constructor for class org.colomoto.biolqm.io.implicanttables.ImplicantTableImport

INAFormat - Class in org.colomoto.biolqm.io.petrinet

PNML is an xml-based format for Petri net models.

INAFormat() - Constructor for class org.colomoto.biolqm.io.petrinet.INAFormat

incGroup(int, int, List<String>) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

inclusion() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceList

incPriorities(int, int, List<String>) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

InitialStateFactory - Class in org.colomoto.biolqm.tool.simulation

InitialStateFactory() - Constructor for class org.colomoto.biolqm.tool.simulation.InitialStateFactory

input() - Method in interface org.colomoto.biolqm.io.StreamProvider

Get the default stream.

input(String) - Method in interface org.colomoto.biolqm.io.StreamProvider

Get a custom stream, specifying a pattern.

input(String) - Method in class org.colomoto.biolqm.io.StreamProviderFileImpl

INTEGER - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

INTEGER() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.CountContext

INTEGER - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

INTEGER() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TtlineContext

INTEGER(int) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TtlineContext

INTEGER() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.VaridContext

InteractionPerturbation - Class in org.colomoto.biolqm.modifier.perturbation

A perturbation which removes the effect of a component on another (i.e.

InteractionPerturbation(NodeInfo, NodeInfo, int) - Constructor for class org.colomoto.biolqm.modifier.perturbation.InteractionPerturbation

InteractionSearcher - Class in org.colomoto.biolqm.helper.inferinteraction

Extract detailed interactions from a logical model.

InteractionSearcher(LogicalModel) - Constructor for class org.colomoto.biolqm.helper.inferinteraction.InteractionSearcher

isAvailable() - Static method in class org.colomoto.biolqm.helper.clingo.ClingoLauncher

isAvailable() - Method in class org.colomoto.biolqm.helper.HelperTool

isBoolean() - Method in interface org.colomoto.biolqm.LogicalModel

Check if this model is Boolean.

isBoolean() - Method in class org.colomoto.biolqm.LogicalModelImpl

isEmpty() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

isEmpty() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClassGroup

isInput() - Method in class org.colomoto.biolqm.NodeInfo

isSanitizeIDs() - Method in class org.colomoto.biolqm.modifier.sanitize.SanitizeModifier

isValid(int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

isValidId(String) - Static method in class org.colomoto.common.xml.XMLWriter

Indicates if the given string is a valid GINsim ID (contains only a-z, A-Z, 0-9, "_" characters, not starting with a digit)

iterator() - Method in class org.colomoto.biolqm.helper.implicants.ImplicantSearcher

iterator() - Method in class org.colomoto.biolqm.helper.implicants.RestrictedPathSearcher

iterator() - Method in class org.colomoto.biolqm.tool.fixpoints.StructuralNodeOrderer

iterator() - Method in class org.colomoto.biolqm.tool.simulation.deterministic.DeterministicSimulation

iterator() - Method in class org.colomoto.biolqm.tool.simulation.random.RandomWalkSimulation

ITNETBaseListener - Class in org.colomoto.biolqm.io.antlr

This class provides an empty implementation of ITNETListener, which can be extended to create a listener which only needs to handle a subset of the available methods.

ITNETBaseListener() - Constructor for class org.colomoto.biolqm.io.antlr.ITNETBaseListener

ITNETLexer - Class in org.colomoto.biolqm.io.antlr

ITNETLexer(CharStream) - Constructor for class org.colomoto.biolqm.io.antlr.ITNETLexer

ITNETListener - Interface in org.colomoto.biolqm.io.antlr

This interface defines a complete listener for a parse tree produced by ITNETParser.

ITNETParser - Class in org.colomoto.biolqm.io.antlr

ITNETParser(TokenStream) - Constructor for class org.colomoto.biolqm.io.antlr.ITNETParser

ITNETParser.CurvarContext - Class in org.colomoto.biolqm.io.antlr

ITNETParser.LineContext - Class in org.colomoto.biolqm.io.antlr

ITNETParser.MaxContext - Class in org.colomoto.biolqm.io.antlr

ITNETParser.ModelContext - Class in org.colomoto.biolqm.io.antlr

ITNETParser.TableContext - Class in org.colomoto.biolqm.io.antlr

ITNETParser.TargetContext - Class in org.colomoto.biolqm.io.antlr

ITNETParser.TtlineContext - Class in org.colomoto.biolqm.io.antlr

ITNETParser.VarContext - Class in org.colomoto.biolqm.io.antlr

J

JBDDModel - Class in org.colomoto.biolqm.tool.fixpoints

JBDDModel(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.fixpoints.JBDDModel

JOKER - Static variable in interface org.colomoto.biolqm.helper.state.StateList

JOKER - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

JOKER - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

JOKER() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TtlineContext

JOKER(int) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TtlineContext

K

keepExtra - Variable in class org.colomoto.biolqm.modifier.reduction.ReductionModifier

L

LayoutInfo(int, int, int, int) - Constructor for class org.colomoto.biolqm.ModelLayout.LayoutInfo

LayoutInfo(int, int) - Constructor for class org.colomoto.biolqm.ModelLayout.LayoutInfo

len - Variable in class org.colomoto.biolqm.io.petrinet.AbstractPNEncoder

length - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpace

line() - Method in class org.colomoto.biolqm.io.antlr.CNetParser

line() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TableContext

line(int) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TableContext

line() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser

line() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TableContext

line(int) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TableContext

LineContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.CNetParser.LineContext

LineContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.ITNETParser.LineContext

lmodel - Variable in class org.colomoto.biolqm.io.sbml.SBMLQualBundle

load(StreamProvider) - Method in interface org.colomoto.biolqm.io.LogicalModelFormat

Load a file in this format and build a logical model for it.

load(File) - Method in interface org.colomoto.biolqm.io.LogicalModelFormat

Load a file in this format and build a logical model for it.

load(String) - Method in interface org.colomoto.biolqm.io.LogicalModelFormat

Load a file in this format and build a logical model for it.

load(String) - Static method in class org.colomoto.biolqm.service.LQMServiceManager

Load a model guessing the format.

load(String, String) - Static method in class org.colomoto.biolqm.service.LQMServiceManager

Load a model from file.

load_instances(Class<T>) - Static method in class org.colomoto.biolqm.service.ExtensionLoader

Discover and load a list of services.

loadEngine(String) - Static method in class org.colomoto.biolqm.LQMLauncher

Detect and load script engines

loadExtensions(String, Class<?>) - Static method in class org.colomoto.biolqm.service.ExtensionLoader

Trigger the loading of extensions.

loadFile(File) - Static method in class org.colomoto.biolqm.io.sbml.SBMLqualHelper

loadModel() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

loadSettings() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

LogicalModel - Interface in org.colomoto.biolqm

A LogicalModel is a ready to use object containing all necessary information to perform simulations and analysis, without the editing facilities provided by a full RegulatoryGraph.

LogicalModel2GINML - Class in org.colomoto.biolqm.io.ginml

Encoder to transform a LogicalModel into a GINML file.

LogicalModel2GINML(LogicalModel) - Constructor for class org.colomoto.biolqm.io.ginml.LogicalModel2GINML

LogicalModelComparator - Class in org.colomoto.biolqm

Test if two logical models share the same variables and equivalent functions

LogicalModelComparator() - Constructor for class org.colomoto.biolqm.LogicalModelComparator

LogicalModelFormat - Interface in org.colomoto.biolqm.io

Description of an available file format.

LogicalModelImpl - Class in org.colomoto.biolqm

Implementation of the LogicalModel interface.

LogicalModelImpl(MDDManager, List<NodeInfo>, int[], List<NodeInfo>, int[]) - Constructor for class org.colomoto.biolqm.LogicalModelImpl

LogicalModelImpl(List<NodeInfo>, MDDManager, int[]) - Constructor for class org.colomoto.biolqm.LogicalModelImpl

LogicalModelPerturbation - Interface in org.colomoto.biolqm.modifier.perturbation

Common interface for perturbations.

LogicalModelUpdater - Interface in org.colomoto.biolqm.tool.simulation

Common interface for all updaters.

LQMLauncher - Class in org.colomoto.biolqm

Entry point to launch the bioLQM toolbox.

LQMLauncher() - Constructor for class org.colomoto.biolqm.LQMLauncher

LQMServiceManager - Class in org.colomoto.biolqm.service

Static service manager: list available "services" in LQM: formats modifiers

LQMServiceManager(String[]) - Constructor for class org.colomoto.biolqm.service.LQMServiceManager

Create an instance, storing command-line arguments

M

MaBoSSEncoder - Class in org.colomoto.biolqm.io.maboss

Export a Boolean(ized) LogicalModel into MaBoSS format

MaBoSSEncoder(LogicalModel) - Constructor for class org.colomoto.biolqm.io.maboss.MaBoSSEncoder

MaBoSSFormat - Class in org.colomoto.biolqm.io.maboss

MaBoSSFormat() - Constructor for class org.colomoto.biolqm.io.maboss.MaBoSSFormat

main(String[]) - Static method in class org.colomoto.biolqm.helper.implicants.Formula

main(String[]) - Static method in class org.colomoto.biolqm.helper.state.SimpleStateList

main(String[]) - Static method in class org.colomoto.biolqm.LQMLauncher

The main entry point.

max - Variable in class org.colomoto.biolqm.helper.state.Range

max() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser

max() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TableContext

max - Variable in class org.colomoto.biolqm.modifier.perturbation.RangePerturbation

MaxContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.ITNETParser.MaxContext

MDD2PrimeImplicants - Class in org.colomoto.biolqm.helper.implicants

MDD2PrimeImplicants(MDDManager) - Constructor for class org.colomoto.biolqm.helper.implicants.MDD2PrimeImplicants

method - Variable in class org.colomoto.biolqm.tool.fixpoints.FixpointTask

min - Variable in class org.colomoto.biolqm.helper.state.Range

min - Variable in class org.colomoto.biolqm.modifier.perturbation.RangePerturbation

MNetBaseListener - Class in org.colomoto.biolqm.io.antlr

This class provides an empty implementation of MNetListener, which can be extended to create a listener which only needs to handle a subset of the available methods.

