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

A

abs - Variable in class org.w3._1998.math.mathml.Apply

active - Variable in class org.sbml._2001.ns.celldesigner.Region

activity - Variable in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

activity - Variable in class org.sbml._2001.ns.celldesigner.SpeciesAlias

addAdditionalProducts(ReactionWrapper, Process) - Method in class fr.curie.cd2sbgnml.model.GenericReactionModel

addAdditionalReactants(ReactionWrapper, Process) - Method in class fr.curie.cd2sbgnml.model.GenericReactionModel

addModifiers(ReactionWrapper, Process) - Method in class fr.curie.cd2sbgnml.model.GenericReactionModel

AlgebraicRule - Class in org.sbml.sbml.level2.version4

Java class for AlgebraicRule complex type.

AlgebraicRule() - Constructor for class org.sbml.sbml.level2.version4.AlgebraicRule

algebraicRuleOrAssignmentRuleOrRateRule - Variable in class org.sbml.sbml.level2.version4.OriginalModel.ListOfRules

alias - Variable in class org.sbml._2001.ns.celldesigner.BaseProduct

alias - Variable in class org.sbml._2001.ns.celldesigner.BaseReactant

alias - Variable in class org.sbml._2001.ns.celldesigner.LinkTarget

alias - Variable in class org.sbml._2001.ns.celldesigner.ProductLink

alias - Variable in class org.sbml._2001.ns.celldesigner.ReactantLink

alias - Variable in class org.sbml._2001.ns.celldesigner.SpeciesReferenceAnnotationType.Extension

aliases - Variable in class org.sbml._2001.ns.celldesigner.Modification

AliasInfoWrapper - Class in fr.curie.cd2sbgnml.xmlcdwrappers

AliasInfoWrapper() - Constructor for class fr.curie.cd2sbgnml.xmlcdwrappers.AliasInfoWrapper

AliasInfoWrapper(float, String, String) - Constructor for class fr.curie.cd2sbgnml.xmlcdwrappers.AliasInfoWrapper

AliasWrapper - Class in fr.curie.cd2sbgnml.xmlcdwrappers

Wraps speciesAlias and complexSpeciesAlias xml entities as they have a lot in common.

AliasWrapper(String, AliasWrapper.AliasType, SpeciesWrapper) - Constructor for class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

AliasWrapper(SpeciesAlias, SpeciesWrapper) - Constructor for class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

Parse speciesAlias from CellDesigner file.

AliasWrapper(ComplexSpeciesAlias, SpeciesWrapper) - Constructor for class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

Parse complexSpeciesAlias from CellDesigner file.

AliasWrapper.AliasType - Enum in fr.curie.cd2sbgnml.xmlcdwrappers

The different aliases possible.

AnchorPoint - Enum in fr.curie.cd2sbgnml.graphics

The possible anchor points as defined by CellDesigner (except the CENTER value that is implicit in CellDesigner if no anchor point is defined, or sometimes when it is set to INACTIVE).

and - Variable in class org.w3._1998.math.mathml.Apply

angle(Point2D, Point2D) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

return the signed angle in radian between 2 vectors at origin

angle(Point2D) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

return angle from origin

angle - Variable in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasInfoWrapper

angle - Variable in class fr.curie.cd2sbgnml.xmlcdwrappers.ResidueWrapper

angle - Variable in class org.sbml._2001.ns.celldesigner.BindingRegion

angle - Variable in class org.sbml._2001.ns.celldesigner.Info

angle - Variable in class org.sbml._2001.ns.celldesigner.ModificationResidue

angle - Variable in class org.sbml._2001.ns.celldesigner.StructuralStateAngle

annotation - Variable in class org.sbml._2001.ns.celldesigner.Species

Annotation() - Constructor for class org.sbml._2001.ns.celldesigner.Species.Annotation

annotation - Variable in class org.sbml.sbml.level2.version4.Compartment

annotation - Variable in class org.sbml.sbml.level2.version4.Model

annotation - Variable in class org.sbml.sbml.level2.version4.ModifierSpeciesReference

annotation - Variable in class org.sbml.sbml.level2.version4.Reaction

annotation - Variable in class org.sbml.sbml.level2.version4.Species

annotation - Variable in class org.sbml.sbml.level2.version4.SpeciesReference

Annotation - Class in org.w3._1998.math.mathml

Java class for Annotation complex type.

Annotation() - Constructor for class org.w3._1998.math.mathml.Annotation

annotationOrAnnotationXml - Variable in class org.w3._1998.math.mathml.Semantics

AnnotationXml - Class in org.w3._1998.math.mathml

Java class for Annotation-xml complex type.

AnnotationXml() - Constructor for class org.w3._1998.math.mathml.AnnotationXml

AntisenseRNA - Class in org.sbml._2001.ns.celldesigner

For antisense RNA.

AntisenseRNA() - Constructor for class org.sbml._2001.ns.celldesigner.AntisenseRNA

antisenseRNA - Variable in class org.sbml._2001.ns.celldesigner.ListOfAntisenseRNAs

antisensernaReference - Variable in class org.sbml._2001.ns.celldesigner.SpeciesIdentity

any - Variable in class org.sbml._2001.ns.celldesigner.CompartmentAnnotationType

any - Variable in class org.sbml._2001.ns.celldesigner.ModelAnnotationType

any - Variable in class org.sbml._2001.ns.celldesigner.Notes

any - Variable in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType

any - Variable in class org.sbml._2001.ns.celldesigner.SpeciesAnnotationType

any - Variable in class org.sbml._2001.ns.celldesigner.SpeciesReferenceAnnotationType

any - Variable in class org.sbml.sbml.level2.version4.SBase.Notes

any - Variable in class org.w3._1998.math.mathml.AnnotationXml

App - Class in fr.curie.cd2sbgnml

App() - Constructor for class fr.curie.cd2sbgnml.App

App.ConvertionChoice - Enum in fr.curie.cd2sbgnml

This enum describes the 2 possible directions of convertion.

App.TextOutputStream - Class in fr.curie.cd2sbgnml

Apply - Class in org.w3._1998.math.mathml

Java class for Apply complex type.

Apply() - Constructor for class org.w3._1998.math.mathml.Apply

apply - Variable in class org.w3._1998.math.mathml.Lambda

apply - Variable in class org.w3._1998.math.mathml.Math

apply - Variable in class org.w3._1998.math.mathml.NodeContainer

apply - Variable in class org.w3._1998.math.mathml.Otherwise

apply - Variable in class org.w3._1998.math.mathml.Semantics

applyCorrection(List<Point2D.Float>, float, float) - Static method in class fr.curie.cd2sbgnml.SBGNML2CD

Apply correcting factor inplace to a the coordinates of a list of points

arccos - Variable in class org.w3._1998.math.mathml.Apply

arccosh - Variable in class org.w3._1998.math.mathml.Apply

arccot - Variable in class org.w3._1998.math.mathml.Apply

arccoth - Variable in class org.w3._1998.math.mathml.Apply

arccsc - Variable in class org.w3._1998.math.mathml.Apply

arccsch - Variable in class org.w3._1998.math.mathml.Apply

arcsec - Variable in class org.w3._1998.math.mathml.Apply

arcsech - Variable in class org.w3._1998.math.mathml.Apply

arcsin - Variable in class org.w3._1998.math.mathml.Apply

arcsinh - Variable in class org.w3._1998.math.mathml.Apply

arctan - Variable in class org.w3._1998.math.mathml.Apply

arctanh - Variable in class org.w3._1998.math.mathml.Apply

arm - Variable in class org.sbml._2001.ns.celldesigner.LineDirection

AssignmentRule - Class in org.sbml.sbml.level2.version4

Java class for AssignmentRule complex type.

AssignmentRule() - Constructor for class org.sbml.sbml.level2.version4.AssignmentRule

AssocDissoc - Class in fr.curie.cd2sbgnml.model

Represents the association or dissociation glyphs.

AssocDissoc(Glyph, String, StyleInfo) - Constructor for class fr.curie.cd2sbgnml.model.AssocDissoc

AssocDissoc(Point2D.Float, String, StyleInfo) - Constructor for class fr.curie.cd2sbgnml.model.AssocDissoc

AssociationReactionModel - Class in fr.curie.cd2sbgnml.model

Used for the construction of an association reaction.

AssociationReactionModel(ReactionWrapper) - Constructor for class fr.curie.cd2sbgnml.model.AssociationReactionModel

B

backupSize - Variable in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

BackupSize() - Constructor for class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias.BackupSize

backupView - Variable in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

baseLinkProcessingStep1(ReactantWrapper, Glyph, Arc, Point2D.Float, boolean, SBGNML2CD.ReactionFeatures) - Method in class fr.curie.cd2sbgnml.SBGNML2CD

BaseProduct - Class in org.sbml._2001.ns.celldesigner

Base product.

BaseProduct() - Constructor for class org.sbml._2001.ns.celldesigner.BaseProduct

baseProduct - Variable in class org.sbml._2001.ns.celldesigner.BaseProducts

BaseProducts - Class in org.sbml._2001.ns.celldesigner

List of base products.

BaseProducts() - Constructor for class org.sbml._2001.ns.celldesigner.BaseProducts

baseProducts - Variable in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

BaseReactant - Class in org.sbml._2001.ns.celldesigner

Base reactant.

BaseReactant() - Constructor for class org.sbml._2001.ns.celldesigner.BaseReactant

baseReactant - Variable in class org.sbml._2001.ns.celldesigner.BaseReactants

BaseReactants - Class in org.sbml._2001.ns.celldesigner

List of base reactants.

