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

A

AbstractDeterministicUpdater - Class in org.colomoto.biolqm.tool.simulation.updater

Base class to build updaters with a single successor.

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

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, LogicalModelFormat.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

AbstractModelModifierService - Class in org.colomoto.biolqm.modifier

A base class handling service discovery for model modifier services.

AbstractModelModifierService(String, String, String) - Constructor for class org.colomoto.biolqm.modifier.AbstractModelModifierService

Shared constructor for model modifier.

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

Base class for updaters which yield multiple successors.

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

AbstractPerturbation - Class in org.colomoto.biolqm.modifier.perturbation

Base class for Perturbations.

AbstractPerturbation() - Constructor for class org.colomoto.biolqm.modifier.perturbation.AbstractPerturbation

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.updater

Base class for random updaters.

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

AbstractTool<R,S> - Class in org.colomoto.biolqm.tool

Base class for the boring parts of tool declaration classes.

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

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

add(int[], boolean) - Method in class org.colomoto.biolqm.tool.simulation.updater.PriorityClasses

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_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

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"

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

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

addOutput(int) - Method in class org.colomoto.biolqm.io.avatar.AvatarClause

Adds the output value given the inputted restrictions

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

addRestriction(String, int) - Method in class org.colomoto.biolqm.io.avatar.AvatarClause

Adds a restriction

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

Add a state to the result of this simulation.

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

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

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

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 class org.colomoto.biolqm.modifier.perturbation.AbstractPerturbation

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

Apply the perturbation.

args - Variable in class org.colomoto.biolqm.LQMScriptLauncher

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

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

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

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

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

Create a new asynchronous updater.

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

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

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

AvatarClause - Class in org.colomoto.biolqm.io.avatar

Defines an Avatar clause (how the state of a component changes as a function of its regulators)

AvatarClause() - Constructor for class org.colomoto.biolqm.io.avatar.AvatarClause

AvatarLogicalModelException - Exception in org.colomoto.biolqm.io.avatar

Exception associated with the loading and exportation of Avatar files

AvatarLogicalModelException(String) - Constructor for exception org.colomoto.biolqm.io.avatar.AvatarLogicalModelException

Creates a new Avatar exception with a dedicated message

AvatarLogicalModelException(String, Throwable) - Constructor for exception org.colomoto.biolqm.io.avatar.AvatarLogicalModelException

Creates a new Avatar exception with a detail message and nested exception

AvatarUtils - Class in org.colomoto.biolqm.io.avatar

Facilities for the management of logical models for simulations

AvatarUtils() - Constructor for class org.colomoto.biolqm.io.avatar.AvatarUtils

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.

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

Base class for all updaters.

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

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

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

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

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

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

booleanize(LogicalModel) - Static method in class org.colomoto.biolqm.modifier.booleanize.Booleanizer

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

Construct a Boolean version of a multi-valued model.

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

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() - 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() - 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

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?

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

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

Does this format supports import operation?

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

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 interface org.colomoto.biolqm.LogicalModel

Make a copy of this model.

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

clone() - Method in class org.colomoto.biolqm.tool.simulation.updater.PriorityClasses

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.

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

Export logical model into cnet truth tables.

CNetExport() - 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

collapse(boolean) - Method in class org.colomoto.biolqm.tool.simulation.updater.PriorityClasses

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

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

Compare two logical models.

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

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

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

Create a new full updater.

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

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

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.

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

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

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

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

D

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

decPriority(int, int, int) - Method in class org.colomoto.biolqm.tool.simulation.updater.PriorityClasses

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

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

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

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

doGetResult() - Method in class org.colomoto.biolqm.tool.stablestate.StableStateSearcher

doGetResult() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceIdentifier

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

Placeholder for the actual implementation.

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

DontCare - Static variable in class org.colomoto.biolqm.tool.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.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().

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().

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().

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

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().

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().

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().

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().

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().

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

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().

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().

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().

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

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

equals(Object) - Method in class org.colomoto.biolqm.tool.simulation.updater.PriorityClasses

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().

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().

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().

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

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().

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().

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().

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().

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().

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

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().

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().

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().

export(LogicalModel, OutputStreamProvider) - Method in class org.colomoto.biolqm.io.AbstractFormat

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.AbstractFormat

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.bnet.BNetExport

Export a logical model into logical functions.

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.bnet.BNetFormat

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.booleannet.BooleanNetExport

Export a logical model into logical functions.

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.booleannet.BooleanNetFormat

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.boolsim.BoolSimExport

Export a logical model into logical functions.

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.boolsim.BoolSimFormat

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.cnet.CNetExport

Export a logical model into cnet truth tables.

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.cnet.CNetFormat

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.functions.BooleanFunctionExport

Export a logical model into logical functions.

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.functions.BooleanFunctionFormat

export(OutputStream) - Method in class org.colomoto.biolqm.io.ginml.AbstractGINMLWriter

Start the GINML export.

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.ginml.GINMLFormat

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.gna.GNAExport

Export a logical model into logical functions.

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.gna.GNAFormat

export(LogicalModel, OutputStreamProvider) - Method in interface org.colomoto.biolqm.io.LogicalModelFormat

Export a logical model to this format.

export(LogicalModel, OutputStreamProvider) - Method in class org.colomoto.biolqm.io.maboss.MaBoSSFormat

export(PNConfig, OutputStreamProvider) - Method in class org.colomoto.biolqm.io.petrinet.AbstractPNEncoder

export(LogicalModel, PNConfig, OutputStreamProvider) - Method in class org.colomoto.biolqm.io.petrinet.PNFormat

export(LogicalModel, OutputStreamProvider) - Method in class org.colomoto.biolqm.io.petrinet.PNFormat

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.pint.PintExport

Export a logical model into automata network transitions

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.pint.PintFormat

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.sbml.SBMLFormat

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

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.truthtable.TruthTableExport

Exports a logical model into a truth table.

export(LogicalModel, OutputStream) - Method in class org.colomoto.biolqm.io.truthtable.TruthTableFormat

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

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

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

Helper class to support extensions.