MNetBaseListener() - Constructor for class org.colomoto.biolqm.io.antlr.MNetBaseListener

MNetExport - Class in org.colomoto.biolqm.io.mnet

Export logical model into a list of multi-valued functions.

MNetExport(LogicalModel) - Constructor for class org.colomoto.biolqm.io.mnet.MNetExport

MNetFormat - Class in org.colomoto.biolqm.io.mnet

MNetFormat() - Constructor for class org.colomoto.biolqm.io.mnet.MNetFormat

MNetImport - Class in org.colomoto.biolqm.io.mnet

Simple import reading multi-valued logical functions from a text file.

MNetImport() - Constructor for class org.colomoto.biolqm.io.mnet.MNetImport

MNetLexer - Class in org.colomoto.biolqm.io.antlr

MNetLexer(CharStream) - Constructor for class org.colomoto.biolqm.io.antlr.MNetLexer

MNetListener - Interface in org.colomoto.biolqm.io.antlr

This interface defines a complete listener for a parse tree produced by MNetParser.

MNetParser - Class in org.colomoto.biolqm.io.antlr

MNetParser(TokenStream) - Constructor for class org.colomoto.biolqm.io.antlr.MNetParser

MNetParser.AndContext - Class in org.colomoto.biolqm.io.antlr

MNetParser.AndExprContext - Class in org.colomoto.biolqm.io.antlr

MNetParser.AssignContext - Class in org.colomoto.biolqm.io.antlr

MNetParser.ExprContext - Class in org.colomoto.biolqm.io.antlr

MNetParser.ModelContext - Class in org.colomoto.biolqm.io.antlr

MNetParser.NotContext - Class in org.colomoto.biolqm.io.antlr

MNetParser.OrContext - Class in org.colomoto.biolqm.io.antlr

MNetParser.OrExprContext - Class in org.colomoto.biolqm.io.antlr

MNetParser.SimpleExprContext - Class in org.colomoto.biolqm.io.antlr

MNetParser.ValContext - Class in org.colomoto.biolqm.io.antlr

MNetParser.VarContext - Class in org.colomoto.biolqm.io.antlr

model() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

model() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

model() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser

model() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser

model() - Method in class org.colomoto.biolqm.io.antlr.CNetParser

model() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser

model() - Method in class org.colomoto.biolqm.io.antlr.MNetParser

model - Variable in class org.colomoto.biolqm.io.BaseExporter

model - Variable in class org.colomoto.biolqm.io.sbml.SBMLQualBundle

model - Variable in class org.colomoto.biolqm.tool.AbstractToolTask

model - Variable in class org.colomoto.biolqm.tool.fixpoints.StructuralNodeOrderer

model - Variable in class org.colomoto.biolqm.tool.simulation.BaseUpdater

model - Variable in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

ModelContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BNetParser.ModelContext

ModelContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ModelContext

ModelContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanNetParser.ModelContext

ModelContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BoolsimParser.ModelContext

ModelContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.CNetParser.ModelContext

ModelContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.ITNETParser.ModelContext

ModelContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.MNetParser.ModelContext

ModelExporter - Interface in org.colomoto.biolqm.io

Model exporters are tasks dedicated to exporting a model in a specific format.

ModelGrouping - Class in org.colomoto.biolqm.tool.simulation.grouping

ModelGrouping(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

ModelGrouping(LogicalModel, String) - Constructor for class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

ModelGrouping.RankedClass - Class in org.colomoto.biolqm.tool.simulation.grouping

ModelGrouping.RankedClassGroup - Class in org.colomoto.biolqm.tool.simulation.grouping

ModelLayout - Class in org.colomoto.biolqm

Simple storage for layout information

ModelLayout() - Constructor for class org.colomoto.biolqm.ModelLayout

ModelLayout.LayoutInfo - Class in org.colomoto.biolqm

ModelLoader - Interface in org.colomoto.biolqm.io

Model loaders are tasks dedicated to loading a model from a specific format.

ModelModifier - Interface in org.colomoto.biolqm.modifier

Model Modifiers are tasks dedicated to the construction of modified logical models.

ModelModifierService - Interface in org.colomoto.biolqm.modifier

A service providing modifiers for logical models.

ModelReducer - Class in org.colomoto.biolqm.modifier.reduction

Wrap ReduceOperation to properly remove variables from models.

ModelReducer(LogicalModel) - Constructor for class org.colomoto.biolqm.modifier.reduction.ModelReducer

ModelTask - Interface in org.colomoto.biolqm.service

Model Tasks are tasks which return a model.

ModelToolService<R,T extends ToolTask<R>> - Interface in org.colomoto.biolqm.tool

Simple tool description interface.

modeNames - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

modeNames - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

modeNames - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

modeNames - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

modeNames - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

modeNames - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

modeNames - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

modify(LogicalModel, String) - Method in interface org.colomoto.biolqm.modifier.ModelModifierService

Setup a modifier and directly retrieve the modified model.

modify(LogicalModel) - Method in interface org.colomoto.biolqm.modifier.ModelModifierService

Apply a modifier with the default parameters.

modify(LogicalModel, String) - Static method in class org.colomoto.biolqm.service.LQMServiceManager

Construct a modified model.

modify(LogicalModel, String, String) - Static method in class org.colomoto.biolqm.service.LQMServiceManager

Construct a modified model.

MultiplePerturbation<P extends LogicalModelPerturbation> - Class in org.colomoto.biolqm.modifier.perturbation

A multiple perturbation is a list of perturbations all applied together.

MultiplePerturbation(List<P>) - Constructor for class org.colomoto.biolqm.modifier.perturbation.MultiplePerturbation

Create a multiple perturbation

MultipleSuccessorSimulation - Class in org.colomoto.biolqm.tool.simulation.multiplesuccessor

Common structure for simulations with updaters yielding multiple successors.

MultipleSuccessorSimulation(MultipleSuccessorsUpdater) - Constructor for class org.colomoto.biolqm.tool.simulation.multiplesuccessor.MultipleSuccessorSimulation

MultipleSuccessorSimulation(MultipleSuccessorsUpdater, SimulationStrategy) - Constructor for class org.colomoto.biolqm.tool.simulation.multiplesuccessor.MultipleSuccessorSimulation

MultipleSuccessorsUpdater - Interface in org.colomoto.biolqm.tool.simulation.multiplesuccessor

Updaters which can yield multiple successors for a single state.

MultivaluedSupport - Enum in org.colomoto.biolqm.service

N

negatePrimes() - Method in class org.colomoto.biolqm.helper.implicants.Formula

NEGATIVE - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

NEGATIVE - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

NEGATIVE() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.OpContext

newBundle() - Static method in class org.colomoto.biolqm.io.sbml.SBMLqualHelper

Create a new Bundle, with an empty qualitative model

newBundle(boolean) - Static method in class org.colomoto.biolqm.io.sbml.SBMLqualHelper

NEWLINE - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AssignContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AssignContext

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.HeaderContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.HeaderContext

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.ModelContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.ModelContext

NEWLINE - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

NEWLINE - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AssignContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AssignContext

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ModelContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ModelContext

NEWLINE - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

NEWLINE - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.AssignContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.AssignContext

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.ModelContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.ModelContext

NEWLINE - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

NEWLINE - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.AssignContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.AssignContext

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.ModelContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.ModelContext

NEWLINE - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

NEWLINE - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.LineContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.LineContext

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.ModelContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.ModelContext

NEWLINE - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TableContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TableContext

NEWLINE - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.LineContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.LineContext

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.ModelContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.ModelContext

NEWLINE - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TableContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TableContext

NEWLINE - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AssignContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AssignContext

NEWLINE() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.ModelContext

NEWLINE(int) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.ModelContext

NEWLINE - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

next() - Method in class org.colomoto.biolqm.helper.state.PatternStateIterator

nextState - Variable in class org.colomoto.biolqm.tool.simulation.multiplesuccessor.AbstractMultipleSuccessorUpdater

nfree - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpace

nodeChange(byte[], int) - Method in class org.colomoto.biolqm.tool.simulation.BaseUpdater

Test if a component is ready to change its state.