BaseReactants() - Constructor for class org.sbml._2001.ns.celldesigner.BaseReactants

baseReactants - Variable in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

BindingRegion - Class in org.sbml._2001.ns.celldesigner

Java class for bindingRegion complex type.

BindingRegion() - Constructor for class org.sbml._2001.ns.celldesigner.BindingRegion

bindingRegion - Variable in class org.sbml._2001.ns.celldesigner.ListOfBindingRegions

bindingSite - Variable in class org.sbml._2001.ns.celldesigner.EndPointInBlockDiagram

bindingSite - Variable in class org.sbml._2001.ns.celldesigner.StartingPointInBlockDiagram

BindingSiteInBlockDiagram - Class in org.sbml._2001.ns.celldesigner

Binding site on the left side of a block(protein).

BindingSiteInBlockDiagram() - Constructor for class org.sbml._2001.ns.celldesigner.BindingSiteInBlockDiagram

bindingSiteInBlockDiagram - Variable in class org.sbml._2001.ns.celldesigner.ListOfBindingSitesInBlockDiagram

Block - Class in org.sbml._2001.ns.celldesigner

Block(protein) on canvas.

Block() - Constructor for class org.sbml._2001.ns.celldesigner.Block

block - Variable in class org.sbml._2001.ns.celldesigner.BlockDiagram

BlockDiagram - Class in org.sbml._2001.ns.celldesigner

Block diagram for a protein.

BlockDiagram() - Constructor for class org.sbml._2001.ns.celldesigner.BlockDiagram

blockDiagram - Variable in class org.sbml._2001.ns.celldesigner.ListOfBlockDiagrams

BOMskip(Reader) - Static method in class fr.curie.cd2sbgnml.SBGNSBFCModel

Skip BOM char.

boundaryCondition - Variable in class org.sbml._2001.ns.celldesigner.Species

boundaryCondition - Variable in class org.sbml.sbml.level2.version4.OriginalSpecies

Bounds - Class in org.sbml._2001.ns.celldesigner

Bound of an object on canvas.

Bounds() - Constructor for class org.sbml._2001.ns.celldesigner.Bounds

bounds - Variable in class org.sbml._2001.ns.celldesigner.CompartmentAlias

bounds - Variable in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

bounds - Variable in class org.sbml._2001.ns.celldesigner.LayerCompartmentAlias

bounds - Variable in class org.sbml._2001.ns.celldesigner.LayerFreeLine

bounds - Variable in class org.sbml._2001.ns.celldesigner.LayerSpeciesAlias

bounds - Variable in class org.sbml._2001.ns.celldesigner.SpeciesAlias

bounds2Rect(Bounds) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.Utils

BoxSize - Class in org.sbml._2001.ns.celldesigner

Box size.

BoxSize() - Constructor for class org.sbml._2001.ns.celldesigner.BoxSize

boxSize - Variable in class org.sbml._2001.ns.celldesigner.BriefView

boxSize - Variable in class org.sbml._2001.ns.celldesigner.UsualView

BriefView - Class in org.sbml._2001.ns.celldesigner

Data for drawing object with brief (compact) view.

BriefView() - Constructor for class org.sbml._2001.ns.celldesigner.BriefView

briefView - Variable in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

briefView - Variable in class org.sbml._2001.ns.celldesigner.SpeciesAlias

buildLineWrapper(String, List<Point2D.Float>, Point2D.Float) - Method in class fr.curie.cd2sbgnml.SBGNML2CD

buildLineWrapperWithProcess(Map<String, List<Point2D.Float>>, String, Point2D.Float) - Method in class fr.curie.cd2sbgnml.SBGNML2CD

Bvar - Class in org.w3._1998.math.mathml

Java class for Bvar complex type.

Bvar() - Constructor for class org.w3._1998.math.mathml.Bvar

bvar - Variable in class org.w3._1998.math.mathml.Lambda

C

canvas - Variable in class org.sbml._2001.ns.celldesigner.BlockDiagram

Canvas - Class in org.sbml._2001.ns.celldesigner

Canvas size of block diagrams.

Canvas() - Constructor for class org.sbml._2001.ns.celldesigner.Canvas

Catalyzed - Class in org.sbml._2001.ns.celldesigner

Catalyzed reaction.

Catalyzed() - Constructor for class org.sbml._2001.ns.celldesigner.Catalyzed

catalyzed - Variable in class org.sbml._2001.ns.celldesigner.ListOfCatalyzedReactions

CD2SBGNML - Class in fr.curie.cd2sbgnml

CD2SBGNML() - Constructor for class fr.curie.cd2sbgnml.CD2SBGNML

Cd2SbgnmlScript - Class in fr.curie.cd2sbgnml

Cd2SbgnmlScript() - Constructor for class fr.curie.cd2sbgnml.Cd2SbgnmlScript

CdShape - Enum in fr.curie.cd2sbgnml.graphics

All the general shapes a CellDesigner glyph can take.

ceiling - Variable in class org.w3._1998.math.mathml.Apply

CellDesignerSBFCModel - Class in fr.curie.cd2sbgnml

CellDesignerSBFCModel() - Constructor for class fr.curie.cd2sbgnml.CellDesignerSBFCModel

CellDesignerSBFCModel(Sbml) - Constructor for class fr.curie.cd2sbgnml.CellDesignerSBFCModel

charge - Variable in class org.sbml._2001.ns.celldesigner.Species

charge - Variable in class org.sbml.sbml.level2.version4.OriginalSpecies

ci - Variable in class org.w3._1998.math.mathml.Apply

ci - Variable in class org.w3._1998.math.mathml.Bvar

Ci - Class in org.w3._1998.math.mathml

Java class for Ci complex type.

Ci() - Constructor for class org.w3._1998.math.mathml.Ci

ci - Variable in class org.w3._1998.math.mathml.Lambda

ci - Variable in class org.w3._1998.math.mathml.Math

ci - Variable in class org.w3._1998.math.mathml.NodeContainer

ci - Variable in class org.w3._1998.math.mathml.Otherwise

ci - Variable in class org.w3._1998.math.mathml.Semantics

clazz - Variable in class org.sbml._2001.ns.celldesigner.CompartmentAlias

clazz - Variable in class org.sbml._2001.ns.celldesigner.SpeciesIdentity

clazz - Variable in class org.w3._1998.math.mathml.Annotation

clazz - Variable in class org.w3._1998.math.mathml.AnnotationXml

clazz - Variable in class org.w3._1998.math.mathml.Ci

clazz - Variable in class org.w3._1998.math.mathml.Cn

clazz - Variable in class org.w3._1998.math.mathml.Csymbol

clazz - Variable in class org.w3._1998.math.mathml.MathBase

Cn - Class in org.w3._1998.math.mathml

Java class for Cn complex type.

Cn() - Constructor for class org.w3._1998.math.mathml.Cn

cn - Variable in class org.w3._1998.math.mathml.Lambda

cn - Variable in class org.w3._1998.math.mathml.Math

cn - Variable in class org.w3._1998.math.mathml.NodeContainer

cn - Variable in class org.w3._1998.math.mathml.Otherwise

cn - Variable in class org.w3._1998.math.mathml.Semantics

color - Variable in class org.sbml._2001.ns.celldesigner.Line

color - Variable in class org.sbml._2001.ns.celldesigner.LineType2

color - Variable in class org.sbml._2001.ns.celldesigner.Paint

compartment - Variable in class org.sbml._2001.ns.celldesigner.CompartmentAlias

compartment - Variable in class org.sbml._2001.ns.celldesigner.Species

Compartment - Class in org.sbml.sbml.level2.version4

Redefined compartment.

Compartment() - Constructor for class org.sbml.sbml.level2.version4.Compartment

compartment - Variable in class org.sbml.sbml.level2.version4.OriginalModel.ListOfCompartments

compartment - Variable in class org.sbml.sbml.level2.version4.OriginalSpecies

CompartmentAlias - Class in org.sbml._2001.ns.celldesigner

For compartment aliases.

CompartmentAlias() - Constructor for class org.sbml._2001.ns.celldesigner.CompartmentAlias

compartmentAlias - Variable in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

compartmentAlias - Variable in class org.sbml._2001.ns.celldesigner.ListOfCompartmentAliases

compartmentAlias - Variable in class org.sbml._2001.ns.celldesigner.SpeciesAlias

CompartmentAnnotationType - Class in org.sbml._2001.ns.celldesigner

Annotation for compartment.

CompartmentAnnotationType() - Constructor for class org.sbml._2001.ns.celldesigner.CompartmentAnnotationType

CompartmentAnnotationType.Extension - Class in org.sbml._2001.ns.celldesigner

Java class for anonymous complex type.

CompartmentWrapper - Class in fr.curie.cd2sbgnml.xmlcdwrappers

CompartmentWrapper(String, String, Rectangle2D) - Constructor for class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

complexSpecies - Variable in class org.sbml._2001.ns.celldesigner.Species.Annotation

complexSpecies - Variable in class org.sbml._2001.ns.celldesigner.SpeciesAnnotationType.Extension

ComplexSpeciesAlias - Class in org.sbml._2001.ns.celldesigner

For species aliases of complex species.

ComplexSpeciesAlias() - Constructor for class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

complexSpeciesAlias - Variable in class org.sbml._2001.ns.celldesigner.ListOfComplexSpeciesAliases

ComplexSpeciesAlias() - Constructor for class org.sbml._2001.ns.celldesigner.ListOfComplexSpeciesAliases.ComplexSpeciesAlias

complexSpeciesAlias - Variable in class org.sbml._2001.ns.celldesigner.ListOfComplexSpeciesAliases.ComplexSpeciesAlias

complexSpeciesAlias - Variable in class org.sbml._2001.ns.celldesigner.SpeciesAlias

ComplexSpeciesAlias.BackupSize - Class in org.sbml._2001.ns.celldesigner

Java class for anonymous complex type.