ExtensionLoader() - Constructor for class org.colomoto.biolqm.ExtensionLoader

F

fileWriter(String) - Method in class org.colomoto.biolqm.LQMScriptLauncher

Open a file for writing.

findNextRequiredNegation(int, byte[]) - Method in class org.colomoto.biolqm.tool.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.

flag - Variable in enum org.colomoto.biolqm.io.LogicalModelFormat.MultivaluedSupport

Formula - Class in org.colomoto.biolqm.tool.implicants

Formula(List<Term>) - Constructor for class org.colomoto.biolqm.tool.implicants.Formula

Formula(List<Term>, int[]) - Constructor for class org.colomoto.biolqm.tool.implicants.Formula

FUNC_DUAL - Static variable in class org.colomoto.biolqm.tool.inferinteraction.InteractionSearcher

FUNC_NEGATIVE - Static variable in class org.colomoto.biolqm.tool.inferinteraction.InteractionSearcher

FUNC_NON - Static variable in class org.colomoto.biolqm.tool.inferinteraction.InteractionSearcher

FUNC_POSITIVE - Static variable in class org.colomoto.biolqm.tool.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() - Method in class org.colomoto.biolqm.tool.stablestate.StableASP

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

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

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.

getChildrenWithSingleNode(int, int) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Creates a state where only a single component is initialized (others as -1)

getClass(int) - Method in class org.colomoto.biolqm.tool.simulation.updater.PriorityClasses

getClassLoader() - Static method in class org.colomoto.biolqm.ExtensionLoader

Retrieve a class loader covering the extensions.

getComponent(String) - Method in interface org.colomoto.biolqm.LogicalModel

Retrieve a component by name.

getComponent(String) - Method in class org.colomoto.biolqm.LogicalModelImpl

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

getConfig() - Method in class org.colomoto.biolqm.io.petrinet.PNFormat

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.modifier.AbstractModelModifierService

getDescription() - Method in interface org.colomoto.biolqm.modifier.ModelModifierService

Provide a brief description of parameters for the help message

getEmptySuccessors() - Static method in class org.colomoto.biolqm.tool.simulation.updater.AbstractMultipleSuccessorUpdater

getErrors() - Method in class org.colomoto.biolqm.io.antlr.ErrorListener

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

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

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

getFormat(String) - Method in class org.colomoto.biolqm.LQMScriptLauncher

Retrieve a format descriptor.

getFormat(String) - Static method in class org.colomoto.biolqm.LQMServiceManager

Get the format declaration for a given ID.

getFormat(Class<T>) - Static method in class org.colomoto.biolqm.LQMServiceManager

Get the format descriptor instance for a given class.

getFormats() - Static method in class org.colomoto.biolqm.LQMServiceManager

Get the available formats.

getFreeChildren(int) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Creates a state (int array) where components are initialized as -1

getFreeState(int) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Creates a state (byte array) where components are initialized as -1

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

getHelp() - Method in class org.colomoto.biolqm.tool.AbstractTool

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

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

get the ID of the format.

getID() - Method in class org.colomoto.biolqm.modifier.AbstractModelModifierService

getID() - Method in interface org.colomoto.biolqm.Service

get the ID of the service.

getID() - Method in class org.colomoto.biolqm.tool.AbstractTool

getIdentityChildren(int) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Creates an identity node array (e.g.

getInclusiontree() - 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.

getInitialstate() - Method in class org.colomoto.biolqm.io.petrinet.PNConfig

getInitialStates() - Method in interface org.colomoto.biolqm.StatefulLogicalModel

Gets the set of initial states defining a portion of the state-space

getInitialStates() - Method in class org.colomoto.biolqm.StatefulLogicalModelImpl

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.stablestate.StableStateTool

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.stablestate.StableStateSearcher

Convenience method to retrieve the MDDManager in which the result is stored.

getModel(Reader) - Static method in class org.colomoto.biolqm.io.bnet.BNetImport

Entry point to parse a full model.

getModel(Reader) - Static method in class org.colomoto.biolqm.io.booleannet.BooleanNetImport

Entry point to parse a full model.

getModel(Reader) - Static method in class org.colomoto.biolqm.io.boolsim.BoolSimImport

Entry point to parse a full model.

getModel(Reader) - Static method in class org.colomoto.biolqm.io.functions.BooleanFunctionImport

Entry point to parse a full model.

getModel() - Method in class org.colomoto.biolqm.io.sbml.SBMLqualImport

getModel(File) - Method in class org.colomoto.biolqm.io.truthtable.TruthTableImport

getModel() - Method in class org.colomoto.biolqm.modifier.booleanize.Booleanizer

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 interface org.colomoto.biolqm.tool.simulation.LogicalModelUpdater

getModel() - Method in class org.colomoto.biolqm.tool.simulation.updater.BaseUpdater

getModel() - Method in class org.colomoto.biolqm.tool.simulation.updater.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

getModifiedModel(LogicalModel, String) - Method in class org.colomoto.biolqm.modifier.AbstractModelModifierService

getModifiedModel(LogicalModel) - Method in class org.colomoto.biolqm.modifier.booleanize.ModelBooleanizerService

getModifiedModel() - Method in interface org.colomoto.biolqm.modifier.ModelModifier