NodeInfo - Class in org.colomoto.biolqm

Contains the basic information of a regulatory component : nodeID : a unique identifier for the gene display name (optional) max : the maximal activity level

NodeInfo(String) - Constructor for class org.colomoto.biolqm.NodeInfo

NodeInfo(String, byte) - Constructor for class org.colomoto.biolqm.NodeInfo

NodeInfo(String, String, byte) - Constructor for class org.colomoto.biolqm.NodeInfo

NodeInfoHolder - Interface in org.colomoto.biolqm

An object containing a NodeInfo

nodeOrder - Variable in class org.colomoto.biolqm.io.petrinet.AbstractPNEncoder

nodes - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceList

not() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

not() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.SimpleExprContext

not(int) - Method in class org.colomoto.biolqm.io.antlr.BNetParser.SimpleExprContext

NOT - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

NOT - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

not() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

NOT() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.NotContext

not() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.SimpleExprContext

not(int) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.SimpleExprContext

NOT - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

NOT - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

not() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser

NOT() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.NotContext

not() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.SimpleExprContext

not(int) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.SimpleExprContext

NOT - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

NOT - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

not() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser

NOT() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.NotContext

not() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.SimpleExprContext

not(int) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.SimpleExprContext

not() - Method in class org.colomoto.biolqm.io.antlr.ExpressionStack

not() - Method in class org.colomoto.biolqm.io.antlr.MNetParser

not() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.SimpleExprContext

not(int) - Method in class org.colomoto.biolqm.io.antlr.MNetParser.SimpleExprContext

NotContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BNetParser.NotContext

NotContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.NotContext

NotContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanNetParser.NotContext

NotContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BoolsimParser.NotContext

NotContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.MNetParser.NotContext

npercolated - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpace

O

op() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.AssignContext

op() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser

OpContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BoolsimParser.OpContext

openTag(String) - Method in class org.colomoto.common.xml.XMLWriter

Open a tag in the XML output file

openTag(String, String[]) - Method in class org.colomoto.common.xml.XMLWriter

Open a tag and add it the specified attributes.

operator(Operator) - Method in class org.colomoto.biolqm.io.antlr.ExpressionStack

Operator - Enum in org.colomoto.biolqm.io.antlr

Operator supported in function parsers

or() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

or() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.OrExprContext

OR - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

OR - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

OR() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.OrExprContext

OR - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

OR - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

OR() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.OrExprContext

or() - Method in class org.colomoto.biolqm.io.antlr.MNetParser

or() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.OrExprContext

OrContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BNetParser.OrContext

OrContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.MNetParser.OrContext

OrExprContext(BNetParser.ExprContext) - Constructor for class org.colomoto.biolqm.io.antlr.BNetParser.OrExprContext

OrExprContext(BooleanFunctionParser.ExprContext) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.OrExprContext

OrExprContext(BooleanNetParser.ExprContext) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanNetParser.OrExprContext

OrExprContext(MNetParser.ExprContext) - Constructor for class org.colomoto.biolqm.io.antlr.MNetParser.OrExprContext

org.colomoto.biolqm - package 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 - package org.colomoto.biolqm.helper

org.colomoto.biolqm.helper.clingo - package org.colomoto.biolqm.helper.clingo

org.colomoto.biolqm.helper.implicants - package org.colomoto.biolqm.helper.implicants

org.colomoto.biolqm.helper.inferinteraction - package org.colomoto.biolqm.helper.inferinteraction

Infer interactions and their signs from a logical model.

org.colomoto.biolqm.helper.state - package org.colomoto.biolqm.helper.state

org.colomoto.biolqm.io - package org.colomoto.biolqm.io

Input/Output for Logical Model.

org.colomoto.biolqm.io.antlr - package org.colomoto.biolqm.io.antlr

Parser implementations using the antlr parser generator.

org.colomoto.biolqm.io.bnet - package org.colomoto.biolqm.io.bnet

The format used by boolnet and pyboolnet

org.colomoto.biolqm.io.booleannet - package org.colomoto.biolqm.io.booleannet

The format used by booleannet and related tools in Reka Albert's group

org.colomoto.biolqm.io.boolsim - package org.colomoto.biolqm.io.boolsim

The format used by boolsim/GenYsis.

org.colomoto.biolqm.io.cnet - package org.colomoto.biolqm.io.cnet

The format used by boolnet and pyboolnet

org.colomoto.biolqm.io.functions - package org.colomoto.biolqm.io.functions

logical functions.

org.colomoto.biolqm.io.ginml - package org.colomoto.biolqm.io.ginml

GINML support.

org.colomoto.biolqm.io.gna - package org.colomoto.biolqm.io.gna

GNA (non-xml) support.

org.colomoto.biolqm.io.implicanttables - package org.colomoto.biolqm.io.implicanttables

Implicant table format.

org.colomoto.biolqm.io.maboss - package org.colomoto.biolqm.io.maboss

The format used by MaBoSS - https://maboss.curie.fr/

org.colomoto.biolqm.io.mnet - package org.colomoto.biolqm.io.mnet

A custom text format for multi-valued networks

org.colomoto.biolqm.io.petrinet - package org.colomoto.biolqm.io.petrinet

Petri net support.

org.colomoto.biolqm.io.pint - package org.colomoto.biolqm.io.pint

The format used by Pint - http://loicpauleve.name/pint

org.colomoto.biolqm.io.sbml - package org.colomoto.biolqm.io.sbml

SBML qual support.

org.colomoto.biolqm.io.truthtable - package org.colomoto.biolqm.io.truthtable

TruthTable file reader.

org.colomoto.biolqm.modifier - package org.colomoto.biolqm.modifier

Modifications of logical models.

org.colomoto.biolqm.modifier.booleanize - package org.colomoto.biolqm.modifier.booleanize

Construct Boolean versions of Multi-valued models

org.colomoto.biolqm.modifier.buffer - package org.colomoto.biolqm.modifier.buffer

Expand a model using "buffer components".

org.colomoto.biolqm.modifier.perturbation - package org.colomoto.biolqm.modifier.perturbation

Perturbation of logical models: local modifications of its logical functions.

org.colomoto.biolqm.modifier.reduction - package org.colomoto.biolqm.modifier.reduction

model modification: remove components from the core.

org.colomoto.biolqm.modifier.reverse - package org.colomoto.biolqm.modifier.reverse

model modification: creates a new model capable of generating the reverse dynamics.

org.colomoto.biolqm.modifier.sanitize - package org.colomoto.biolqm.modifier.sanitize

Cleanups and sanity-checks, preserving the same model

org.colomoto.biolqm.modifier.submodel - package org.colomoto.biolqm.modifier.submodel

org.colomoto.biolqm.modifier.subspace - package org.colomoto.biolqm.modifier.subspace

org.colomoto.biolqm.service - package org.colomoto.biolqm.service

org.colomoto.biolqm.tool - package org.colomoto.biolqm.tool

Tool definition, used to run actions from the command-line interface.

org.colomoto.biolqm.tool.attractor - package org.colomoto.biolqm.tool.attractor

Identification of the stable states of a logical model.

org.colomoto.biolqm.tool.fixpoints - package org.colomoto.biolqm.tool.fixpoints

Identification of the stable states of a logical model.

org.colomoto.biolqm.tool.simulation - package org.colomoto.biolqm.tool.simulation

Some tools to run simulations on logical models.

org.colomoto.biolqm.tool.simulation.deterministic - package org.colomoto.biolqm.tool.simulation.deterministic

Implementation of updating schemes: update the state of a model (i.e.

org.colomoto.biolqm.tool.simulation.grouping - package org.colomoto.biolqm.tool.simulation.grouping

org.colomoto.biolqm.tool.simulation.multiplesuccessor - package org.colomoto.biolqm.tool.simulation.multiplesuccessor

Implementation of updating schemes: update the state of a model (i.e.

org.colomoto.biolqm.tool.simulation.random - package org.colomoto.biolqm.tool.simulation.random

Implementation of updating schemes: update the state of a model (i.e.

org.colomoto.biolqm.tool.trapspaces - package org.colomoto.biolqm.tool.trapspaces

org.colomoto.biolqm.widgets - package org.colomoto.biolqm.widgets

org.colomoto.common.task - package org.colomoto.common.task

Task interface and tools: callables which can run in background.

org.colomoto.common.xml - package org.colomoto.common.xml

Helper to deal with XML files.

output() - Method in interface org.colomoto.biolqm.io.StreamProvider

Get a single stream.

output(String) - Method in interface org.colomoto.biolqm.io.StreamProvider

Get a custom stream, specifying a pattern.

output(String) - Method in class org.colomoto.biolqm.io.StreamProviderFileImpl

P

PanelChangedEventListener - Interface in org.colomoto.biolqm.widgets

panelChangedOccurred() - Method in interface org.colomoto.biolqm.widgets.PanelChangedEventListener

parseFile(File) - Static method in class org.colomoto.biolqm.io.sbml.SBMLqualHelper

parseInitialState(LogicalModel, String) - Static method in class org.colomoto.biolqm.tool.simulation.InitialStateFactory

parseInputStream(InputStream) - Static method in class org.colomoto.biolqm.io.sbml.SBMLqualHelper

parseMax(String) - Method in class org.colomoto.biolqm.tool.simulation.random.RandomWalkTask

parseSeed(String) - Method in class org.colomoto.biolqm.tool.simulation.random.RandomWalkTask

pattern - Variable in class org.colomoto.biolqm.modifier.reduction.ReductionModifier

pattern - Variable in class org.colomoto.biolqm.tool.fixpoints.FixpointTask

pattern - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpace

PATTERN_commentID - Static variable in class org.colomoto.biolqm.io.cnet.CNetImport

PatternReduction - Class in org.colomoto.biolqm.modifier.reduction

PatternReduction(LogicalModel, StatePattern) - Constructor for class org.colomoto.biolqm.modifier.reduction.PatternReduction

PatternStateIterator - Class in org.colomoto.biolqm.helper.state

Iterator over all states covered by a state pattern.

PatternStateIterator(byte[]) - Constructor for class org.colomoto.biolqm.helper.state.PatternStateIterator

Create an iterator over all states in a Boolean pattern.