ComplexSpeciesAlias.Font - Class in org.sbml._2001.ns.celldesigner

Java class for anonymous complex type.

connectPolicy - Variable in class org.sbml._2001.ns.celldesigner.ConnectScheme

ConnectScheme - Class in org.sbml._2001.ns.celldesigner

Connection scheme.

ConnectScheme() - Constructor for class org.sbml._2001.ns.celldesigner.ConnectScheme

connectScheme - Variable in class org.sbml._2001.ns.celldesigner.Modification

connectScheme - Variable in class org.sbml._2001.ns.celldesigner.ProductLink

connectScheme - Variable in class org.sbml._2001.ns.celldesigner.ReactantLink

connectScheme - Variable in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

constant - Variable in class org.sbml._2001.ns.celldesigner.Species

constant - Variable in class org.sbml.sbml.level2.version4.OriginalCompartment

constant - Variable in class org.sbml.sbml.level2.version4.OriginalSpecies

constant - Variable in class org.sbml.sbml.level2.version4.Parameter

content - Variable in class org.w3._1998.math.mathml.Cn

convert(GeneralModel) - Method in class fr.curie.cd2sbgnml.CD2SBGNML

convert(String, String) - Static method in class fr.curie.cd2sbgnml.Cd2SbgnmlScript

convert(GeneralModel) - Method in class fr.curie.cd2sbgnml.SBGNML2CD

convert(String, String) - Static method in class fr.curie.cd2sbgnml.Sbgnml2CdScript

convertPoints(List<Point2D.Float>, List<AffineTransform>) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

Apply a list of affine transforms to a list of points.

cos - Variable in class org.w3._1998.math.mathml.Apply

cosh - Variable in class org.w3._1998.math.mathml.Apply

cot - Variable in class org.w3._1998.math.mathml.Apply

coth - Variable in class org.w3._1998.math.mathml.Apply

create(ReactionWrapper) - Static method in class fr.curie.cd2sbgnml.model.ReactionModelFactory

create(Sbml) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

createActivity(String) - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of JAXBElement<String>}

createAlgebraicRule() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of AlgebraicRule

createAlias(String) - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of JAXBElement<String>}

createAnnotation() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of Annotation

createAnnotationXml() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of AnnotationXml

createAntisenseRNA() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of AntisenseRNA

createAntisensernaReference(String) - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of JAXBElement<String>}

createApply() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of Apply

createApplyApply(Apply) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<Apply>}

createApplyCi(Ci) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<Ci>}

createApplyCn(Cn) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<Cn>}

createApplyCsymbol(Csymbol) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<Csymbol>}

createApplyExponentiale(MathBase) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<MathBase>}

createApplyFalse(MathBase) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<MathBase>}

createApplyInfinity(MathBase) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<MathBase>}

createApplyNotanumber(MathBase) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<MathBase>}

createApplyPi(MathBase) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<MathBase>}

createApplyPiecewise(Piecewise) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<Piecewise>}

createApplySemantics(Semantics) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<Semantics>}

createApplyTrue(MathBase) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<MathBase>}

createAssignmentRule() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of AssignmentRule

createBaseProduct() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of BaseProduct

createBaseProducts() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of BaseProducts

createBaseReactant() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of BaseReactant

createBaseReactants() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of BaseReactants

createBindingRegion() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of BindingRegion

createBindingSiteInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of BindingSiteInBlockDiagram

createBlock() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Block

createBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of BlockDiagram

createBounds() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Bounds

createBoxSize() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of BoxSize

createBriefView() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of BriefView

createBvar() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of Bvar

createCanvas() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Canvas

createCatalyzed() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Catalyzed

createCi() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of Ci

createClass(String) - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of JAXBElement<String>}

createCn() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of Cn

createCnSep(SepType) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<SepType>}

createCompartment() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of Compartment

createCompartmentAlias() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of CompartmentAlias

createCompartmentAnnotationType() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of CompartmentAnnotationType

createCompartmentAnnotationTypeExtension() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of CompartmentAnnotationType.Extension

createComplexSpecies(String) - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of JAXBElement<String>}

createComplexSpeciesAlias() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ComplexSpeciesAlias

createComplexSpeciesAliasBackupSize() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ComplexSpeciesAlias.BackupSize

createComplexSpeciesAliasFont() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ComplexSpeciesAlias.Font

createConnectScheme() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ConnectScheme

createCsymbol() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of Csymbol

createDegradedInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of DegradedInBlockDiagram

createDegradedShapeInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of DegradedShapeInBlockDiagram

createDoubleLine() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of DoubleLine

createEditPoints() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of EditPoints

createEffectInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of EffectInBlockDiagram

createEffectSiteInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of EffectSiteInBlockDiagram

createEffectTargetInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of EffectTargetInBlockDiagram

createEndPointInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of EndPointInBlockDiagram

createEvent() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of Event

createEventAssignment() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of EventAssignment

createExternalConnectionInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ExternalConnectionInBlockDiagram

createExternalNameForResidue() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ExternalNameForResidue

createFunctionDefinition() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of FunctionDefinition

createGene() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Gene

createGeneReference(String) - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of JAXBElement<String>}

createGroup() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Group

createHalo() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Halo

createHomodimer(BigInteger) - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of JAXBElement<BigInteger>}

createHypothetical(Boolean) - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of JAXBElement<Boolean>}

createInfo() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Info

createInnerPosition() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of InnerPosition

createInternalLinkInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of InternalLinkInBlockDiagram

createInternalOperatorInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of InternalOperatorInBlockDiagram

createInternalOperatorValueInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of InternalOperatorValueInBlockDiagram

createKeyInfo() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of KeyInfo

createKineticLaw() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of KineticLaw

createLambda() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of Lambda

createLayer() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Layer

createLayerCompartmentAlias() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of LayerCompartmentAlias

createLayerFreeLine() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of LayerFreeLine

createLayerLineBounds() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of LayerLineBounds

createLayerSpeciesAlias() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of LayerSpeciesAlias

createLayerSpeciesAliasFont() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of LayerSpeciesAlias.Font

createLine() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Line

createLineDirection() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of LineDirection

createLineType2() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of LineType2

createLinkAnchor() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of LinkAnchor

createLinkTarget() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of LinkTarget

createListOfAntisenseRNAs() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfAntisenseRNAs

createListOfBindingRegions() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfBindingRegions

createListOfBindingSitesInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfBindingSitesInBlockDiagram

createListOfBlockDiagrams() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfBlockDiagrams

createListOfCatalyzedReactions() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfCatalyzedReactions

createListOfCompartmentAliases() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfCompartmentAliases

createListOfComplexSpeciesAliases() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfComplexSpeciesAliases

createListOfComplexSpeciesAliasesComplexSpeciesAlias() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfComplexSpeciesAliases.ComplexSpeciesAlias

createListOfEffectSitesInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfEffectSitesInBlockDiagram

createListOfEventAssignments() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of ListOfEventAssignments

createListOfExternalConnectionsInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfExternalConnectionsInBlockDiagram

createListOfExternalNamesForResidue() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfExternalNamesForResidue

createListOfFreeLines() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfFreeLines

createListOfGateMember() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfGateMember

createListOfGenes() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfGenes

createListOfGroups() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfGroups

createListOfIncludedSpecies() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfIncludedSpecies

createListOfInternalLinksInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfInternalLinksInBlockDiagram

createListOfInternalOperatorsInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfInternalOperatorsInBlockDiagram

createListOfLayers() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfLayers

createListOfLineDirection() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfLineDirection

createListOfModification() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfModification

createListOfModificationResidues() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfModificationResidues

createListOfModifications() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfModifications

createListOfModificationsModification() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfModifications.Modification

createListOfModifierSpeciesReferences() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of ListOfModifierSpeciesReferences

createListOfParameters() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of ListOfParameters

createListOfProductLinks() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfProductLinks

createListOfProteins() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfProteins

createListOfReactantLinks() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfReactantLinks

createListOfRegions() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfRegions

createListOfRegionsRegion() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfRegions.Region

createListOfResiduesInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfResiduesInBlockDiagram

createListOfRNAs() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfRNAs

createListOfSpeciesAliases() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfSpeciesAliases

createListOfSpeciesReferences() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of ListOfSpeciesReferences

createListOfSpeciesTag() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfSpeciesTag

createListOfSquares() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfSquares

createListOfStructuralStates() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfStructuralStates

createListOfTexts() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ListOfTexts

createListOfUnits() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of ListOfUnits

createMath() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of Math

createMath(Math) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<Math>}

createMathBase() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of MathBase

createMathField() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of MathField

createModel() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of Model

createModelAnnotationType() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ModelAnnotationType

createModelAnnotationTypeExtension() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ModelAnnotationType.Extension

createModelDisplay() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ModelDisplay

createModelVersion(BigDecimal) - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of JAXBElement<BigDecimal>}

createModification() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Modification

createModificationResidue() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ModificationResidue

createModifierSpeciesReference() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of ModifierSpeciesReference

createName(String) - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of JAXBElement<String>}

createNodeContainer() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of NodeContainer

createNotes() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Notes

createOffset() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Offset

createOriginalCompartment() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of OriginalCompartment