Apply the modifier and retrieve the new model

getModifiedModel(LogicalModel, String) - Method in interface org.colomoto.biolqm.modifier.ModelModifierService

Setup a modifier and directly retrieve the modified model.

getModifiedModel() - Method in class org.colomoto.biolqm.modifier.perturbation.PerturbationModifier

getModifiedModel() - Method in class org.colomoto.biolqm.modifier.reduction.ReductionModifier

getModifiedModel() - Method in class org.colomoto.biolqm.modifier.reverse.ModelReverser

getModifiedModel(LogicalModel) - Method in class org.colomoto.biolqm.modifier.reverse.ModelReverserService

Shorthand to retrieve a modified model without requiring a parameter String.

getModifiedModel() - Method in class org.colomoto.biolqm.modifier.subspace.SubSpaceRestriction

getModifier(String) - Method in class org.colomoto.biolqm.LQMScriptLauncher

Retrieve a modifier service.

getModifier(String) - Static method in class org.colomoto.biolqm.LQMServiceManager

Get the service for a given ID.

getModifier(Class<T>) - Static method in class org.colomoto.biolqm.LQMServiceManager

Get the service instance for a given class.

getModifier(LogicalModel, String) - Method in class org.colomoto.biolqm.modifier.booleanize.ModelBooleanizerService

getModifier(LogicalModel) - Method in class org.colomoto.biolqm.modifier.booleanize.ModelBooleanizerService

getModifier(LogicalModel, String) - Method in interface org.colomoto.biolqm.modifier.ModelModifierService

Setup a new modifier object.

getModifier(LogicalModel, String) - Method in class org.colomoto.biolqm.modifier.perturbation.PerturbationService

getModifier(LogicalModel, String) - Method in class org.colomoto.biolqm.modifier.reduction.ModelReductionService

getModifier(LogicalModel, ReductionSettings) - Method in class org.colomoto.biolqm.modifier.reduction.ModelReductionService

getModifier(LogicalModel, String) - Method in class org.colomoto.biolqm.modifier.reverse.ModelReverserService

getModifier(LogicalModel) - Method in class org.colomoto.biolqm.modifier.reverse.ModelReverserService

Shorthand to retrieve a modifier without requiring a parameter String.

getModifier(LogicalModel, String) - Method in class org.colomoto.biolqm.modifier.subspace.SubSpaceService

getModifiers() - Static method in class org.colomoto.biolqm.LQMServiceManager

Get the available model modifier services.

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

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

Precise type of support for multivalued models.

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

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

Get a longer name for the format.

getName() - Method in class org.colomoto.biolqm.modifier.AbstractModelModifierService

getName() - Method in interface org.colomoto.biolqm.Service

Get a longer name for the service.

getName() - Method in interface org.colomoto.biolqm.StatefulLogicalModel

Returns the model's name (by default the associated filename)

getName() - Method in class org.colomoto.biolqm.StatefulLogicalModelImpl

getName() - Method in class org.colomoto.biolqm.tool.AbstractTool

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

getNodeInfo() - Method in interface org.colomoto.biolqm.NodeInfoHolder

Get the internal NodeInfo.

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

Deprecated.

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

Deprecated.

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

getNumVars() - Method in class org.colomoto.biolqm.tool.implicants.Term

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

getOracles() - Method in interface org.colomoto.biolqm.StatefulLogicalModel

Gets the stored oracles

getOracles() - Method in class org.colomoto.biolqm.StatefulLogicalModelImpl

getOutput() - Method in class org.colomoto.biolqm.io.avatar.AvatarClause

Returns the target state of the regulated component

getOutputStream() - Method in class org.colomoto.biolqm.io.OutputStreamProvider

Get a single stream.

getOutputStream(String) - Method in class org.colomoto.biolqm.io.OutputStreamProvider

Get a custom stream, specifying a pattern.

getPaths() - Method in class org.colomoto.biolqm.tool.stablestate.StableStateSearcher

Get the path (variable assignment) corresponding to stable states.

getPrimes(int, int) - Method in class org.colomoto.biolqm.tool.implicants.MDD2PrimeImplicants

Extract the prime implicants from a MDD-represented function.

getProcessBuilder(String...) - Method in class org.colomoto.biolqm.HelperTool

getProgram() - Method in class org.colomoto.biolqm.tool.stablestate.StableASP

getQualBundle() - Method in class org.colomoto.biolqm.io.sbml.SBMLqualImport

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.tool.implicants.ImplicantSearcher

getRegulatorList() - Method in class org.colomoto.biolqm.tool.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.tool.implicants.ImplicantSearcher

getRegulators() - Method in class org.colomoto.biolqm.tool.implicants.RestrictedPathSearcher

Retrieve the list of regulators on which this searcher is restricted.

getRestrictions() - Method in class org.colomoto.biolqm.io.avatar.AvatarClause

Returns the list of restrictions imposing a well-defined state in the current component

getResult(LogicalModel) - Method in class org.colomoto.biolqm.tool.AbstractTool

getResult(LogicalModel, String) - Method in class org.colomoto.biolqm.tool.AbstractTool

getResult(LogicalModel, String...) - Method in class org.colomoto.biolqm.tool.AbstractTool

getResult(LogicalModel, Object) - Method in class org.colomoto.biolqm.tool.attractor.AttractorTool

getResult(LogicalModel, S) - Method in interface org.colomoto.biolqm.tool.LogicalModelTool

Get the analysis result with a custom setting.

getResult(LogicalModel) - Method in interface org.colomoto.biolqm.tool.LogicalModelTool

Get the analysis result.

getResult(LogicalModel, String) - Method in interface org.colomoto.biolqm.tool.LogicalModelTool

Get the analysis result.