PatternStateIterator(byte[], byte[]) - Constructor for class org.colomoto.biolqm.helper.state.PatternStateIterator

Create an iterator over all states in a multi-valued pattern.

percolate - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

percolated - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpace

performTask() - Method in class org.colomoto.biolqm.io.BaseExporter

performTask() - Method in class org.colomoto.biolqm.io.bnet.BNetImport

performTask() - Method in class org.colomoto.biolqm.io.booleannet.BooleanNetImport

performTask() - Method in class org.colomoto.biolqm.io.boolsim.BoolSimImport

performTask() - Method in class org.colomoto.biolqm.io.cnet.CNetImport

performTask() - Method in class org.colomoto.biolqm.io.functions.BooleanFunctionImport

performTask() - Method in class org.colomoto.biolqm.io.implicanttables.ImplicantTableImport

performTask() - Method in class org.colomoto.biolqm.io.mnet.MNetImport

performTask() - Method in class org.colomoto.biolqm.io.sbml.SBMLqualImport

performTask() - Method in class org.colomoto.biolqm.io.truthtable.TruthTableImport

performTask() - Method in class org.colomoto.biolqm.modifier.booleanize.BooleanizeModifier

performTask() - Method in class org.colomoto.biolqm.modifier.buffer.BufferingModifier

performTask() - Method in class org.colomoto.biolqm.modifier.perturbation.PerturbationModifier

performTask() - Method in class org.colomoto.biolqm.modifier.reduction.PatternReduction

performTask() - Method in class org.colomoto.biolqm.modifier.reduction.ReductionModifier

performTask() - Method in class org.colomoto.biolqm.modifier.reverse.ReverseModifier

performTask() - Method in class org.colomoto.biolqm.modifier.sanitize.SanitizeModifier

performTask() - Method in class org.colomoto.biolqm.modifier.submodel.SubmodelModifier

performTask() - Method in class org.colomoto.biolqm.modifier.subspace.SubSpaceModifier

performTask() - Method in class org.colomoto.biolqm.tool.attractor.SATAttractorFinder

performTask() - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointSearcher

performTask() - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointTask

performTask() - Method in class org.colomoto.biolqm.tool.simulation.deterministic.TraceTask

performTask() - Method in class org.colomoto.biolqm.tool.simulation.random.RandomWalkTask

performTask() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

performTask() - Method in class org.colomoto.common.task.AbstractTask

Placeholder for the actual implementation.

PerturbationModifier - Class in org.colomoto.biolqm.modifier.perturbation

PerturbationModifier(LogicalModel) - Constructor for class org.colomoto.biolqm.modifier.perturbation.PerturbationModifier

perturbations - Variable in class org.colomoto.biolqm.modifier.perturbation.MultiplePerturbation

PerturbationService - Class in org.colomoto.biolqm.modifier.perturbation

Service to apply perturbations to Logical Models.

PerturbationService() - Constructor for class org.colomoto.biolqm.modifier.perturbation.PerturbationService

Public constructor which should only be used for service discovery.

PetriNetFormat - Class in org.colomoto.biolqm.io.petrinet

Base format for the PN formats

PetriNetFormat(String, String) - Constructor for class org.colomoto.biolqm.io.petrinet.PetriNetFormat

pickSuccessor(byte[]) - Method in interface org.colomoto.biolqm.tool.simulation.random.RandomUpdater

Get the successor of a state state.

pickSuccessor(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.random.RandomUpdaterWithRates

pickSuccessor(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.random.RandomUpdaterWrapper

PintExport - Class in org.colomoto.biolqm.io.pint

Export logical model into the Pint format.

PintExport(LogicalModel) - Constructor for class org.colomoto.biolqm.io.pint.PintExport

PintFormat - Class in org.colomoto.biolqm.io.pint

PintFormat() - Constructor for class org.colomoto.biolqm.io.pint.PintFormat

PNEncoderAPNN - Class in org.colomoto.biolqm.io.petrinet

Export a regulatory graph to petri net (APNN format).

PNEncoderAPNN(LogicalModel) - Constructor for class org.colomoto.biolqm.io.petrinet.PNEncoderAPNN

PNEncoderINA - Class in org.colomoto.biolqm.io.petrinet

Export a regulatory graph to Petri net (INA format).

PNEncoderINA(LogicalModel) - Constructor for class org.colomoto.biolqm.io.petrinet.PNEncoderINA

PNEncoderPNML - Class in org.colomoto.biolqm.io.petrinet

Export a regulatory graph to Petri net (PNML format).

PNEncoderPNML(LogicalModel) - Constructor for class org.colomoto.biolqm.io.petrinet.PNEncoderPNML

PNMLFormat - Class in org.colomoto.biolqm.io.petrinet

PNML is an xml-based format for Petri net models.

PNMLFormat() - Constructor for class org.colomoto.biolqm.io.petrinet.PNMLFormat

POSITIVE - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

POSITIVE() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.OpContext

POSITIVE - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

preventForbiddenStates(MDDManager, List<NodeInfo>, int[]) - Static method in class org.colomoto.biolqm.modifier.booleanize.BooleanizeModifier

Ensure that a booleanized model has no transition leading to forbidden states.

print() - Method in class org.colomoto.biolqm.tool.fixpoints.JBDDModel

PriorityClassPanel - Class in org.colomoto.biolqm.widgets

PriorityClassPanel(ModelGrouping, boolean) - Constructor for class org.colomoto.biolqm.widgets.PriorityClassPanel

PriorityUpdater - Class in org.colomoto.biolqm.tool.simulation.multiplesuccessor

Draft for a priority updater: components are grouped in groups, which can be updated synchronously or asynchronously.

PriorityUpdater(LogicalModel, String) - Constructor for class org.colomoto.biolqm.tool.simulation.multiplesuccessor.PriorityUpdater

PriorityUpdater(ModelGrouping) - Constructor for class org.colomoto.biolqm.tool.simulation.multiplesuccessor.PriorityUpdater

project_on_components(Iterable<String>) - Method in interface org.colomoto.biolqm.helper.state.StateList

Project the list of states on a subset of components

purgeFixed - Variable in class org.colomoto.biolqm.modifier.reduction.ReductionModifier

Q

qmodel - Variable in class org.colomoto.biolqm.io.sbml.SBMLQualBundle

R

random - Variable in class org.colomoto.biolqm.tool.simulation.random.AbstractRandomUpdater

RandomUpdater - Interface in org.colomoto.biolqm.tool.simulation.random

Interface for random (stochastic) updaters.

RandomUpdaterWithRates - Class in org.colomoto.biolqm.tool.simulation.random

Updater picking a random successor in the asynchronous scheme, with optional rates.

RandomUpdaterWithRates(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.simulation.random.RandomUpdaterWithRates

Create a new random random

RandomUpdaterWithRates(LogicalModel, double[]) - Constructor for class org.colomoto.biolqm.tool.simulation.random.RandomUpdaterWithRates

RandomUpdaterWrapper - Class in org.colomoto.biolqm.tool.simulation.random

Random random which wraps a MultipleSuccessorUpdater and picks one of the successors.

RandomUpdaterWrapper(MultipleSuccessorsUpdater) - Constructor for class org.colomoto.biolqm.tool.simulation.random.RandomUpdaterWrapper

RandomWalkService - Class in org.colomoto.biolqm.tool.simulation.random

RandomWalkService() - Constructor for class org.colomoto.biolqm.tool.simulation.random.RandomWalkService

RandomWalkSimulation - Class in org.colomoto.biolqm.tool.simulation.random

A simple simulation engine for random updaters.

RandomWalkSimulation(RandomUpdater, byte[], int) - Constructor for class org.colomoto.biolqm.tool.simulation.random.RandomWalkSimulation

RandomWalkTask - Class in org.colomoto.biolqm.tool.simulation.random

RandomWalkTask(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.simulation.random.RandomWalkTask

Range - Class in org.colomoto.biolqm.helper.state

Range() - Constructor for class org.colomoto.biolqm.helper.state.Range

Range(int, int) - Constructor for class org.colomoto.biolqm.helper.state.Range

RangePerturbation - Class in org.colomoto.biolqm.modifier.perturbation

Simple perturbation to restrict the value of a component in a range.

RangePerturbation(NodeInfo, int, int) - Constructor for class org.colomoto.biolqm.modifier.perturbation.RangePerturbation

Create a range restriction.

RangeRestrictionOperation - Class in org.colomoto.biolqm.modifier.perturbation

Operation used to restrict the values reached in a MDD into a specific range.

RangeRestrictionOperation(MDDManager, int, int) - Constructor for class org.colomoto.biolqm.modifier.perturbation.RangeRestrictionOperation

RankedClass(ModelGrouping.RankedClassGroup) - Constructor for class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

RankedClass(LogicalModel, String) - Constructor for class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

RankedClassGroup(int[]) - Constructor for class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClassGroup

RankedClassGroup(LogicalModel, String) - Constructor for class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClassGroup

rawByteArray() - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointList

read(Reader) - Static method in class org.colomoto.biolqm.helper.implicants.Formula

read(Reader) - Static method in class org.colomoto.biolqm.helper.implicants.Term

reader() - Method in interface org.colomoto.biolqm.io.StreamProvider

reader(String) - Method in interface org.colomoto.biolqm.io.StreamProvider

readintArray(int[][]) - Static method in class org.colomoto.biolqm.helper.implicants.Formula

readintArray(int[]) - Static method in class org.colomoto.biolqm.helper.implicants.Term

reduce - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

reduceFixed(LogicalModel, boolean) - Static method in class org.colomoto.biolqm.modifier.reduction.FixedComponentRemover

ReduceOperation - Class in org.colomoto.biolqm.modifier.reduction

Rewrite a logical function to remove a regulator.

ReduceOperation(MDDManager) - Constructor for class org.colomoto.biolqm.modifier.reduction.ReduceOperation

reducePrimeImplicantsToSubset() - Method in class org.colomoto.biolqm.helper.implicants.Formula

reduceToPrimeImplicants() - Method in class org.colomoto.biolqm.helper.implicants.Formula

ReductionModifier - Class in org.colomoto.biolqm.modifier.reduction

ReductionModifier(LogicalModel) - Constructor for class org.colomoto.biolqm.modifier.reduction.ReductionModifier

ReductionModifier(LogicalModel, String) - Constructor for class org.colomoto.biolqm.modifier.reduction.ReductionModifier

ReductionService - Class in org.colomoto.biolqm.modifier.reduction

Orchestrator for model reduction tools

ReductionService() - Constructor for class org.colomoto.biolqm.modifier.reduction.ReductionService

Public constructor which should only be used for service discovery.

register(Service) - Static method in class org.colomoto.biolqm.service.LQMServiceManager

Register a service after initial service discovery.

regulator - Variable in class org.colomoto.biolqm.modifier.perturbation.InteractionPerturbation

RegulatorRemovalOperation - Class in org.colomoto.biolqm.modifier.perturbation

Operation used to remove a regulator (by assigning it a fixed value) from a MDD.