createOriginalModel() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of OriginalModel

createOriginalModelListOfCompartments() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of OriginalModel.ListOfCompartments

createOriginalModelListOfEvents() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of OriginalModel.ListOfEvents

createOriginalModelListOfFunctionDefinitions() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of OriginalModel.ListOfFunctionDefinitions

createOriginalModelListOfParameters() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of OriginalModel.ListOfParameters

createOriginalModelListOfReactions() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of OriginalModel.ListOfReactions

createOriginalModelListOfRules() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of OriginalModel.ListOfRules

createOriginalModelListOfSpecies() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of OriginalModel.ListOfSpecies

createOriginalModelListOfUnitDefinitions() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of OriginalModel.ListOfUnitDefinitions

createOriginalModifierSpeciesReference() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of OriginalModifierSpeciesReference

createOriginalReaction() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of OriginalReaction

createOriginalSpecies() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of OriginalSpecies

createOriginalSpeciesReference() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of OriginalSpeciesReference

createOtherwise() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of Otherwise

createPaint() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Paint

createParameter() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of Parameter

createPiece() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of Piece

createPieceApply(Apply) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<Apply>}

createPieceCi(Ci) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<Ci>}

createPieceCn(Cn) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<Cn>}

createPieceCsymbol(Csymbol) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<Csymbol>}

createPieceExponentiale(MathBase) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<MathBase>}

createPieceFalse(MathBase) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<MathBase>}

createPieceInfinity(MathBase) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<MathBase>}

createPieceNotanumber(MathBase) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<MathBase>}

createPiecePi(MathBase) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<MathBase>}

createPiecePiecewise(Piecewise) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<Piecewise>}

createPieceSemantics(Semantics) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<Semantics>}

createPieceTrue(MathBase) - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of JAXBElement<MathBase>}

createPiecewise() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of Piecewise

createPoint() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Point

createPositionToCompartment(String) - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of JAXBElement<String>}

createProductLink() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ProductLink

createProtein() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Protein

createProteinReference(String) - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of JAXBElement<String>}

createRateRule() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of RateRule

createReactantLink() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ReactantLink

createReaction() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of Reaction

createReactionAnnotationType() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ReactionAnnotationType

createReactionAnnotationTypeExtension() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ReactionAnnotationType.Extension

createReactionType(String) - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of JAXBElement<String>}

createRegion() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Region

createResidueInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of ResidueInBlockDiagram

createRNA() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of RNA

createRnaReference(String) - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of JAXBElement<String>}

createSBaseNotes() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of SBase.Notes

createSbml() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of Sbml

createSemantics() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of Semantics

createSepType() - Method in class org.w3._1998.math.mathml.ObjectFactory

Create an instance of SepType

createSingleLine() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of SingleLine

createSpecies() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Species

createSpecies() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of Species

createSpeciesAlias() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of SpeciesAlias

createSpeciesAliasFont() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of SpeciesAlias.Font

createSpeciesAnnotation() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of Species.Annotation

createSpeciesAnnotationType() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of SpeciesAnnotationType

createSpeciesAnnotationTypeExtension() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of SpeciesAnnotationType.Extension

createSpeciesIdentity() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of SpeciesIdentity

createSpeciesReference() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of SpeciesReference

createSpeciesReferenceAnnotationType() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of SpeciesReferenceAnnotationType

createSpeciesReferenceAnnotationTypeExtension() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of SpeciesReferenceAnnotationType.Extension

createSpeciesTag() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of SpeciesTag

createStartingPointInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of StartingPointInBlockDiagram

createState() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of State

createStoichiometryMath() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of StoichiometryMath

createStructuralStateAngle() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of StructuralStateAngle

createStructuralStates() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of StructuralStates

createTagBounds() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of TagBounds

createTagEdgeLine() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of TagEdgeLine

createUnit() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of Unit

createUnitDefinition() - Method in class org.sbml.sbml.level2.version4.ObjectFactory

Create an instance of UnitDefinition

createUsualView() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of UsualView

createView() - Method in class org.sbml._2001.ns.celldesigner.ObjectFactory

Create an instance of View

csc - Variable in class org.w3._1998.math.mathml.Apply

csch - Variable in class org.w3._1998.math.mathml.Apply

csymbol - Variable in class org.w3._1998.math.mathml.Apply

Csymbol - Class in org.w3._1998.math.mathml

Java class for Csymbol complex type.

Csymbol() - Constructor for class org.w3._1998.math.mathml.Csymbol

csymbol - Variable in class org.w3._1998.math.mathml.Lambda

csymbol - Variable in class org.w3._1998.math.mathml.Math

csymbol - Variable in class org.w3._1998.math.mathml.NodeContainer

csymbol - Variable in class org.w3._1998.math.mathml.Otherwise

csymbol - Variable in class org.w3._1998.math.mathml.Semantics

CsymbolURI - Enum in org.w3._1998.math.mathml

Java class for CsymbolURI.

D

DefaultNamespacePrefixMapper() - Constructor for class fr.curie.cd2sbgnml.xmlcdwrappers.Utils.DefaultNamespacePrefixMapper

definitionURL - Variable in class org.w3._1998.math.mathml.Ci

definitionURL - Variable in class org.w3._1998.math.mathml.Csymbol

definitionURL - Variable in class org.w3._1998.math.mathml.Semantics

degrade - Variable in class org.sbml._2001.ns.celldesigner.EndPointInBlockDiagram

degradedInBlockDiagram - Variable in class org.sbml._2001.ns.celldesigner.BlockDiagram

DegradedInBlockDiagram - Class in org.sbml._2001.ns.celldesigner

Degradation of a protein represented by the block.

DegradedInBlockDiagram() - Constructor for class org.sbml._2001.ns.celldesigner.DegradedInBlockDiagram

degradedShapeInBlockDiagram - Variable in class org.sbml._2001.ns.celldesigner.DegradedInBlockDiagram

DegradedShapeInBlockDiagram - Class in org.sbml._2001.ns.celldesigner

Degradation symbol.

DegradedShapeInBlockDiagram() - Constructor for class org.sbml._2001.ns.celldesigner.DegradedShapeInBlockDiagram

degree - Variable in class org.w3._1998.math.mathml.Apply

delay - Variable in class org.sbml.sbml.level2.version4.Event

direct - Variable in class org.sbml._2001.ns.celldesigner.KeyInfo

DissociationReactionModel - Class in fr.curie.cd2sbgnml.model

Used for the construction of an dissociation reaction.

DissociationReactionModel(ReactionWrapper) - Constructor for class fr.curie.cd2sbgnml.model.DissociationReactionModel

divide - Variable in class org.w3._1998.math.mathml.Apply

doubleLine - Variable in class org.sbml._2001.ns.celldesigner.CompartmentAlias

DoubleLine - Class in org.sbml._2001.ns.celldesigner

Double line type to draw object.

DoubleLine() - Constructor for class org.sbml._2001.ns.celldesigner.DoubleLine

E

EditPoints - Class in org.sbml._2001.ns.celldesigner

Edit points.

EditPoints() - Constructor for class org.sbml._2001.ns.celldesigner.EditPoints

editPoints - Variable in class org.sbml._2001.ns.celldesigner.Modification

editPoints - Variable in class org.sbml._2001.ns.celldesigner.ProductLink

editPoints - Variable in class org.sbml._2001.ns.celldesigner.ReactantLink

editPoints - Variable in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

editPointsAsStringList() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

EffectInBlockDiagram - Class in org.sbml._2001.ns.celldesigner

Type and targets of an effect.

EffectInBlockDiagram() - Constructor for class org.sbml._2001.ns.celldesigner.EffectInBlockDiagram

effectInBlockDiagram - Variable in class org.sbml._2001.ns.celldesigner.EffectSiteInBlockDiagram

effectSite - Variable in class org.sbml._2001.ns.celldesigner.EndPointInBlockDiagram

EffectSiteInBlockDiagram - Class in org.sbml._2001.ns.celldesigner

Effect site on the lower side of a block(protein).

EffectSiteInBlockDiagram() - Constructor for class org.sbml._2001.ns.celldesigner.EffectSiteInBlockDiagram

effectSiteInBlockDiagram - Variable in class org.sbml._2001.ns.celldesigner.ListOfEffectSitesInBlockDiagram

effectTargetInBlockDiagram - Variable in class org.sbml._2001.ns.celldesigner.EffectInBlockDiagram

EffectTargetInBlockDiagram - Class in org.sbml._2001.ns.celldesigner

Target protein of an effect.

EffectTargetInBlockDiagram() - Constructor for class org.sbml._2001.ns.celldesigner.EffectTargetInBlockDiagram

ellipsePerimeterPointFromAngle(float, float, float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

Assuming the ellipse is aligned to axis and center of ellipse is 0,0

encoding - Variable in class org.w3._1998.math.mathml.Annotation

encoding - Variable in class org.w3._1998.math.mathml.AnnotationXml

encoding - Variable in class org.w3._1998.math.mathml.Csymbol

EndPointInBlockDiagram - Class in org.sbml._2001.ns.celldesigner

End point (residue, binding site, effect site, operator, link, degrade) of the link.

EndPointInBlockDiagram() - Constructor for class org.sbml._2001.ns.celldesigner.EndPointInBlockDiagram

endPointInBlockDiagram - Variable in class org.sbml._2001.ns.celldesigner.InternalLinkInBlockDiagram

eq - Variable in class org.w3._1998.math.mathml.Apply

Event - Class in org.sbml.sbml.level2.version4

Java class for Event complex type.