getResult(LogicalModel, String...) - Method in interface org.colomoto.biolqm.tool.LogicalModelTool

Get the analysis result.

getResult(LogicalModel, Object) - Method in class org.colomoto.biolqm.tool.stablestate.StableJBDD

getResult(LogicalModel, StableStateMethod) - Method in class org.colomoto.biolqm.tool.stablestate.StableStateTool

getResult(LogicalModel, TrapSpaceSettings) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTool

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

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

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

getSettings() - Method in class org.colomoto.biolqm.modifier.reduction.ModelReductionService

getSettings(String) - Method in class org.colomoto.biolqm.modifier.reduction.ModelReductionService

getSettings() - Method in class org.colomoto.biolqm.tool.AbstractTool

getSettings(String) - Method in class org.colomoto.biolqm.tool.AbstractTool

getSettings(String...) - Method in class org.colomoto.biolqm.tool.AbstractTool

getSettings() - Method in interface org.colomoto.biolqm.tool.LogicalModelTool

Construct a default setting object.

getSettings(String) - Method in interface org.colomoto.biolqm.tool.LogicalModelTool

Construct a default setting object.

getSettings(String...) - Method in interface org.colomoto.biolqm.tool.LogicalModelTool

Construct a default setting object.

getSettings(String...) - Method in class org.colomoto.biolqm.tool.stablestate.StableStateTool

getSettings(String[]) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTool

getSingleSuccessors(byte[]) - Static method in class org.colomoto.biolqm.tool.simulation.updater.AbstractMultipleSuccessorUpdater

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

getStable(MDDManager, int, int, MDDVariable) - Method in class org.colomoto.biolqm.tool.stablestate.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.

getSuccessor(byte[]) - Method in interface org.colomoto.biolqm.tool.simulation.DeterministicUpdater

Get the successor of a state state.

getSuccessor(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.updater.BlockSequentialUpdater

getSuccessor(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.updater.SequentialUpdater

getSuccessor(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.updater.SynchronousUpdater

getSuccessors(byte[]) - Method in interface org.colomoto.biolqm.tool.simulation.MultipleSuccessorsUpdater

Get all successors for a given state.

getSuccessors(List<byte[]>) - Static method in class org.colomoto.biolqm.tool.simulation.updater.AbstractMultipleSuccessorUpdater

getSuccessors(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.updater.AsynchronousUpdater

getSuccessors(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.updater.CompleteUpdater

getSuccessors(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.updater.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, TrapSpaceSettings) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTool

getTerms() - Method in class org.colomoto.biolqm.tool.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.

getTool(String) - Method in class org.colomoto.biolqm.LQMScriptLauncher

Retrieve a tool service.

getTool(String) - Static method in class org.colomoto.biolqm.LQMServiceManager

Get the tool declaration for a given ID.

getTool(Class<T>) - Static method in class org.colomoto.biolqm.LQMServiceManager

Get the tool service instance for a given class.

getTools() - Static method in class org.colomoto.biolqm.LQMServiceManager

Get the available tools.

getVarsValue(int) - Method in class org.colomoto.biolqm.tool.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

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.stablestate.JBDDModel

globalAsynchronousFunction() - Method in class org.colomoto.biolqm.tool.stablestate.JBDDModel

globalFunctions() - Method in class org.colomoto.biolqm.tool.stablestate.JBDDModel

globalStable() - Method in class org.colomoto.biolqm.tool.stablestate.JBDDModel

globalSynchronousFunction() - Method in class org.colomoto.biolqm.tool.stablestate.JBDDModel

GNAExport - Class in org.colomoto.biolqm.io.gna

Exports a logical model into the non-xml GNA format.

GNAExport() - 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

H

handle(ClingoResult) - Method in interface org.colomoto.biolqm.helper.clingo.ClingoResultHandler

handle(ClingoResult) - Method in class org.colomoto.biolqm.tool.stablestate.StableASP

handle(ClingoResult) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverASP

handleDuplicates - Variable in class org.colomoto.biolqm.modifier.reduction.ReductionSettings

handleFixed - Variable in class org.colomoto.biolqm.modifier.reduction.ReductionSettings

handleOutputs - Variable in class org.colomoto.biolqm.modifier.reduction.ReductionSettings

hasErrors() - Method in class org.colomoto.biolqm.io.antlr.ErrorListener

hashCode() - Method in class org.colomoto.biolqm.tool.implicants.Term

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

hasReduction() - Method in class org.colomoto.biolqm.modifier.reduction.ReductionSettings

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

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

HELP_LINE - Static variable in class org.colomoto.biolqm.tool.stablestate.StableStateTool

HELP_LINE - Static variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTool

HELP_MESSAGE - Static variable in class org.colomoto.biolqm.tool.stablestate.StableStateTool

HELP_MESSAGE - Static variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTool

HelperTool - Class in org.colomoto.biolqm

Locate and call external tools.

HelperTool(String) - Constructor for class org.colomoto.biolqm.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.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.modifier.booleanize.ModelBooleanizerService

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.ModelReductionService

The identifier used to retrieve this service by name

ID - Static variable in class org.colomoto.biolqm.modifier.reverse.ModelReverserService

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

ImplicantSearcher - Class in org.colomoto.biolqm.tool.implicants

Restrict the paths given by a PathSearcher to the list of actual regulators

ImplicantSearcher(MDDManager, int) - Constructor for class org.colomoto.biolqm.tool.implicants.ImplicantSearcher

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

importFile(File) - Method in class org.colomoto.biolqm.io.bnet.BNetFormat

importFile(File) - Method in class org.colomoto.biolqm.io.booleannet.BooleanNetFormat

importFile(File) - Method in class org.colomoto.biolqm.io.boolsim.BoolSimFormat

importFile(File) - Method in class org.colomoto.biolqm.io.functions.BooleanFunctionFormat

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

Import a file in this format and build a logical model for it.

importFile(File) - Method in class org.colomoto.biolqm.io.sbml.SBMLFormat

importFile(File) - Method in class org.colomoto.biolqm.io.truthtable.TruthTableFormat

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

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

incPriority(int, int, int) - Method in class org.colomoto.biolqm.tool.simulation.updater.PriorityClasses

initialStates - Variable in class org.colomoto.biolqm.StatefulLogicalModelImpl

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.tool.inferinteraction

Extract detailed interactions from a logical model.