RegulatorRemovalOperation(MDDManager, MDDVariable, int) - Constructor for class org.colomoto.biolqm.modifier.perturbation.RegulatorRemovalOperation

regulators - Variable in class org.colomoto.biolqm.helper.implicants.Formula

regValue - Variable in class org.colomoto.biolqm.modifier.perturbation.InteractionPerturbation

remove(int) - Method in class org.colomoto.biolqm.modifier.reduction.ModelReducer

Remove a selected variable.

remove(int, int, MDDVariable) - Method in class org.colomoto.biolqm.modifier.reduction.ReduceOperation

Remove regulator from its target node.

remove(int, int, int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

Removes a given variable/split pair from a class, if it exists.

remove(int, int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

remove(int, int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClassGroup

Removes a given variable/split pair from a class, if it exists.

removeActionListener(PanelChangedEventListener) - Method in class org.colomoto.biolqm.widgets.PriorityClassPanel

removeDuplicateComponents(LogicalModel) - Static method in class org.colomoto.biolqm.modifier.reduction.DuplicateRemover

removeGrp(int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

removePseudoOutputs() - Method in class org.colomoto.biolqm.modifier.reduction.ModelReducer

Find outputs and pseudo-outputs in the model and remove them all.

removePseudoOutputs(boolean) - Method in class org.colomoto.biolqm.modifier.reduction.ModelReducer

Remove all (pseudo-)outputs from the model.

reportAmbiguity(Parser, DFA, int, int, boolean, BitSet, ATNConfigSet) - Method in class org.colomoto.biolqm.io.antlr.ErrorListener

reportAttemptingFullContext(Parser, DFA, int, int, BitSet, ATNConfigSet) - Method in class org.colomoto.biolqm.io.antlr.ErrorListener

reportContextSensitivity(Parser, DFA, int, int, int, ATNConfigSet) - Method in class org.colomoto.biolqm.io.antlr.ErrorListener

reset(byte[]) - Method in class org.colomoto.biolqm.helper.state.PatternStateIterator

Assign a new pattern to this iterator and start over.

reset(int[]) - Method in class org.colomoto.biolqm.helper.state.PatternStateIterator

Assign a new pattern to this iterator and start over.

restrict(int) - Method in class org.colomoto.biolqm.modifier.perturbation.RangeRestrictionOperation

Compute a range-restricted version of a MDD

restrict(int) - Method in class org.colomoto.biolqm.modifier.perturbation.RegulatorRemovalOperation

Remove a regulator from a MDD.

RestrictedPathSearcher - Class in org.colomoto.biolqm.helper.implicants

Restrict the paths given by a PathSearcher to the list of actual regulators

RestrictedPathSearcher(MDDManager) - Constructor for class org.colomoto.biolqm.helper.implicants.RestrictedPathSearcher

RestrictedPathSearcher(MDDManager, int) - Constructor for class org.colomoto.biolqm.helper.implicants.RestrictedPathSearcher

restrictValues(byte[], List<NodeInfo>) - Method in class org.colomoto.biolqm.modifier.perturbation.FixedValuePerturbation

restrictValues(byte[], List<NodeInfo>) - Method in class org.colomoto.biolqm.modifier.perturbation.InteractionPerturbation

restrictValues(byte[], List<NodeInfo>) - Method in interface org.colomoto.biolqm.modifier.perturbation.LogicalModelPerturbation

Apply the perturbation(s) directly to a state, i.e., restricts the values of the state in the valid range of the perturbation(s).

restrictValues(byte[], List<NodeInfo>) - Method in class org.colomoto.biolqm.modifier.perturbation.MultiplePerturbation

restrictValues(byte[], List<NodeInfo>) - Method in class org.colomoto.biolqm.modifier.perturbation.RangePerturbation

reverse(MDDVariable, int) - Method in class org.colomoto.biolqm.modifier.reverse.ReverseOperation

Reverse a node.

ReverseModifier - Class in org.colomoto.biolqm.modifier.reverse

Wrap ReverseOperation to properly create a new model capable of generating the reverse dynamics.

ReverseModifier(LogicalModel) - Constructor for class org.colomoto.biolqm.modifier.reverse.ReverseModifier

Prepare a Model modifier for model reversal.

ReverseOperation - Class in org.colomoto.biolqm.modifier.reverse

Reverse a node according to a given variable.

ReverseOperation(MDDManager) - Constructor for class org.colomoto.biolqm.modifier.reverse.ReverseOperation

ReverseService - Class in org.colomoto.biolqm.modifier.reverse

Wrap the reverser code into the ModelModifier interface.

ReverseService() - Constructor for class org.colomoto.biolqm.modifier.reverse.ReverseService

Public constructor which should only be used for service discovery.

RULE_and - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

RULE_and - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

RULE_assign - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

RULE_assign - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

RULE_assign - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

RULE_assign - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

RULE_assign - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

RULE_count - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

RULE_curvar - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

RULE_curvar - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

RULE_expr - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

RULE_expr - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

RULE_expr - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

RULE_expr - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

RULE_expr - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

RULE_header - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

RULE_line - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

RULE_line - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

RULE_max - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

RULE_model - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

RULE_model - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

RULE_model - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

RULE_model - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

RULE_model - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

RULE_model - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

RULE_model - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

RULE_not - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

RULE_not - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

RULE_not - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

RULE_not - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

RULE_not - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

RULE_op - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

RULE_or - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

RULE_or - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

RULE_table - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

RULE_table - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

RULE_target - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

RULE_ttline - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

RULE_ttline - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

RULE_val - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

RULE_val - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

RULE_val - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

RULE_val - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

RULE_var - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

RULE_var - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

RULE_var - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

RULE_var - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

RULE_var - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

RULE_var - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

RULE_varid - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

ruleNames - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

ruleNames - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

ruleNames - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

ruleNames - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

ruleNames - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

ruleNames - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

ruleNames - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

ruleNames - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

ruleNames - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

ruleNames - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

ruleNames - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

ruleNames - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

ruleNames - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

ruleNames - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

run() - Method in class org.colomoto.biolqm.helper.clingo.ClingoLauncher

run() - Method in class org.colomoto.biolqm.helper.inferinteraction.InteractionSearcher

run() - Method in class org.colomoto.common.task.AbstractTask

runSimulation(Iterator<byte[]>) - Method in class org.colomoto.biolqm.tool.simulation.multiplesuccessor.MultipleSuccessorSimulation

runSimulation() - Method in class org.colomoto.biolqm.tool.simulation.multiplesuccessor.MultipleSuccessorSimulation

S

SanitizeModifier - Class in org.colomoto.biolqm.modifier.sanitize

SanitizeModifier(LogicalModel) - Constructor for class org.colomoto.biolqm.modifier.sanitize.SanitizeModifier

SanitizeService - Class in org.colomoto.biolqm.modifier.sanitize

A service for model cleanups and sanity checks.

SanitizeService() - Constructor for class org.colomoto.biolqm.modifier.sanitize.SanitizeService

Public constructor which should only be used for service discovery.

SATAttractorFinder - Class in org.colomoto.biolqm.tool.attractor

Identification of synchronous attractors using a SAT solver, as proposed by E.

SATAttractorFinder(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.attractor.SATAttractorFinder

save(LogicalModel, String, String) - Static method in class org.colomoto.biolqm.service.LQMServiceManager

Save a model to file

SBMLFormat - Class in org.colomoto.biolqm.io.sbml

Format description for SBML files, using the qual extension.

SBMLFormat() - Constructor for class org.colomoto.biolqm.io.sbml.SBMLFormat

SBMLQualBundle - Class in org.colomoto.biolqm.io.sbml

Simple wrapper to get together a SBMLDocument, its enclosed model and qualitative model.

SBMLQualBundle(SBMLDocument, Model, QualModelPlugin) - Constructor for class org.colomoto.biolqm.io.sbml.SBMLQualBundle

SBMLQualBundle(SBMLDocument, Model, QualModelPlugin, LayoutModelPlugin) - Constructor for class org.colomoto.biolqm.io.sbml.SBMLQualBundle

SBMLqualExport - Class in org.colomoto.biolqm.io.sbml

SBML export using JSBML and the "qual" extension.

SBMLqualExport(LogicalModel) - Constructor for class org.colomoto.biolqm.io.sbml.SBMLqualExport

SBMLqualExport(LogicalModel, boolean) - Constructor for class org.colomoto.biolqm.io.sbml.SBMLqualExport

SBMLqualHelper - Class in org.colomoto.biolqm.io.sbml

Helper to create new SBML documents from scratch or from files using JSBML.

SBMLqualHelper() - Constructor for class org.colomoto.biolqm.io.sbml.SBMLqualHelper

SBMLqualImport - Class in org.colomoto.biolqm.io.sbml

Crude SBML import using JSBML and the qual extension.