Event() - Constructor for class org.sbml.sbml.level2.version4.Event

event - Variable in class org.sbml.sbml.level2.version4.OriginalModel.ListOfEvents

EventAssignment - Class in org.sbml.sbml.level2.version4

Java class for EventAssignment complex type.

EventAssignment() - Constructor for class org.sbml.sbml.level2.version4.EventAssignment

eventAssignment - Variable in class org.sbml.sbml.level2.version4.ListOfEventAssignments

ex - Variable in class org.sbml._2001.ns.celldesigner.LayerLineBounds

exp - Variable in class org.w3._1998.math.mathml.Apply

exponent - Variable in class org.sbml.sbml.level2.version4.Unit

exponentiale - Variable in class org.w3._1998.math.mathml.Lambda

exponentiale - Variable in class org.w3._1998.math.mathml.Math

exponentiale - Variable in class org.w3._1998.math.mathml.NodeContainer

exponentiale - Variable in class org.w3._1998.math.mathml.Otherwise

exponentiale - Variable in class org.w3._1998.math.mathml.Semantics

extension - Variable in class org.sbml._2001.ns.celldesigner.CompartmentAnnotationType

Extension() - Constructor for class org.sbml._2001.ns.celldesigner.CompartmentAnnotationType.Extension

extension - Variable in class org.sbml._2001.ns.celldesigner.ModelAnnotationType

Extension() - Constructor for class org.sbml._2001.ns.celldesigner.ModelAnnotationType.Extension

extension - Variable in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType

Extension() - Constructor for class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

extension - Variable in class org.sbml._2001.ns.celldesigner.SpeciesAnnotationType

Extension() - Constructor for class org.sbml._2001.ns.celldesigner.SpeciesAnnotationType.Extension

extension - Variable in class org.sbml._2001.ns.celldesigner.SpeciesReferenceAnnotationType

Extension() - Constructor for class org.sbml._2001.ns.celldesigner.SpeciesReferenceAnnotationType.Extension

ExternalConnectionInBlockDiagram - Class in org.sbml._2001.ns.celldesigner

External connection to a residue.

ExternalConnectionInBlockDiagram() - Constructor for class org.sbml._2001.ns.celldesigner.ExternalConnectionInBlockDiagram

externalConnectionInBlockDiagram - Variable in class org.sbml._2001.ns.celldesigner.ListOfExternalConnectionsInBlockDiagram

ExternalNameForResidue - Class in org.sbml._2001.ns.celldesigner

External protein name connecting to residues.

ExternalNameForResidue() - Constructor for class org.sbml._2001.ns.celldesigner.ExternalNameForResidue

externalNameForResidue - Variable in class org.sbml._2001.ns.celldesigner.ListOfExternalNamesForResidue

ey - Variable in class org.sbml._2001.ns.celldesigner.LayerLineBounds

F

factorial - Variable in class org.w3._1998.math.mathml.Apply

fast - Variable in class org.sbml.sbml.level2.version4.OriginalReaction

floor - Variable in class org.w3._1998.math.mathml.Apply

font - Variable in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Font() - Constructor for class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias.Font

font - Variable in class org.sbml._2001.ns.celldesigner.LayerSpeciesAlias

Font() - Constructor for class org.sbml._2001.ns.celldesigner.LayerSpeciesAlias.Font

font - Variable in class org.sbml._2001.ns.celldesigner.SpeciesAlias

Font() - Constructor for class org.sbml._2001.ns.celldesigner.SpeciesAlias.Font

fr.curie.cd2sbgnml - package fr.curie.cd2sbgnml

fr.curie.cd2sbgnml.graphics - package fr.curie.cd2sbgnml.graphics

Classes to deal with pure geometry problems.

fr.curie.cd2sbgnml.model - package fr.curie.cd2sbgnml.model

Higher abstraction of xml wrappers.

fr.curie.cd2sbgnml.xmlcdwrappers - package fr.curie.cd2sbgnml.xmlcdwrappers

fromListOfModifications(ListOfModification, ModelWrapper) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

fromReaction(Reaction, ModelWrapper) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

fromValue(String) - Static method in enum org.sbml.sbml.level2.version4.UnitKind

fromValue(String) - Static method in enum org.w3._1998.math.mathml.CsymbolURI

FunctionDefinition - Class in org.sbml.sbml.level2.version4

Java class for FunctionDefinition complex type.

FunctionDefinition() - Constructor for class org.sbml.sbml.level2.version4.FunctionDefinition

functionDefinition - Variable in class org.sbml.sbml.level2.version4.OriginalModel.ListOfFunctionDefinitions

G

gateMember - Variable in class org.sbml._2001.ns.celldesigner.ListOfGateMember

Gene - Class in org.sbml._2001.ns.celldesigner

For gene.

Gene() - Constructor for class org.sbml._2001.ns.celldesigner.Gene

gene - Variable in class org.sbml._2001.ns.celldesigner.ListOfGenes

geneReference - Variable in class org.sbml._2001.ns.celldesigner.SpeciesIdentity

GenericReactionElement - Class in fr.curie.cd2sbgnml.model

The most basic abstraction of what is something that is involved in a reaction.

GenericReactionElement(Glyph, String) - Constructor for class fr.curie.cd2sbgnml.model.GenericReactionElement

GenericReactionModel - Class in fr.curie.cd2sbgnml.model

Contains parts that are common to simple, association and dissociation reactions.

GenericReactionModel(ReactionWrapper) - Constructor for class fr.curie.cd2sbgnml.model.GenericReactionModel

GeometryUtils - Class in fr.curie.cd2sbgnml.graphics

Util class containing only static methods, dealing with geometry objects.

GeometryUtils() - Constructor for class fr.curie.cd2sbgnml.graphics.GeometryUtils

geq - Variable in class org.w3._1998.math.mathml.Apply

getAbs() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the abs property.

getAbsoluteAnchorCoordinate(AnchorPoint) - Method in class fr.curie.cd2sbgnml.model.ReactantModel

getAbsoluteAnchorCoords(int) - Method in class fr.curie.cd2sbgnml.model.Process

getAbsoluteAnchorPoint(CdShape, Rectangle2D.Float, AnchorPoint) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

getAbsolutePoint(Point2D.Float, Point2D.Float, Point2D.Float, Point2D.Float) - Static method in class fr.curie.cd2sbgnml.model.GenericReactionModel

Given a 3-point coordinate system, gets the absolute coordinates of a relative point

getActivity() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Gets the value of the activity property.

getActivity() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAlias

Gets the value of the activity property.

getAdditionalProducts() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getAdditionalReactants() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getAlgebraicRuleOrAssignmentRuleOrRateRule() - Method in class org.sbml.sbml.level2.version4.OriginalModel.ListOfRules

Gets the value of the algebraicRuleOrAssignmentRuleOrRateRule property.

getAlias() - Method in class org.sbml._2001.ns.celldesigner.BaseProduct

Gets the value of the alias property.

getAlias() - Method in class org.sbml._2001.ns.celldesigner.BaseReactant

Gets the value of the alias property.

getAlias() - Method in class org.sbml._2001.ns.celldesigner.LinkTarget

Gets the value of the alias property.

getAlias() - Method in class org.sbml._2001.ns.celldesigner.ProductLink

Gets the value of the alias property.

getAlias() - Method in class org.sbml._2001.ns.celldesigner.ReactantLink

Gets the value of the alias property.

getAlias() - Method in class org.sbml._2001.ns.celldesigner.SpeciesReferenceAnnotationType.Extension

Gets the value of the alias property.

getAliases() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LogicGateWrapper

getAliases() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getAliases() - Method in class org.sbml._2001.ns.celldesigner.Modification

Gets the value of the aliases property.

getAliasId() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getAliasType() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

getAliasW() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getAliasWrapperFor(String) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getAllPoints() - Method in class fr.curie.cd2sbgnml.graphics.Link

getAllStyles(List<StyleInfo>, Sbml) - Method in class fr.curie.cd2sbgnml.CD2SBGNML

getAnchorPoint() - Method in class fr.curie.cd2sbgnml.model.ReactantModel

getAnchorPoint() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getAnd() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the and property.

getAngle() - Method in class org.sbml._2001.ns.celldesigner.BindingRegion

Gets the value of the angle property.

getAngle() - Method in class org.sbml._2001.ns.celldesigner.Info

Gets the value of the angle property.

getAngle() - Method in class org.sbml._2001.ns.celldesigner.ModificationResidue

Gets the value of the angle property.

getAngle() - Method in class org.sbml._2001.ns.celldesigner.StructuralStateAngle

Gets the value of the angle property.

getAngleOfAuxUnit(Rectangle2D, Rectangle2D) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

getAnnotation() - Method in class org.sbml._2001.ns.celldesigner.Species

Gets the value of the annotation property.

getAnnotation() - Method in class org.sbml.sbml.level2.version4.Compartment

Gets the value of the annotation property.

getAnnotation() - Method in class org.sbml.sbml.level2.version4.Model

Gets the value of the annotation property.

getAnnotation() - Method in class org.sbml.sbml.level2.version4.ModifierSpeciesReference

Gets the value of the annotation property.

getAnnotation() - Method in class org.sbml.sbml.level2.version4.Reaction

Gets the value of the annotation property.

getAnnotation() - Method in class org.sbml.sbml.level2.version4.Species

Gets the value of the annotation property.

getAnnotation() - Method in class org.sbml.sbml.level2.version4.SpeciesReference

Gets the value of the annotation property.

getAnnotationOrAnnotationXml() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the annotationOrAnnotationXml property.