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

isAvailable() - Static method in class org.colomoto.biolqm.helper.clingo.ClingoLauncher

isAvailable() - Method in class org.colomoto.biolqm.HelperTool

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

Check if this model is Boolean.

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

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

isSync(int) - Method in class org.colomoto.biolqm.tool.simulation.updater.PriorityClasses

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, "_" or "-" characters)

iterator() - Method in class org.colomoto.biolqm.tool.implicants.ImplicantSearcher

iterator() - Method in class org.colomoto.biolqm.tool.implicants.RestrictedPathSearcher

iterator() - Method in class org.colomoto.biolqm.tool.simulation.SingleSuccessorSimulation

iterator() - Method in class org.colomoto.biolqm.tool.stablestate.StructuralNodeOrderer

J

JBDDModel - Class in org.colomoto.biolqm.tool.stablestate

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

L

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

length - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpace

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

load_instances(Class<T>) - Static method in class org.colomoto.biolqm.ExtensionLoader

Discover and load a list of services.

loadEngine(String) - Static method in class org.colomoto.biolqm.LQMScriptLauncher

Detect and load script engines

loadExtensions(String, Class<?>) - Static method in class org.colomoto.biolqm.ExtensionLoader

Trigger the loading of extensions.

loadFile(File) - Static method in class org.colomoto.biolqm.io.sbml.SBMLqualHelper

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

Load a model from file.

loadModel(String) - Method in class org.colomoto.biolqm.LQMScriptLauncher

Load a model guessing the format.

loadModel(String, String) - Method in class org.colomoto.biolqm.LQMScriptLauncher

Load a model from a file.

loadModel() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceIdentifier

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.

LogicalModelFormat.MultivaluedSupport - Enum in org.colomoto.biolqm.io

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.

LogicalModelTool<R,S> - Interface in org.colomoto.biolqm.tool

Simple tool description interface.

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

LQMScriptLauncher - Class in org.colomoto.biolqm

Wrap common API to provide convenient access in scripts.

LQMScriptLauncher(String[]) - Constructor for class org.colomoto.biolqm.LQMScriptLauncher

Create a scripting environment with access to the command line arguments

LQMServiceManager - Class in org.colomoto.biolqm

Static service manager: list available "services" in LQM: formats modifiers

LQMServiceManager() - Constructor for class org.colomoto.biolqm.LQMServiceManager

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.LQMLauncher

The main entry point.

main(String[]) - Static method in class org.colomoto.biolqm.tool.implicants.Formula

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

MDD2PrimeImplicants - Class in org.colomoto.biolqm.tool.implicants

MDD2PrimeImplicants(MDDManager) - Constructor for class org.colomoto.biolqm.tool.implicants.MDD2PrimeImplicants

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

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

model - Variable in class org.colomoto.biolqm.tool.simulation.updater.BaseUpdater

model - Variable in class org.colomoto.biolqm.tool.stablestate.StructuralNodeOrderer

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

A service for model booleanization.

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

Public constructor which should only be used for service discovery.

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

ModelModifier - Interface in org.colomoto.biolqm.modifier

Generic interface for modifications of 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

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

Orchestrator for model reduction tools

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

Public constructor which should only be used for service discovery.

ModelReverser - Class in org.colomoto.biolqm.modifier.reverse

Wrap ReverseOperation to properly create a new model capable of generating the reverse dynamics.

ModelReverser(LogicalModel) - Constructor for class org.colomoto.biolqm.modifier.reverse.ModelReverser

Prepare a Model modifier for model reversal.

ModelReverserService - Class in org.colomoto.biolqm.modifier.reverse

Wrap the reverser code into the ModelModifier interface.

ModelReverserService() - Constructor for class org.colomoto.biolqm.modifier.reverse.ModelReverserService

Public constructor which should only be used for service discovery.

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

modifyModel(LogicalModel, String) - Method in class org.colomoto.biolqm.LQMScriptLauncher

Construct a modified model.

modifyModel(LogicalModel, String, String) - Method in class org.colomoto.biolqm.LQMScriptLauncher

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

Common structure for simulations with updaters yielding multiple successors.

MultipleSuccessorSimulation(MultipleSuccessorsUpdater) - Constructor for class org.colomoto.biolqm.tool.simulation.MultipleSuccessorSimulation

MultipleSuccessorSimulation(MultipleSuccessorsUpdater, SimulationStrategy) - Constructor for class org.colomoto.biolqm.tool.simulation.MultipleSuccessorSimulation

MultipleSuccessorsUpdater - Interface in org.colomoto.biolqm.tool.simulation

Updaters which can yield multiple successors for a single state.

N

name - Variable in class org.colomoto.biolqm.StatefulLogicalModelImpl

negatePrimes() - Method in class org.colomoto.biolqm.tool.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

nextState - Variable in class org.colomoto.biolqm.tool.simulation.updater.AbstractMultipleSuccessorUpdater

nfree - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpace

nodeChange(byte[], int) - Method in class org.colomoto.biolqm.tool.simulation.updater.BaseUpdater

Test if a component is ready to change its state.