SBMLqualImport() - Constructor for class org.colomoto.biolqm.io.sbml.SBMLqualImport

scale(float) - Method in class org.colomoto.biolqm.ModelLayout

scale(float, float) - Method in class org.colomoto.biolqm.ModelLayout

selectAttractors(List<TrapSpace>) - Static method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

sempred(RuleContext, int, int) - Method in class org.colomoto.biolqm.io.antlr.BNetParser

sempred(RuleContext, int, int) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

sempred(RuleContext, int, int) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser

sempred(RuleContext, int, int) - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser

sempred(RuleContext, int, int) - Method in class org.colomoto.biolqm.io.antlr.MNetParser

SEP - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

SEP() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.LineContext

SEP - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

SEP() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TableContext

SEPCLASS - Static variable in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

SEPGROUP - Static variable in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

SEPVAR - Static variable in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

SequentialUpdater - Class in org.colomoto.biolqm.tool.simulation.deterministic

Updater for the sequential scheme: all components are updated one after the other in a single successor.

SequentialUpdater(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.SequentialUpdater

Create a new sequential updater, using the default order

SequentialUpdater(LogicalModel, String) - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.SequentialUpdater

Create a new sequential updater, using a custom order

SequentialUpdater(LogicalModel, int[]) - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.SequentialUpdater

Create a new sequential updater, using a custom order

Service - Interface in org.colomoto.biolqm.service

Simple service description interface.

set(NodeInfo, int, int, int, int) - Method in class org.colomoto.biolqm.ModelLayout

setBooleanizedGroup(NodeInfo[]) - Method in class org.colomoto.biolqm.NodeInfo

setDestination(StreamProvider) - Method in class org.colomoto.biolqm.io.BaseExporter

setDestination(StreamProvider) - Method in interface org.colomoto.biolqm.io.ModelExporter

Define the destination at which the model will be exported.

setDestination(File) - Method in interface org.colomoto.biolqm.io.ModelExporter

Define the destination at which the model will be exported.

setDestination(String) - Method in interface org.colomoto.biolqm.io.ModelExporter

Define the destination at which the model will be exported.

setExtra(boolean) - Method in interface org.colomoto.biolqm.helper.state.StateList

Include or hide extra components.

setExtra(boolean) - Method in class org.colomoto.biolqm.helper.state.StateListProjection

setExtra(boolean) - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointList

setExtra(boolean) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceList

setInitialCondition(byte[]) - Method in class org.colomoto.biolqm.io.sbml.SBMLqualExport

Apply an initial condition to the exported model.

setInitialState(byte[]) - Method in class org.colomoto.biolqm.io.petrinet.AbstractPNEncoder

setInput(boolean) - Method in class org.colomoto.biolqm.NodeInfo

setMax(byte) - Method in class org.colomoto.biolqm.NodeInfo

setMinsolutions(boolean) - Method in class org.colomoto.biolqm.helper.clingo.ClingoLauncher

setName(String) - Method in class org.colomoto.biolqm.NodeInfo

setNode(int) - Method in class org.colomoto.biolqm.helper.implicants.ImplicantSearcher

setNode(int) - Method in class org.colomoto.biolqm.helper.implicants.RestrictedPathSearcher

setNodeID(String) - Method in class org.colomoto.biolqm.NodeInfo

setParameter(String) - Method in class org.colomoto.biolqm.modifier.buffer.BufferingModifier

setParameter(String) - Method in interface org.colomoto.common.task.Task

setParameters(String[]) - Method in class org.colomoto.biolqm.modifier.perturbation.PerturbationModifier

setParameters(String[]) - Method in class org.colomoto.biolqm.modifier.reduction.ReductionModifier

setParameters(String[]) - Method in class org.colomoto.biolqm.modifier.sanitize.SanitizeModifier

setParameters(String[]) - Method in class org.colomoto.biolqm.modifier.submodel.SubmodelModifier

setParameters(String[]) - Method in class org.colomoto.biolqm.modifier.subspace.SubSpaceModifier

setParameters(String[]) - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointTask

setParameters(String[]) - Method in class org.colomoto.biolqm.tool.simulation.deterministic.TraceTask

setParameters(String[]) - Method in class org.colomoto.biolqm.tool.simulation.random.RandomWalkTask

setParameters(String[]) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

setParameters(String[]) - Method in interface org.colomoto.common.task.Task

setParameters(String) - Method in interface org.colomoto.common.task.Task

setPattern(byte[]) - Method in class org.colomoto.biolqm.modifier.subspace.SubSpaceModifier

setPosition(NodeInfo, int, int) - Method in class org.colomoto.biolqm.ModelLayout

setSanitizeIDs(boolean) - Method in class org.colomoto.biolqm.modifier.sanitize.SanitizeModifier

setSeed(long) - Method in class org.colomoto.biolqm.tool.simulation.random.AbstractRandomUpdater

setSeed(long) - Method in interface org.colomoto.biolqm.tool.simulation.random.RandomUpdater

Set the seed for the random generator (for reproducibility in tests, NOT for real use)

setSeed(long) - Method in class org.colomoto.biolqm.tool.simulation.random.RandomUpdaterWrapper

setSolutionLimit(int) - Method in class org.colomoto.biolqm.helper.clingo.ClingoLauncher

setSource(StreamProvider) - Method in class org.colomoto.biolqm.io.BaseLoader

setSource(StreamProvider) - Method in interface org.colomoto.biolqm.io.ModelLoader

Define the source from which the model will be loaded.

setSource(File) - Method in interface org.colomoto.biolqm.io.ModelLoader

Define the source file from which the model will be loaded.

setSource(String) - Method in interface org.colomoto.biolqm.io.ModelLoader

Define the source from which the model will be loaded.

shortString() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpace

show() - Method in interface org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolver

show() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverASP

show() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverFunctionASP

showasp - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

SimpleExprContext(BNetParser.ExprContext) - Constructor for class org.colomoto.biolqm.io.antlr.BNetParser.SimpleExprContext

SimpleExprContext(BooleanFunctionParser.ExprContext) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.SimpleExprContext

SimpleExprContext(BooleanNetParser.ExprContext) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanNetParser.SimpleExprContext

SimpleExprContext(BoolsimParser.ExprContext) - Constructor for class org.colomoto.biolqm.io.antlr.BoolsimParser.SimpleExprContext

SimpleExprContext(MNetParser.ExprContext) - Constructor for class org.colomoto.biolqm.io.antlr.MNetParser.SimpleExprContext

SimpleStateList - Class in org.colomoto.biolqm.helper.state

SimulationStrategy - Enum in org.colomoto.biolqm.tool.simulation.multiplesuccessor

size() - Method in interface org.colomoto.biolqm.helper.state.StateList

get the number of states or patterns in the list.

size - Variable in class org.colomoto.biolqm.tool.simulation.BaseUpdater

size() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

size() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClassGroup

size() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

It's the number of classes

solve(TrapSpaceList) - Method in interface org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolver

solve(TrapSpaceList) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverASP

solve(TrapSpaceList) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverBDD

solve(TrapSpaceList) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverFunctionASP

split(int, int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

Splits a variable in two (in the current/selected class).

split(int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClassGroup

Splits a variable in two (in the current/selected group).

split(int, int, String) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

SplittingType - Enum in org.colomoto.biolqm.tool.simulation.grouping

stable() - Method in class org.colomoto.biolqm.tool.fixpoints.JBDDModel

StableASP - Class in org.colomoto.biolqm.tool.fixpoints

Use the clingo ASP solver to assemble the stability constraints and identify stable states.

StableASP(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.fixpoints.StableASP

StableOperation - Class in org.colomoto.biolqm.tool.fixpoints

MDD operation used to build a stability condition.

StableOperation() - Constructor for class org.colomoto.biolqm.tool.fixpoints.StableOperation

state - Variable in class org.colomoto.biolqm.tool.simulation.multiplesuccessor.AbstractMultipleSuccessorUpdater

StateList - Interface in org.colomoto.biolqm.helper.state

StateListProjection - Class in org.colomoto.biolqm.helper.state

Group a list of states after projecting it on a subset of components.

StateListProjection(StateList, Iterable<String>) - Constructor for class org.colomoto.biolqm.helper.state.StateListProjection

StateListProjection(StateList, int[]) - Constructor for class org.colomoto.biolqm.helper.state.StateListProjection

StatePattern - Class in org.colomoto.biolqm.helper.state

StatePattern() - Constructor for class org.colomoto.biolqm.helper.state.StatePattern

StreamProvider - Interface in org.colomoto.biolqm.io

Provide Input or Output stream objects for the loading and saving operations filters.

StreamProviderFileImpl - Class in org.colomoto.biolqm.io

Provide input streams from the file system.

streams - Variable in class org.colomoto.biolqm.io.BaseExporter

streams - Variable in class org.colomoto.biolqm.io.BaseLoader

StructuralNodeOrderer - Class in org.colomoto.biolqm.tool.fixpoints

Sort nodes of a LogicalModel according to the new regulators they introduce.

StructuralNodeOrderer(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.fixpoints.StructuralNodeOrderer

SubmodelModifier - Class in org.colomoto.biolqm.modifier.submodel

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).

SubmodelModifier(LogicalModel) - Constructor for class org.colomoto.biolqm.modifier.submodel.SubmodelModifier

SubmodelService - Class in org.colomoto.biolqm.modifier.submodel

SubmodelService() - Constructor for class org.colomoto.biolqm.modifier.submodel.SubmodelService

Public constructor which should only be used for service discovery.

SubSpaceModifier - Class in org.colomoto.biolqm.modifier.subspace

Model Modifier to restrict a model into a subspace.