getAnnotations() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getAnnotations() - Method in interface fr.curie.cd2sbgnml.xmlcdwrappers.IAnnotationsFeature

getAnnotations() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getAnnotations() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getAntisenseRNA(String) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getAntisenseRNA() - Method in class org.sbml._2001.ns.celldesigner.ListOfAntisenseRNAs

Gets the value of the antisenseRNA property.

getAntisensernaReference() - Method in class org.sbml._2001.ns.celldesigner.SpeciesIdentity

Gets the value of the antisensernaReference property.

getAny() - Method in class org.sbml._2001.ns.celldesigner.CompartmentAnnotationType

Gets the value of the any property.

getAny() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType

Gets the value of the any property.

getAny() - Method in class org.sbml._2001.ns.celldesigner.Notes

Gets the value of the any property.

getAny() - Method in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType

Gets the value of the any property.

getAny() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAnnotationType

Gets the value of the any property.

getAny() - Method in class org.sbml._2001.ns.celldesigner.SpeciesReferenceAnnotationType

Gets the value of the any property.

getAny() - Method in class org.sbml.sbml.level2.version4.SBase.Notes

Gets the value of the any property.

getAny() - Method in class org.w3._1998.math.mathml.AnnotationXml

Gets the value of the any property.

getApply() - Method in class org.w3._1998.math.mathml.Lambda

Gets the value of the apply property.

getApply() - Method in class org.w3._1998.math.mathml.Math

Gets the value of the apply property.

getApply() - Method in class org.w3._1998.math.mathml.NodeContainer

Gets the value of the apply property.

getApply() - Method in class org.w3._1998.math.mathml.Otherwise

Gets the value of the apply property.

getApply() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the apply property.

getArc(LinkModel) - Method in class fr.curie.cd2sbgnml.CD2SBGNML

getArccos() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the arccos property.

getArccosh() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the arccosh property.

getArccot() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the arccot property.

getArccoth() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the arccoth property.

getArccsc() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the arccsc property.

getArccsch() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the arccsch property.

getArcsec() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the arcsec property.

getArcsech() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the arcsech property.

getArcsin() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the arcsin property.

getArcsinh() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the arcsinh property.

getArctan() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the arctan property.

getArctanh() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the arctanh property.

getArm() - Method in class org.sbml._2001.ns.celldesigner.LineDirection

Gets the value of the arm property.

getAsModification() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getAssocDissoc() - Method in class fr.curie.cd2sbgnml.model.GenericReactionModel

getAssocDissocPoints(List<ReactantWrapper>, Glyph, Point2D.Float, Arc, boolean) - Method in class fr.curie.cd2sbgnml.SBGNML2CD

getAuxUnitBboxFromAngle(Rectangle2D.Float, String, float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

getAuxUnitBboxFromPoint(Rectangle2D.Float, String, Point2D) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

getAuxUnitBboxFromRelativeTopRatio(Rectangle2D.Float, String, float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

getAxis() - Method in class fr.curie.cd2sbgnml.model.Process

getBackupSize() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Gets the value of the backupSize property.

getBackupView() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Gets the value of the backupView property.

getBaseEditPoints(Reaction) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

Get the list of edit points for the base reaction

getBaseProduct() - Method in class org.sbml._2001.ns.celldesigner.BaseProducts

Gets the value of the baseProduct property.

getBaseProducts() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getBaseProducts() - Method in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

Gets the value of the baseProducts property.

getBaseReactant() - Method in class org.sbml._2001.ns.celldesigner.BaseReactants

Gets the value of the baseReactant property.

getBaseReactants() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getBaseReactants() - Method in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

Gets the value of the baseReactants property.

getBbox() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getBbox() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.TextWrapper

getBgColor() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.StyleInfo

getBindingRegion() - Method in class org.sbml._2001.ns.celldesigner.ListOfBindingRegions

Gets the value of the bindingRegion property.

getBindingSite() - Method in class org.sbml._2001.ns.celldesigner.EndPointInBlockDiagram

Gets the value of the bindingSite property.

getBindingSite() - Method in class org.sbml._2001.ns.celldesigner.StartingPointInBlockDiagram

Gets the value of the bindingSite property.

getBindingSiteInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ListOfBindingSitesInBlockDiagram

Gets the value of the bindingSiteInBlockDiagram property.

getBLGReactantTypes(List<Arc>) - Static method in class fr.curie.cd2sbgnml.SBGNUtils

Determines which arcs are baseReactants and the baseProduct for a boolean logic gate reaction type

getBlock() - Method in class org.sbml._2001.ns.celldesigner.BlockDiagram

Gets the value of the block property.

getBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ListOfBlockDiagrams

Gets the value of the blockDiagram property.

getBounds() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

getBounds() - Method in class org.sbml._2001.ns.celldesigner.CompartmentAlias

Gets the value of the bounds property.

getBounds() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Gets the value of the bounds property.

getBounds() - Method in class org.sbml._2001.ns.celldesigner.LayerCompartmentAlias

Gets the value of the bounds property.

getBounds() - Method in class org.sbml._2001.ns.celldesigner.LayerFreeLine

Gets the value of the bounds property.

getBounds() - Method in class org.sbml._2001.ns.celldesigner.LayerSpeciesAlias

Gets the value of the bounds property.

getBounds() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAlias

Gets the value of the bounds property.

getBoxSize() - Method in class org.sbml._2001.ns.celldesigner.BriefView

Gets the value of the boxSize property.

getBoxSize() - Method in class org.sbml._2001.ns.celldesigner.UsualView

Gets the value of the boxSize property.

getBranchPoints(ReactionWrapper, Point2D.Float, Point2D.Float, int) - Static method in class fr.curie.cd2sbgnml.model.GenericReactionModel

already comprises start and end

getBriefView() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Gets the value of the briefView property.

getBriefView() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAlias

Gets the value of the briefView property.

getBvar() - Method in class org.w3._1998.math.mathml.Lambda

Gets the value of the bvar property.

getCanvas() - Method in class org.sbml._2001.ns.celldesigner.BlockDiagram

Gets the value of the canvas property.

getCatalyzed() - Method in class org.sbml._2001.ns.celldesigner.ListOfCatalyzedReactions

Gets the value of the catalyzed property.

getCatalyzedReactions() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getCdClass(ArcClazz) - Static method in class fr.curie.cd2sbgnml.model.LinkModel

getCdClass(String, SpeciesWrapper.ReferenceType) - Static method in class fr.curie.cd2sbgnml.model.ReactantModel

getCdClass() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getCdClass() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getCDCompartment() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getCDCompartmentAlias() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getCDComplexSpeciesAlias() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

Generates the xml for the complexSpeciesAlias element.

getCDConnectScheme() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getCDEditPoints(boolean) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getCDElement() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LogicGateWrapper

getCDElement() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getCDIncludedSpecies() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getCDLine() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getCDLineType2() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getCDNormalSpecies() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getCDReaction() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getCdReactionType() - Method in class fr.curie.cd2sbgnml.model.GenericReactionModel

getCdShape() - Method in class fr.curie.cd2sbgnml.graphics.Glyph

getCdShape(String, SpeciesWrapper.ReferenceType) - Static method in class fr.curie.cd2sbgnml.model.ReactantModel

getCDSpeciesAlias() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

Generates the xml for the speciesAlias element.

getCeiling() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the ceiling property.

getCenter() - Method in class fr.curie.cd2sbgnml.graphics.Glyph

getCenterPoint() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

getCenterPoint() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getCharge() - Method in class org.sbml._2001.ns.celldesigner.Species

Gets the value of the charge property.

getCharge() - Method in class org.sbml.sbml.level2.version4.OriginalSpecies

Gets the value of the charge property.

getCi() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the ci property.

getCi() - Method in class org.w3._1998.math.mathml.Bvar

Gets the value of the ci property.

getCi() - Method in class org.w3._1998.math.mathml.Lambda

Gets the value of the ci property.

getCi() - Method in class org.w3._1998.math.mathml.Math

Gets the value of the ci property.

getCi() - Method in class org.w3._1998.math.mathml.NodeContainer

Gets the value of the ci property.

getCi() - Method in class org.w3._1998.math.mathml.Otherwise

Gets the value of the ci property.

getCi() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the ci property.

getClazz() - Method in class org.sbml._2001.ns.celldesigner.CompartmentAlias

Gets the value of the clazz property.

getClazz() - Method in class org.sbml._2001.ns.celldesigner.SpeciesIdentity

Gets the value of the clazz property.

getClazz() - Method in class org.w3._1998.math.mathml.Annotation

Gets the value of the clazz property.

getClazz() - Method in class org.w3._1998.math.mathml.AnnotationXml

Gets the value of the clazz property.

getClazz() - Method in class org.w3._1998.math.mathml.Ci

Gets the value of the clazz property.

getClazz() - Method in class org.w3._1998.math.mathml.Cn

Gets the value of the clazz property.

getClazz() - Method in class org.w3._1998.math.mathml.Csymbol

Gets the value of the clazz property.

getClazz() - Method in class org.w3._1998.math.mathml.MathBase

Gets the value of the clazz property.

getClosest(List<Point2D.Float>, Point2D.Float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

return the point from the list that is the closest to Point p

getCn() - Method in class org.w3._1998.math.mathml.Lambda

Gets the value of the cn property.

getCn() - Method in class org.w3._1998.math.mathml.Math

Gets the value of the cn property.

getCn() - Method in class org.w3._1998.math.mathml.NodeContainer

Gets the value of the cn property.

getCn() - Method in class org.w3._1998.math.mathml.Otherwise

Gets the value of the cn property.