NodeInfo - Class in org.colomoto.biolqm

Contains the basic informations of a regulatory node (gene) : - nodeID : a unique identifier for the gene - max : the maximal regulatory level

NodeInfo(String) - Constructor for class org.colomoto.biolqm.NodeInfo

NodeInfo(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.stablestate.StableStateList

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

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

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

oracles - Variable in class org.colomoto.biolqm.StatefulLogicalModelImpl

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

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.clingo - package org.colomoto.biolqm.helper.clingo

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

org.colomoto.biolqm.io.avatar - package org.colomoto.biolqm.io.avatar

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.maboss - package org.colomoto.biolqm.io.maboss

The format used by MaBoSS - https://maboss.curie.fr/

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

org.colomoto.biolqm.modifier.booleanize - package org.colomoto.biolqm.modifier.booleanize

Construct Boolean versions of Multi-valued models

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.subspace - package org.colomoto.biolqm.modifier.subspace

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.implicants - package org.colomoto.biolqm.tool.implicants

org.colomoto.biolqm.tool.inferinteraction - package org.colomoto.biolqm.tool.inferinteraction

Infer interactions and their signs from 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.updater - package org.colomoto.biolqm.tool.simulation.updater

Implementation of updating schemes: update the state of a model (i.e.

org.colomoto.biolqm.tool.stablestate - package org.colomoto.biolqm.tool.stablestate

Identification of the stable states of a logical model.

org.colomoto.biolqm.tool.trapspaces - package org.colomoto.biolqm.tool.trapspaces

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.

OutputStreamProvider - Class in org.colomoto.biolqm.io

Provide OutputStream objects to export filters.

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

OutputStreamProvider(File) - Constructor for class org.colomoto.biolqm.io.OutputStreamProvider

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

P

parseFile(File) - Static method in class org.colomoto.biolqm.io.sbml.SBMLqualHelper

parseInputStream(InputStream) - Static method in class org.colomoto.biolqm.io.sbml.SBMLqualHelper

pattern - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpace

percolate - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSettings

percolated - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpace

PerturbationModifier - Class in org.colomoto.biolqm.modifier.perturbation

PerturbationModifier(LogicalModel, LogicalModelPerturbation) - 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.

pickSuccessor(byte[]) - Method in interface org.colomoto.biolqm.tool.simulation.RandomUpdater

Get the successor of a state state.

pickSuccessor(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.updater.RandomUpdaterWithRates

pickSuccessor(byte[]) - Method in class org.colomoto.biolqm.tool.simulation.updater.RandomUpdaterWrapper

PintExport - Class in org.colomoto.biolqm.io.pint

Export logical model into the Pint format.

PintExport() - 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

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

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

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

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

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

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.Booleanizer

Ensure that a booleanized model has no transition leading to forbidden states.

print() - Method in class org.colomoto.biolqm.tool.stablestate.JBDDModel

PriorityClasses - Class in org.colomoto.biolqm.tool.simulation.updater

Internal representation of a set of priority classes.

PriorityClasses() - Constructor for class org.colomoto.biolqm.tool.simulation.updater.PriorityClasses

PriorityUpdater - Class in org.colomoto.biolqm.tool.simulation.updater

Draft for a priority updater: components are grouped in groups, which can be updated synchronously or asynchronously.

PriorityUpdater(LogicalModel, PriorityClasses) - Constructor for class org.colomoto.biolqm.tool.simulation.updater.PriorityUpdater

purgeFixed - Variable in class org.colomoto.biolqm.modifier.reduction.ReductionSettings

Q

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

R

random - Variable in class org.colomoto.biolqm.tool.simulation.updater.AbstractRandomUpdater

RandomUpdater - Interface in org.colomoto.biolqm.tool.simulation

Interface for random (stochastic) updaters.

RandomUpdaterWithRates - Class in org.colomoto.biolqm.tool.simulation.updater

Updater picking a random successor in the asynchronous scheme, with optional rates.

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

Create a new random updater

RandomUpdaterWithRates(LogicalModel, double[]) - Constructor for class org.colomoto.biolqm.tool.simulation.updater.RandomUpdaterWithRates

RandomUpdaterWrapper - Class in org.colomoto.biolqm.tool.simulation.updater

Random updater which wraps a MultipleSuccessorUpdater and picks one of the successors.

RandomUpdaterWrapper(MultipleSuccessorsUpdater) - Constructor for class org.colomoto.biolqm.tool.simulation.updater.RandomUpdaterWrapper

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

read(Reader) - Static method in class org.colomoto.biolqm.tool.implicants.Formula

read(Reader) - Static method in class org.colomoto.biolqm.tool.implicants.Term

readintArray(int[][]) - Static method in class org.colomoto.biolqm.tool.implicants.Formula

readintArray(int[]) - Static method in class org.colomoto.biolqm.tool.implicants.Term

reduce - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSettings

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.tool.implicants.Formula

reduceToPrimeImplicants() - Method in class org.colomoto.biolqm.tool.implicants.Formula

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

ReductionModifier(LogicalModel, ReductionSettings) - Constructor for class org.colomoto.biolqm.modifier.reduction.ReductionModifier

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

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

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

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.tool.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.

removeDuplicateComponents(LogicalModel) - Static method in class org.colomoto.biolqm.modifier.reduction.DuplicateRemover

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

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.tool.implicants

Restrict the paths given by a PathSearcher to the list of actual regulators

RestrictedPathSearcher(MDDManager) - Constructor for class org.colomoto.biolqm.tool.implicants.RestrictedPathSearcher

RestrictedPathSearcher(MDDManager, int) - Constructor for class org.colomoto.biolqm.tool.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() - Method in class org.colomoto.biolqm.modifier.reverse.ModelReverser

Reverse the dynamics of all variables.

reverse(MDDVariable, int) - Method in class org.colomoto.biolqm.modifier.reverse.ReverseOperation

Reverse a node.