SubSpaceModifier(LogicalModel, byte[]) - Constructor for class org.colomoto.biolqm.modifier.subspace.SubSpaceModifier

SubSpaceModifier(LogicalModel) - Constructor for class org.colomoto.biolqm.modifier.subspace.SubSpaceModifier

SubSpaceService - Class in org.colomoto.biolqm.modifier.subspace

Modifier Service for subspace restriction

SubSpaceService() - Constructor for class org.colomoto.biolqm.modifier.subspace.SubSpaceService

switchClasses(int, int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

SynchronousUpdater - Class in org.colomoto.biolqm.tool.simulation.deterministic

Updater for the synchronous scheme: all possible changes are applied in a single successor

SynchronousUpdater(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.SynchronousUpdater

Create a new synchronous updater

syntaxError(Recognizer<?, ?>, Object, int, int, String, RecognitionException) - Method in class org.colomoto.biolqm.io.antlr.ErrorListener

T

T__0 - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

T__0 - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

T__0 - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

T__0 - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

T__0 - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

T__0 - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

T__0 - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

T__0 - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

T__0 - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

T__0 - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

T__0 - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

T__0 - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

T__1 - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

T__1 - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

T__1 - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

T__1 - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

T__1 - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

T__1 - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

T__1 - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

T__1 - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

T__1 - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

T__1 - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

T__1 - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

T__1 - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

T__2 - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

T__2 - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

T__2 - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

T__2 - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

T__2 - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

T__2 - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

T__2 - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

T__2 - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

T__2 - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

T__2 - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

T__3 - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

T__3 - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

T__3 - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

T__3 - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

T__3 - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

T__3 - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

T__4 - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

T__4 - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

T__4 - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

T__4 - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

T__5 - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

T__5 - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

T__5 - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

T__5 - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

T__6 - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

T__6 - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

table() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.ModelContext

table(int) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.ModelContext

table() - Method in class org.colomoto.biolqm.io.antlr.CNetParser

table() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.ModelContext

table(int) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.ModelContext

table() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser

TableContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.CNetParser.TableContext

TableContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.ITNETParser.TableContext

target() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.LineContext

target() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser

target - Variable in class org.colomoto.biolqm.modifier.perturbation.InteractionPerturbation

TargetContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.ITNETParser.TargetContext

Task<T> - Interface in org.colomoto.common.task

Simple task definition.

TaskListener - Interface in org.colomoto.common.task

Listen to a background task.

TaskStatus - Enum in org.colomoto.common.task

List of task status

taskUpdated(Task) - Method in interface org.colomoto.common.task.TaskListener

Notifies a task update (finished or canceled)

Term - Class in org.colomoto.biolqm.helper.implicants

Term(byte[]) - Constructor for class org.colomoto.biolqm.helper.implicants.Term

terminal - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceList

terminal - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

toArray() - Method in class org.colomoto.biolqm.helper.implicants.Formula

toBuffer() - Method in class org.colomoto.common.xml.XMLWriter

ask to store the next calls into a string buffer.

tokenNames - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

Deprecated.

Use BNetLexer.VOCABULARY instead.

tokenNames - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

Deprecated.

Use BNetParser.VOCABULARY instead.

tokenNames - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

Deprecated.

Use BooleanFunctionLexer.VOCABULARY instead.

tokenNames - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

Deprecated.

Use BooleanFunctionParser.VOCABULARY instead.

tokenNames - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

Deprecated.

Use BooleanNetLexer.VOCABULARY instead.

tokenNames - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

Deprecated.

Use BooleanNetParser.VOCABULARY instead.

tokenNames - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

Deprecated.

Use BoolsimLexer.VOCABULARY instead.

tokenNames - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

Deprecated.

Use BoolsimParser.VOCABULARY instead.

tokenNames - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

Deprecated.

Use CNetLexer.VOCABULARY instead.

tokenNames - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

Deprecated.

Use CNetParser.VOCABULARY instead.

tokenNames - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

Deprecated.

Use ITNETLexer.VOCABULARY instead.

tokenNames - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

Deprecated.

Use ITNETParser.VOCABULARY instead.

tokenNames - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

Deprecated.

Use MNetLexer.VOCABULARY instead.

tokenNames - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

Deprecated.

Use MNetParser.VOCABULARY instead.

ToolTask<R> - Interface in org.colomoto.biolqm.tool

toString() - Method in class org.colomoto.biolqm.helper.clingo.ClingoResult

toString() - Method in class org.colomoto.biolqm.helper.implicants.Formula

toString() - Method in class org.colomoto.biolqm.helper.implicants.Term

toString() - Method in class org.colomoto.biolqm.io.AbstractFormat

toString() - Method in class org.colomoto.biolqm.modifier.perturbation.FixedValuePerturbation

toString() - Method in class org.colomoto.biolqm.modifier.perturbation.InteractionPerturbation

toString() - Method in class org.colomoto.biolqm.modifier.perturbation.MultiplePerturbation

toString() - Method in class org.colomoto.biolqm.modifier.perturbation.RangePerturbation

toString() - Method in class org.colomoto.biolqm.NodeInfo

toString() - Method in class org.colomoto.biolqm.service.BaseService

toString() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

toString() - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

toString() - Method in enum org.colomoto.biolqm.tool.simulation.grouping.SplittingType

toString() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpace

TraceService - Class in org.colomoto.biolqm.tool.simulation.deterministic

TraceService() - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.TraceService

TraceTask - Class in org.colomoto.biolqm.tool.simulation.deterministic

TraceTask(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.simulation.deterministic.TraceTask

transform(int, int) - Method in class org.colomoto.biolqm.modifier.booleanize.BooleanizeModifier

Take a Boolean function and transfer it into the new MDDManager, replacing the multi-valued regulators if any.

TrapSpace - Class in org.colomoto.biolqm.tool.trapspaces

TrapSpace(byte[]) - Constructor for class org.colomoto.biolqm.tool.trapspaces.TrapSpace

TrapSpace(byte[], boolean[]) - Constructor for class org.colomoto.biolqm.tool.trapspaces.TrapSpace

TrapSpaceList - Class in org.colomoto.biolqm.tool.trapspaces

TrapSpaceList(TrapSpaceTask, LogicalModel) - Constructor for class org.colomoto.biolqm.tool.trapspaces.TrapSpaceList

TrapSpaceService - Class in org.colomoto.biolqm.tool.trapspaces

TrapSpaceService() - Constructor for class org.colomoto.biolqm.tool.trapspaces.TrapSpaceService

TrapSpaceSolver - Interface in org.colomoto.biolqm.tool.trapspaces

TrapSpaceSolverASP - Class in org.colomoto.biolqm.tool.trapspaces

Use the clingo ASP solver to identify trap spaces.

TrapSpaceSolverASP(LogicalModel, TrapSpaceTask) - Constructor for class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverASP

TrapSpaceSolverBDD - Class in org.colomoto.biolqm.tool.trapspaces

Use BDDs to identify trapspaces.

TrapSpaceSolverBDD(LogicalModel, TrapSpaceTask) - Constructor for class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverBDD

TrapSpaceSolverFunctionASP - Class in org.colomoto.biolqm.tool.trapspaces

Use the clingo ASP solver to identify trap spaces.

TrapSpaceSolverFunctionASP(LogicalModel, TrapSpaceTask) - Constructor for class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverFunctionASP

TrapSpaceTask - Class in org.colomoto.biolqm.tool.trapspaces

TrapSpaceTask(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTask

TruthTableExport - Class in org.colomoto.biolqm.io.truthtable

Exports a logical model into the Truth Table format.

TruthTableExport(LogicalModel) - Constructor for class org.colomoto.biolqm.io.truthtable.TruthTableExport

TruthTableFormat - Class in org.colomoto.biolqm.io.truthtable

Format description for TruthTable (.tt) files.

TruthTableFormat() - Constructor for class org.colomoto.biolqm.io.truthtable.TruthTableFormat

TruthTableImport - Class in org.colomoto.biolqm.io.truthtable

Imports a file in the Truth Table format into a LogicalModel.

TruthTableImport() - Constructor for class org.colomoto.biolqm.io.truthtable.TruthTableImport

TS - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

TS - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

TS() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.VarContext

ttline() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.LineContext

ttline() - Method in class org.colomoto.biolqm.io.antlr.CNetParser

ttline() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.LineContext

ttline() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser

TtlineContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.CNetParser.TtlineContext

TtlineContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.ITNETParser.TtlineContext

U

UID - Static variable in class org.colomoto.biolqm.tool.fixpoints.FixpointService

UID - Static variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceService

UNDEFINED - Static variable in interface org.colomoto.biolqm.helper.state.StateList

UNDEFINED_MAX - Static variable in class org.colomoto.biolqm.NodeInfo

unsplit(int, int, int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClass

Marks a given variable as not split.

unsplit(int, int) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping.RankedClassGroup

Marks a given variable as not split.

unsplit(int, int, String) - Method in class org.colomoto.biolqm.tool.simulation.grouping.ModelGrouping

update(LogicalModel) - Method in class org.colomoto.biolqm.modifier.perturbation.FixedValuePerturbation

update(LogicalModel) - Method in class org.colomoto.biolqm.modifier.perturbation.InteractionPerturbation

update(LogicalModel) - Method in interface org.colomoto.biolqm.modifier.perturbation.LogicalModelPerturbation

Apply the perturbation to a model directly (do not create a modified model).

update(LogicalModel) - Method in class org.colomoto.biolqm.modifier.perturbation.MultiplePerturbation

update(LogicalModel) - Method in class org.colomoto.biolqm.modifier.perturbation.RangePerturbation

update(byte[], int, int, byte[]) - Method in class org.colomoto.biolqm.tool.simulation.BaseUpdater

Create or update the next state.

updatePriorityList() - Method in class org.colomoto.biolqm.widgets.PriorityClassPanel

UpdaterFactory - Class in org.colomoto.biolqm.tool.simulation

Static helper class to construct simulation updaters based on a configuration string

UpdaterFactory() - Constructor for class org.colomoto.biolqm.tool.simulation.UpdaterFactory

useASP() - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointTask

useMDD() - Method in class org.colomoto.biolqm.tool.fixpoints.FixpointTask

V

val() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.SimpleExprContext

val() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

val() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.SimpleExprContext

val() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

val() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.SimpleExprContext

val() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser

val() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.SimpleExprContext

val() - Method in class org.colomoto.biolqm.io.antlr.MNetParser

ValContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BNetParser.ValContext

ValContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ValContext

ValContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanNetParser.ValContext

ValContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.MNetParser.ValContext

value - Variable in class org.colomoto.biolqm.io.antlr.Assignment

VALUE - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

VALUE() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.ValContext

VALUE - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

VALUE - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

VALUE() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ValContext

VALUE - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

VALUE - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

VALUE() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.ValContext

VALUE - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

value(Value) - Method in class org.colomoto.biolqm.io.antlr.ExpressionStack

VALUE - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

VALUE() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.MaxContext

VALUE() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TargetContext

VALUE() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TtlineContext

VALUE(int) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TtlineContext

VALUE - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

VALUE - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

VALUE() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.ValContext

VALUE - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

VALUE() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.VarContext

Value - Enum in org.colomoto.biolqm.io.antlr

Created by aurelien on 10/2/14.

value - Variable in class org.colomoto.biolqm.modifier.perturbation.FixedValuePerturbation

valueOf(String) - Static method in enum org.colomoto.biolqm.io.antlr.Operator

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.colomoto.biolqm.io.antlr.Value

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.colomoto.biolqm.service.MultivaluedSupport

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.colomoto.biolqm.tool.fixpoints.FixpointMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.colomoto.biolqm.tool.simulation.grouping.SplittingType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.colomoto.biolqm.tool.simulation.multiplesuccessor.SimulationStrategy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.colomoto.common.task.TaskStatus

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.colomoto.biolqm.io.antlr.Operator

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.colomoto.biolqm.io.antlr.Value

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.colomoto.biolqm.service.MultivaluedSupport

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.colomoto.biolqm.tool.fixpoints.FixpointMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.colomoto.biolqm.tool.simulation.grouping.SplittingType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.colomoto.biolqm.tool.simulation.multiplesuccessor.SimulationStrategy

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.colomoto.common.task.TaskStatus

Returns an array containing the constants of this enum type, in the order they are declared.

var() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.AssignContext

var() - Method in class org.colomoto.biolqm.io.antlr.BNetParser.SimpleExprContext

var() - Method in class org.colomoto.biolqm.io.antlr.BNetParser

var() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AssignContext

var() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.SimpleExprContext

var() - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

var() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.AssignContext

var() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser.SimpleExprContext

var() - Method in class org.colomoto.biolqm.io.antlr.BooleanNetParser

var() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.AssignContext

var() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser.SimpleExprContext

var() - Method in class org.colomoto.biolqm.io.antlr.BoolsimParser

var() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.CurvarContext

var() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TableContext

var(int) - Method in class org.colomoto.biolqm.io.antlr.ITNETParser.TableContext

var() - Method in class org.colomoto.biolqm.io.antlr.ITNETParser

var() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.AssignContext

var() - Method in class org.colomoto.biolqm.io.antlr.MNetParser.SimpleExprContext

var() - Method in class org.colomoto.biolqm.io.antlr.MNetParser

VarContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BNetParser.VarContext

VarContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanFunctionParser.VarContext

VarContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BooleanNetParser.VarContext

VarContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.BoolsimParser.VarContext

VarContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.ITNETParser.VarContext

VarContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.MNetParser.VarContext

varid() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.CurvarContext

varid() - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TableContext

varid(int) - Method in class org.colomoto.biolqm.io.antlr.CNetParser.TableContext

varid() - Method in class org.colomoto.biolqm.io.antlr.CNetParser

VaridContext(ParserRuleContext, int) - Constructor for class org.colomoto.biolqm.io.antlr.CNetParser.VaridContext

visitErrorNode(ErrorNode) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

visitErrorNode(ErrorNode) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

visitErrorNode(ErrorNode) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

visitErrorNode(ErrorNode) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

visitErrorNode(ErrorNode) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

visitErrorNode(ErrorNode) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

visitErrorNode(ErrorNode) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

visitTerminal(TerminalNode) - Method in class org.colomoto.biolqm.io.antlr.BNetBaseListener

visitTerminal(TerminalNode) - Method in class org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener

visitTerminal(TerminalNode) - Method in class org.colomoto.biolqm.io.antlr.BooleanNetBaseListener

visitTerminal(TerminalNode) - Method in class org.colomoto.biolqm.io.antlr.BoolsimBaseListener

visitTerminal(TerminalNode) - Method in class org.colomoto.biolqm.io.antlr.CNetBaseListener

visitTerminal(TerminalNode) - Method in class org.colomoto.biolqm.io.antlr.ITNETBaseListener

visitTerminal(TerminalNode) - Method in class org.colomoto.biolqm.io.antlr.MNetBaseListener

VOCABULARY - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

VOCABULARY - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

VOCABULARY - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

VOCABULARY - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

VOCABULARY - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

VOCABULARY - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

VOCABULARY - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

VOCABULARY - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

VOCABULARY - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

VOCABULARY - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

VOCABULARY - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

VOCABULARY - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

VOCABULARY - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

VOCABULARY - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

W

width - Variable in class org.colomoto.biolqm.ModelLayout.LayoutInfo

write(Writer) - Method in class org.colomoto.biolqm.io.maboss.MaBoSSEncoder

write(String) - Method in class org.colomoto.common.xml.XMLWriter

Write a String directly (no escaping)

write(char) - Method in class org.colomoto.common.xml.XMLWriter

Write a single character directly t the output

writeConfig(Writer) - Method in class org.colomoto.biolqm.io.maboss.MaBoSSEncoder

writeEdge(XMLWriter, String, String, int, String) - Method in class org.colomoto.biolqm.io.ginml.AbstractGINMLWriter

Write an edge to GINML.

writeEdges(XMLWriter) - Method in class org.colomoto.biolqm.io.ginml.AbstractGINMLWriter

Start writing the edges (interactions).

writeEdges(XMLWriter) - Method in class org.colomoto.biolqm.io.ginml.LogicalModel2GINML

writeEsc(String, boolean) - Method in class org.colomoto.common.xml.XMLWriter

Write a string, using escaping as needed.

writeLogicalParameter(XMLWriter, int, String) - Method in class org.colomoto.biolqm.io.ginml.AbstractGINMLWriter

Write a logical parameter to GINML.

writeNodeDecl(XMLWriter, String, int) - Method in class org.colomoto.biolqm.io.ginml.AbstractGINMLWriter

Write a node declaration to GINML.

writeNodes(XMLWriter) - Method in class org.colomoto.biolqm.io.ginml.AbstractGINMLWriter

Start writing the nodes.

writeNodes(XMLWriter) - Method in class org.colomoto.biolqm.io.ginml.LogicalModel2GINML

writer() - Method in interface org.colomoto.biolqm.io.StreamProvider

writer(String) - Method in interface org.colomoto.biolqm.io.StreamProvider

WS - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

WS - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

WS - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

WS - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

WS - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

WS - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

WS - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

WS - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

WS - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

WS - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

WS - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

WS - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

WS - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

WS - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

X

x - Variable in class org.colomoto.biolqm.ModelLayout.LayoutInfo

XMLWriter - Class in org.colomoto.common.xml

A helper to write well formed XML documents.

XMLWriter(String, String) - Constructor for class org.colomoto.common.xml.XMLWriter

Create a XMLWriter with the path to a file.

XMLWriter(OutputStreamWriter, String) - Constructor for class org.colomoto.common.xml.XMLWriter

Create an XML writer with indenting enabled by default.

XMLWriter(OutputStream, String) - Constructor for class org.colomoto.common.xml.XMLWriter

Create an XML writer with indenting enabled by default.

Y

y - Variable in class org.colomoto.biolqm.ModelLayout.LayoutInfo

_

_ATN - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

_ATN - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

_ATN - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

_ATN - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

_ATN - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

_ATN - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

_ATN - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

_ATN - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

_ATN - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

_ATN - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

_ATN - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

_ATN - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

_ATN - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

_ATN - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

_decisionToDFA - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

_decisionToDFA - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

_decisionToDFA - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

_decisionToDFA - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

_decisionToDFA - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

_decisionToDFA - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

_decisionToDFA - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

_decisionToDFA - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

_decisionToDFA - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

_decisionToDFA - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

_decisionToDFA - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

_decisionToDFA - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

_decisionToDFA - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

_decisionToDFA - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

_serializedATN - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

_serializedATN - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

_serializedATN - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

_serializedATN - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

_serializedATN - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

_serializedATN - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

_serializedATN - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

_serializedATN - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

_serializedATN - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

_serializedATN - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

_serializedATN - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

_serializedATN - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

_serializedATN - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

_serializedATN - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

_sharedContextCache - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

_sharedContextCache - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

_sharedContextCache - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionLexer

_sharedContextCache - Static variable in class org.colomoto.biolqm.io.antlr.BooleanFunctionParser

_sharedContextCache - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetLexer

_sharedContextCache - Static variable in class org.colomoto.biolqm.io.antlr.BooleanNetParser

_sharedContextCache - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimLexer

_sharedContextCache - Static variable in class org.colomoto.biolqm.io.antlr.BoolsimParser

_sharedContextCache - Static variable in class org.colomoto.biolqm.io.antlr.CNetLexer

_sharedContextCache - Static variable in class org.colomoto.biolqm.io.antlr.CNetParser

_sharedContextCache - Static variable in class org.colomoto.biolqm.io.antlr.ITNETLexer

_sharedContextCache - Static variable in class org.colomoto.biolqm.io.antlr.ITNETParser

_sharedContextCache - Static variable in class org.colomoto.biolqm.io.antlr.MNetLexer

_sharedContextCache - Static variable in class org.colomoto.biolqm.io.antlr.MNetParser

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