getCn() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the cn property.

getColor() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.TextWrapper

getColor() - Method in class org.sbml._2001.ns.celldesigner.Line

Gets the value of the color property.

getColor() - Method in class org.sbml._2001.ns.celldesigner.LineType2

Gets the value of the color property.

getColor() - Method in class org.sbml._2001.ns.celldesigner.Paint

Gets the value of the color property.

getCompartment() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getCompartment() - Method in class org.sbml._2001.ns.celldesigner.CompartmentAlias

Gets the value of the compartment property.

getCompartment() - Method in class org.sbml._2001.ns.celldesigner.Species

Gets the value of the compartment property.

getCompartment() - Method in class org.sbml.sbml.level2.version4.OriginalModel.ListOfCompartments

Gets the value of the compartment property.

getCompartment() - Method in class org.sbml.sbml.level2.version4.OriginalSpecies

Gets the value of the compartment property.

getCompartmentAlias() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

getCompartmentAlias() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Gets the value of the compartmentAlias property.

getCompartmentAlias() - Method in class org.sbml._2001.ns.celldesigner.ListOfCompartmentAliases

Gets the value of the compartmentAlias property.

getCompartmentAlias() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAlias

Gets the value of the compartmentAlias property.

getCompartmentAliasFor(String) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getCompartmentBbox(String, float, float, float, float, float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

In some case, a CD compartment only has coordinates, no width or height.

getComplex() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getComplexAlias() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

getComplexSpecies() - Method in class org.sbml._2001.ns.celldesigner.Species.Annotation

Gets the value of the complexSpecies property.

getComplexSpecies() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAnnotationType.Extension

Gets the value of the complexSpecies property.

getComplexSpeciesAlias() - Method in class org.sbml._2001.ns.celldesigner.ListOfComplexSpeciesAliases.ComplexSpeciesAlias

Gets the value of the complexSpeciesAlias property.

getComplexSpeciesAlias() - Method in class org.sbml._2001.ns.celldesigner.ListOfComplexSpeciesAliases

Gets the value of the complexSpeciesAlias property.

getComplexSpeciesAlias() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAlias

Gets the value of the complexSpeciesAlias property.

getComplexSpeciesAliasFor(String) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getConnectPolicy() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getConnectPolicy() - Method in class org.sbml._2001.ns.celldesigner.ConnectScheme

Gets the value of the connectPolicy property.

getConnectScheme() - Method in class org.sbml._2001.ns.celldesigner.Modification

Gets the value of the connectScheme property.

getConnectScheme() - Method in class org.sbml._2001.ns.celldesigner.ProductLink

Gets the value of the connectScheme property.

getConnectScheme() - Method in class org.sbml._2001.ns.celldesigner.ReactantLink

Gets the value of the connectScheme property.

getConnectScheme() - Method in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

Gets the value of the connectScheme property.

getContent() - Method in class org.w3._1998.math.mathml.Cn

Gets the value of the content property.

getCos() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the cos property.

getCosh() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the cosh property.

getCot() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the cot property.

getCoth() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the coth property.

getCsc() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the csc property.

getCsch() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the csch property.

getCsymbol() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the csymbol property.

getCsymbol() - Method in class org.w3._1998.math.mathml.Lambda

Gets the value of the csymbol property.

getCsymbol() - Method in class org.w3._1998.math.mathml.Math

Gets the value of the csymbol property.

getCsymbol() - Method in class org.w3._1998.math.mathml.NodeContainer

Gets the value of the csymbol property.

getCsymbol() - Method in class org.w3._1998.math.mathml.Otherwise

Gets the value of the csymbol property.

getCsymbol() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the csymbol property.

getDefaultNamePoint(String, String, Rectangle2D) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getDefinitionURL() - Method in class org.w3._1998.math.mathml.Ci

Gets the value of the definitionURL property.

getDefinitionURL() - Method in class org.w3._1998.math.mathml.Csymbol

Gets the value of the definitionURL property.

getDefinitionURL() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the definitionURL property.

getDegrade() - Method in class org.sbml._2001.ns.celldesigner.EndPointInBlockDiagram

Gets the value of the degrade property.

getDegradedInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.BlockDiagram

Gets the value of the degradedInBlockDiagram property.

getDegradedShapeInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.DegradedInBlockDiagram

Gets the value of the degradedShapeInBlockDiagram property.

getDegree() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the degree property.

getDelay() - Method in class org.sbml.sbml.level2.version4.Event

Gets the value of the delay property.

getDescription() - Method in class fr.curie.cd2sbgnml.CD2SBGNML

getDescription() - Method in class fr.curie.cd2sbgnml.SBGNML2CD

getDirect() - Method in class org.sbml._2001.ns.celldesigner.KeyInfo

Gets the value of the direct property.

getDivide() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the divide property.

getDoubleLine() - Method in class org.sbml._2001.ns.celldesigner.CompartmentAlias

Gets the value of the doubleLine property.

getEditPoints() - Method in class fr.curie.cd2sbgnml.graphics.Link

getEditPoints() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getEditPoints() - Method in class org.sbml._2001.ns.celldesigner.Modification

Gets the value of the editPoints property.

getEditPoints() - Method in class org.sbml._2001.ns.celldesigner.ProductLink

Gets the value of the editPoints property.

getEditPoints() - Method in class org.sbml._2001.ns.celldesigner.ReactantLink

Gets the value of the editPoints property.

getEditPoints() - Method in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

Gets the value of the editPoints property.

getEditPointsForAdditionalProduct(Reaction, int) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getEditPointsForAdditionalReactant(Reaction, int) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

get edit points for the additional reactant located at position: index in the xml list of additional reactant

getEditPointsForBranch(int) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getEditPointsForModifier(Reaction, int) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

get edit points for the modifier located at position: index in the xml list of modifiers

getEditPointsForModifier() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getEffectInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.EffectSiteInBlockDiagram

Gets the value of the effectInBlockDiagram property.

getEffectSite() - Method in class org.sbml._2001.ns.celldesigner.EndPointInBlockDiagram

Gets the value of the effectSite property.

getEffectSiteInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ListOfEffectSitesInBlockDiagram

Gets the value of the effectSiteInBlockDiagram property.

getEffectTargetInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.EffectInBlockDiagram

Gets the value of the effectTargetInBlockDiagram property.

getEncoding() - Method in class org.w3._1998.math.mathml.Annotation

Gets the value of the encoding property.

getEncoding() - Method in class org.w3._1998.math.mathml.AnnotationXml

Gets the value of the encoding property.

getEncoding() - Method in class org.w3._1998.math.mathml.Csymbol

Gets the value of the encoding property.

getEnd() - Method in class fr.curie.cd2sbgnml.graphics.Link

getEnd() - Method in class fr.curie.cd2sbgnml.model.LinkModel

getEndPointInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.InternalLinkInBlockDiagram

Gets the value of the endPointInBlockDiagram property.

getEq() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the eq property.

getEvent() - Method in class org.sbml.sbml.level2.version4.OriginalModel.ListOfEvents

Gets the value of the event property.

getEventAssignment() - Method in class org.sbml.sbml.level2.version4.ListOfEventAssignments

Gets the value of the eventAssignment property.

getEx() - Method in class org.sbml._2001.ns.celldesigner.LayerLineBounds

Gets the value of the ex property.

getExp() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the exp property.

getExponent() - Method in class org.sbml.sbml.level2.version4.Unit

Gets the value of the exponent property.

getExponentiale() - Method in class org.w3._1998.math.mathml.Lambda

Gets the value of the exponentiale property.

getExponentiale() - Method in class org.w3._1998.math.mathml.Math

Gets the value of the exponentiale property.

getExponentiale() - Method in class org.w3._1998.math.mathml.NodeContainer

Gets the value of the exponentiale property.

getExponentiale() - Method in class org.w3._1998.math.mathml.Otherwise

Gets the value of the exponentiale property.

getExponentiale() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the exponentiale property.

getExtension() - Method in class org.sbml._2001.ns.celldesigner.CompartmentAnnotationType

Gets the value of the extension property.

getExtension() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType

Gets the value of the extension property.

getExtension() - Method in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType

Gets the value of the extension property.

getExtension() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAnnotationType

Gets the value of the extension property.

getExtension() - Method in class org.sbml._2001.ns.celldesigner.SpeciesReferenceAnnotationType

Gets the value of the extension property.

getExtensions() - Method in class fr.curie.cd2sbgnml.CellDesignerSBFCModel

getExternalConnectionInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ListOfExternalConnectionsInBlockDiagram

Gets the value of the externalConnectionInBlockDiagram property.

getExternalNameForResidue() - Method in class org.sbml._2001.ns.celldesigner.ListOfExternalNamesForResidue

Gets the value of the externalNameForResidue property.

getEy() - Method in class org.sbml._2001.ns.celldesigner.LayerLineBounds

Gets the value of the ey property.

getFactorial() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the factorial property.

getFalse() - Method in class org.w3._1998.math.mathml.Lambda

Gets the value of the false property.

getFalse() - Method in class org.w3._1998.math.mathml.Math

Gets the value of the false property.

getFalse() - Method in class org.w3._1998.math.mathml.NodeContainer

Gets the value of the false property.

getFalse() - Method in class org.w3._1998.math.mathml.Otherwise

Gets the value of the false property.

getFalse() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the false property.

getFinalpoint(AnchorPoint, ReactantWrapper, Rectangle2D.Float) - Static method in class fr.curie.cd2sbgnml.SBGNML2CD

getFloor() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the floor property.