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

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

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

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

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

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_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

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

run() - Method in class org.colomoto.biolqm.helper.clingo.ClingoLauncher

run(LogicalModel, String...) - Method in class org.colomoto.biolqm.tool.attractor.AttractorTool

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

run() - Method in class org.colomoto.biolqm.tool.inferinteraction.InteractionSearcher

run(LogicalModel, String...) - Method in interface org.colomoto.biolqm.tool.LogicalModelTool

Run the tool on a logical model.

run(LogicalModel, String...) - Method in class org.colomoto.biolqm.tool.stablestate.StableJBDD

run(LogicalModel, String...) - Method in class org.colomoto.biolqm.tool.stablestate.StableStateTool

run(LogicalModel, String...) - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTool

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

runCLI() - Method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceIdentifier

runSimulation(Iterator<byte[]>) - Method in class org.colomoto.biolqm.tool.simulation.MultipleSuccessorSimulation

runSimulation() - Method in class org.colomoto.biolqm.tool.simulation.MultipleSuccessorSimulation

S

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

saveModel(LogicalModel, String, String) - Static method in class org.colomoto.biolqm.LQMLauncher

Save a model to file

saveModel(LogicalModel, String, String) - Method in class org.colomoto.biolqm.LQMScriptLauncher

Save a model to a 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

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(InputStream) - Constructor for class org.colomoto.biolqm.io.sbml.SBMLqualImport

SBMLqualImport(File) - Constructor for class org.colomoto.biolqm.io.sbml.SBMLqualImport

selectAttractors(List<TrapSpace>) - Static method in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceIdentifier

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

SequentialUpdater - Class in org.colomoto.biolqm.tool.simulation.updater

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.updater.SequentialUpdater

Create a new sequential updater, using the default order

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

Create a new sequential updater, using a custom order

Service - Interface in org.colomoto.biolqm

Simple service description interface.

setBooleanizedGroup(NodeInfo[]) - Method in class org.colomoto.biolqm.NodeInfo

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.PNConfig

setInitialStates(List<byte[]>) - Method in interface org.colomoto.biolqm.StatefulLogicalModel

Changes the set of initial states

setInitialStates(List<byte[]>) - Method in class org.colomoto.biolqm.StatefulLogicalModelImpl

setInput(boolean) - Method in class org.colomoto.biolqm.NodeInfo

setMax(byte) - Method in class org.colomoto.biolqm.NodeInfo

setNode(int) - Method in class org.colomoto.biolqm.tool.implicants.ImplicantSearcher

setNode(int) - Method in class org.colomoto.biolqm.tool.implicants.RestrictedPathSearcher

setNodeID(String) - Method in class org.colomoto.biolqm.NodeInfo

setOracles(List<List<byte[]>>) - Method in interface org.colomoto.biolqm.StatefulLogicalModel

Stores a set of oracles within the model

setOracles(List<List<byte[]>>) - Method in class org.colomoto.biolqm.StatefulLogicalModelImpl

setSeed(long) - Method in interface org.colomoto.biolqm.tool.simulation.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.updater.AbstractRandomUpdater

setSeed(long) - Method in class org.colomoto.biolqm.tool.simulation.updater.RandomUpdaterWrapper

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

showasp - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSettings

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

SimulationStrategy - Enum in org.colomoto.biolqm.tool.simulation

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

A simple simulation engine for updaters with a single successor.

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

SingleSuccessorUpdater - Interface in org.colomoto.biolqm.tool.simulation

General definition of updating methods returning a single successor.

size - Variable in class org.colomoto.biolqm.tool.simulation.updater.BaseUpdater

size() - Method in class org.colomoto.biolqm.tool.simulation.updater.PriorityClasses

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

split(int, int) - Method in class org.colomoto.biolqm.tool.simulation.updater.PriorityClasses

stable() - Method in class org.colomoto.biolqm.tool.stablestate.JBDDModel

StableASP - Class in org.colomoto.biolqm.tool.stablestate

Use the clingo ASP solver to assemble the stability constraints and identify stable states.

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

StableJBDD - Class in org.colomoto.biolqm.tool.stablestate

StableJBDD() - Constructor for class org.colomoto.biolqm.tool.stablestate.StableJBDD

StableOperation - Class in org.colomoto.biolqm.tool.stablestate

MDD operation used to build a stability condition.

StableOperation() - Constructor for class org.colomoto.biolqm.tool.stablestate.StableOperation

StableStateList - Class in org.colomoto.biolqm.tool.stablestate

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

StableStateMethod - Enum in org.colomoto.biolqm.tool.stablestate

StableStateSearcher - Class in org.colomoto.biolqm.tool.stablestate

Perform a stable state search for a given model.

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

Create a new stable state searcher.

StableStateTool - Class in org.colomoto.biolqm.tool.stablestate

StableStateTool() - Constructor for class org.colomoto.biolqm.tool.stablestate.StableStateTool

state - Variable in class org.colomoto.biolqm.tool.simulation.updater.AbstractMultipleSuccessorUpdater

StatefulLogicalModel - Interface in org.colomoto.biolqm

Extension of a logical model with the possibility to store initial states and oracles

StatefulLogicalModelImpl - Class in org.colomoto.biolqm

Extension of a logical model with the possibility to maintain a set of initial states and oracles.
Implements the StatefulLogicalModel interface.

StatefulLogicalModelImpl(MDDManager, List<NodeInfo>, int[], List<NodeInfo>, int[], List<byte[]>, String) - Constructor for class org.colomoto.biolqm.StatefulLogicalModelImpl

Creates a stateful logical model based on a MDD

StatefulLogicalModelImpl(List<NodeInfo>, MDDManager, int[], List<byte[]>, String) - Constructor for class org.colomoto.biolqm.StatefulLogicalModelImpl

Creates a stateful logical model based on a MDD

StatefulLogicalModelImpl(LogicalModel, List<byte[]>) - Constructor for class org.colomoto.biolqm.StatefulLogicalModelImpl

Creates a stateful logical model based on an existing logical model

StructuralNodeOrderer - Class in org.colomoto.biolqm.tool.stablestate

Sort nodes of a LogicalModel according to the new regulators they introduce.

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

SubSpaceRestriction - Class in org.colomoto.biolqm.modifier.subspace

Model Modifier to restrict a model into a subspace.

SubSpaceRestriction(LogicalModel, byte[]) - Constructor for class org.colomoto.biolqm.modifier.subspace.SubSpaceRestriction

SubSpaceService - Class in org.colomoto.biolqm.modifier.subspace

Modifier Service for subspace restriction

SubSpaceService() - Constructor for class org.colomoto.biolqm.modifier.subspace.SubSpaceService

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

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

Deprecated.

supportsMultivalued() - Method in class org.colomoto.biolqm.tool.AbstractTool

supportsMultivalued() - Method in interface org.colomoto.biolqm.tool.LogicalModelTool

Does this tool handle multivalued models?

SynchronousUpdater - Class in org.colomoto.biolqm.tool.simulation.updater

Updater for the synchronous scheme: all possible changes are applied in a single successor

SynchronousUpdater(LogicalModel) - Constructor for class org.colomoto.biolqm.tool.simulation.updater.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__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__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__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__4 - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

T__4 - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

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__6 - Static variable in class org.colomoto.biolqm.io.antlr.BNetLexer

T__6 - Static variable in class org.colomoto.biolqm.io.antlr.BNetParser

target - Variable in class org.colomoto.biolqm.modifier.perturbation.InteractionPerturbation

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.tool.implicants

Term(byte[]) - Constructor for class org.colomoto.biolqm.tool.implicants.Term

terminal - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceList

terminal - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSettings

toArray(List<Integer>) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Converts a list of integers to an array

toArray() - Method in class org.colomoto.biolqm.tool.implicants.Formula

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

ask to store the next calls into a string buffer.

toByteArray(int[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Converts an integer array to a byte array

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.

toOpenString(byte[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

toString() - Method in class org.colomoto.biolqm.helper.clingo.ClingoResult

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

toString() - Method in class org.colomoto.biolqm.io.avatar.AvatarClause

toString(List<byte[]>) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

List of states to string

toString(byte[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Byte array to string

toString(int[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Integer array to string

toString(long[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Long array to string

toString(BigInteger[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

BigInteger array to string

toString(double[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Double array to string

toString(String[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

String array to string

toString(boolean[]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Boolean array to string

toString(int[][]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Integer matrix to string

toString(double[][]) - Static method in class org.colomoto.biolqm.io.avatar.AvatarUtils

Double matrix to string

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.StatefulLogicalModelImpl

toString() - Method in class org.colomoto.biolqm.tool.AbstractTool

toString() - Method in class org.colomoto.biolqm.tool.implicants.Formula

toString() - Method in class org.colomoto.biolqm.tool.implicants.Term

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

transform(int, int) - Method in class org.colomoto.biolqm.modifier.booleanize.Booleanizer

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

TrapSpaceIdentifier - Class in org.colomoto.biolqm.tool.trapspaces

TrapSpaceIdentifier(LogicalModel, TrapSpaceSettings) - Constructor for class org.colomoto.biolqm.tool.trapspaces.TrapSpaceIdentifier

TrapSpaceList - Class in org.colomoto.biolqm.tool.trapspaces

TrapSpaceList(TrapSpaceSettings, LogicalModel) - Constructor for class org.colomoto.biolqm.tool.trapspaces.TrapSpaceList

TrapSpaceSettings - Class in org.colomoto.biolqm.tool.trapspaces

TrapSpaceSettings() - Constructor for class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSettings

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, TrapSpaceSettings) - Constructor for class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverASP

TrapSpaceSolverBDD - Class in org.colomoto.biolqm.tool.trapspaces

Use BDDs to identify trapspaces.

TrapSpaceSolverBDD(LogicalModel, TrapSpaceSettings) - Constructor for class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverBDD

TrapSpaceTool - Class in org.colomoto.biolqm.tool.trapspaces

TrapSpaceTool() - Constructor for class org.colomoto.biolqm.tool.trapspaces.TrapSpaceTool

tree - Variable in class org.colomoto.biolqm.tool.trapspaces.TrapSpaceSettings

TruthTableExport - Class in org.colomoto.biolqm.io.truthtable

Exports a logical model into the Truth Table format.

TruthTableExport() - 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

U

UNDEFINED_MAX - Static variable in class org.colomoto.biolqm.NodeInfo

unsplit(int, int, int) - Method in class org.colomoto.biolqm.tool.simulation.updater.PriorityClasses

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.updater.BaseUpdater

Create or update the next state.

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

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

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 - 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.io.LogicalModelFormat.MultivaluedSupport

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.colomoto.biolqm.tool.simulation.SimulationStrategy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.colomoto.biolqm.tool.stablestate.StableStateMethod

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.io.LogicalModelFormat.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.simulation.SimulationStrategy

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.stablestate.StableStateMethod

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

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

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

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

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

W

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

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

X

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.

_

_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

_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

_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

_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

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