getFont() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Gets the value of the font property.

getFont() - Method in class org.sbml._2001.ns.celldesigner.LayerSpeciesAlias

Gets the value of the font property.

getFont() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAlias

Gets the value of the font property.

getFontSize() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.StyleInfo

getFontSize() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.TextWrapper

getFunctionDefinition() - Method in class org.sbml.sbml.level2.version4.OriginalModel.ListOfFunctionDefinitions

Gets the value of the functionDefinition property.

getGateMember() - Method in class org.sbml._2001.ns.celldesigner.ListOfGateMember

Gets the value of the gateMember property.

getGene(String) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getGene() - Method in class org.sbml._2001.ns.celldesigner.ListOfGenes

Gets the value of the gene property.

getGeneReference() - Method in class org.sbml._2001.ns.celldesigner.SpeciesIdentity

Gets the value of the geneReference property.

getGeq() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the geq property.

getGlyph(AliasWrapper, boolean) - Method in class fr.curie.cd2sbgnml.CD2SBGNML

getGlyph() - Method in class fr.curie.cd2sbgnml.model.GenericReactionElement

getGroup() - Method in class org.sbml._2001.ns.celldesigner.ListOfGroups

Gets the value of the group property.

getGt() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the gt property.

getH() - Method in class org.sbml._2001.ns.celldesigner.Bounds

Gets the value of the h property.

getH() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias.BackupSize

Gets the value of the h property.

getH() - Method in class org.sbml._2001.ns.celldesigner.TagBounds

Gets the value of the h property.

getHalo() - Method in class org.sbml._2001.ns.celldesigner.BlockDiagram

Gets the value of the halo property.

getHeight() - Method in class fr.curie.cd2sbgnml.graphics.Glyph

getHeight() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getHeight() - Method in class org.sbml._2001.ns.celldesigner.Block

Gets the value of the height property.

getHeight() - Method in class org.sbml._2001.ns.celldesigner.BoxSize

Gets the value of the height property.

getHeight() - Method in class org.sbml._2001.ns.celldesigner.Canvas

Gets the value of the height property.

getHeight() - Method in class org.sbml._2001.ns.celldesigner.DegradedShapeInBlockDiagram

Gets the value of the height property.

getHeight() - Method in class org.sbml._2001.ns.celldesigner.Halo

Gets the value of the height property.

getHomodimer() - Method in class org.sbml._2001.ns.celldesigner.State

Gets the value of the homodimer property.

getHtmlDescription() - Method in class fr.curie.cd2sbgnml.CD2SBGNML

getHtmlDescription() - Method in class fr.curie.cd2sbgnml.SBGNML2CD

getId() - Method in class fr.curie.cd2sbgnml.model.GenericReactionElement

getId() - Method in class fr.curie.cd2sbgnml.model.GenericReactionModel

getId() - Method in class fr.curie.cd2sbgnml.model.LinkModel

getId() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

getId() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getId() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getId() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getId() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.StyleInfo

getId() - Method in class org.sbml._2001.ns.celldesigner.AntisenseRNA

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.BindingRegion

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.BindingSiteInBlockDiagram

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.CompartmentAlias

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.DegradedInBlockDiagram

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.EffectSiteInBlockDiagram

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.ExternalNameForResidue

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.Gene

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.Group

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.InternalLinkInBlockDiagram

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.InternalOperatorInBlockDiagram

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.Layer

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.ModificationResidue

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.Protein

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.Region

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.ResidueInBlockDiagram

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.RNA

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.Species

Gets the value of the id property.

getId() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAlias

Gets the value of the id property.

getId() - Method in class org.sbml.sbml.level2.version4.Event

Gets the value of the id property.

getId() - Method in class org.sbml.sbml.level2.version4.FunctionDefinition

Gets the value of the id property.

getId() - Method in class org.sbml.sbml.level2.version4.OriginalCompartment

Gets the value of the id property.

getId() - Method in class org.sbml.sbml.level2.version4.OriginalModel

Gets the value of the id property.

getId() - Method in class org.sbml.sbml.level2.version4.OriginalReaction

Gets the value of the id property.

getId() - Method in class org.sbml.sbml.level2.version4.OriginalSpecies

Gets the value of the id property.

getId() - Method in class org.sbml.sbml.level2.version4.Parameter

Gets the value of the id property.

getId() - Method in class org.sbml.sbml.level2.version4.UnitDefinition

Gets the value of the id property.

getId() - Method in class org.w3._1998.math.mathml.Annotation

Gets the value of the id property.

getId() - Method in class org.w3._1998.math.mathml.AnnotationXml

Gets the value of the id property.

getId() - Method in class org.w3._1998.math.mathml.Ci

Gets the value of the id property.

getId() - Method in class org.w3._1998.math.mathml.Cn

Gets the value of the id property.

getId() - Method in class org.w3._1998.math.mathml.Csymbol

Gets the value of the id property.

getId() - Method in class org.w3._1998.math.mathml.MathBase

Gets the value of the id property.

getIncludedAliasWrapperFor(String) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getIncludedSpecies(String) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getIndex() - Method in class org.sbml._2001.ns.celldesigner.LineDirection

Gets the value of the index property.

getInfinity() - Method in class org.w3._1998.math.mathml.Lambda

Gets the value of the infinity property.

getInfinity() - Method in class org.w3._1998.math.mathml.Math

Gets the value of the infinity property.

getInfinity() - Method in class org.w3._1998.math.mathml.NodeContainer

Gets the value of the infinity property.

getInfinity() - Method in class org.w3._1998.math.mathml.Otherwise

Gets the value of the infinity property.

getInfinity() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the infinity property.

getInfo() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

getInfo() - Method in class org.sbml._2001.ns.celldesigner.CompartmentAlias

Gets the value of the info property.

getInfo() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Gets the value of the info property.

getInfo() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAlias

Gets the value of the info property.

getInfoAngle() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getInfoState() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getInitialAmount() - Method in class org.sbml._2001.ns.celldesigner.Species

Gets the value of the initialAmount property.

getInitialAmount() - Method in class org.sbml.sbml.level2.version4.OriginalSpecies

Gets the value of the initialAmount property.

getInitialConcentration() - Method in class org.sbml._2001.ns.celldesigner.Species

Gets the value of the initialConcentration property.

getInitialConcentration() - Method in class org.sbml.sbml.level2.version4.OriginalSpecies

Gets the value of the initialConcentration property.

getInnerPosition() - Method in class org.sbml._2001.ns.celldesigner.BriefView

Gets the value of the innerPosition property.

getInnerPosition() - Method in class org.sbml._2001.ns.celldesigner.UsualView

Gets the value of the innerPosition property.

getInnerWidth() - Method in class org.sbml._2001.ns.celldesigner.DoubleLine

Gets the value of the innerWidth property.

getInternalLinkInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ListOfInternalLinksInBlockDiagram

Gets the value of the internalLinkInBlockDiagram property.

getInternalOperatorInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ListOfInternalOperatorsInBlockDiagram

Gets the value of the internalOperatorInBlockDiagram property.

getInternalOperatorValueInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.InternalOperatorInBlockDiagram

Gets the value of the internalOperatorValueInBlockDiagram property.

getKeyInfo() - Method in class org.sbml._2001.ns.celldesigner.SpeciesTag

Gets the value of the keyInfo property.

getKind() - Method in class org.sbml.sbml.level2.version4.Unit

Gets the value of the kind property.

getKineticLaw() - Method in class org.sbml.sbml.level2.version4.OriginalReaction

Gets the value of the kineticLaw property.

getLabel() - Method in class fr.curie.cd2sbgnml.graphics.Glyph

getLabel() - Method in class org.sbml._2001.ns.celldesigner.Info

Gets the value of the label property.

getLambda() - Method in class org.w3._1998.math.mathml.Math

Gets the value of the lambda property.

getLambda() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the lambda property.

getLayer() - Method in class org.sbml._2001.ns.celldesigner.ListOfLayers

Gets the value of the layer property.

getLayerCompartmentAlias() - Method in class org.sbml._2001.ns.celldesigner.ListOfSquares

Gets the value of the layerCompartmentAlias property.

getLayerFreeLine() - Method in class org.sbml._2001.ns.celldesigner.ListOfFreeLines

Gets the value of the layerFreeLine property.

getLayerNotes() - Method in class org.sbml._2001.ns.celldesigner.LayerSpeciesAlias

Gets the value of the layerNotes property.

getLayerSpeciesAlias() - Method in class org.sbml._2001.ns.celldesigner.ListOfTexts

Gets the value of the layerSpeciesAlias property.

getLengthForString(String) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

Return an estimation of a pixel width taken by a string s usdfs dfsdf sdfsd f -> fill a width of 80 in CellDesigner -> 5 / letter with a minimum margin of 5.

getLeq() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the leq property.

getLevel() - Method in class org.sbml.sbml.level2.version4.Sbml

Gets the value of the level property.

getLine() - Method in class org.sbml._2001.ns.celldesigner.LayerFreeLine

Gets the value of the line property.

getLine() - Method in class org.sbml._2001.ns.celldesigner.Modification

Gets the value of the line property.

getLine() - Method in class org.sbml._2001.ns.celldesigner.ProductLink

Gets the value of the line property.

getLine() - Method in class org.sbml._2001.ns.celldesigner.ReactantLink

Gets the value of the line property.

getLine() - Method in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

Gets the value of the line property.

getLineColor() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getLineColor() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.StyleInfo

getLineDirection() - Method in class org.sbml._2001.ns.celldesigner.ListOfLineDirection

Gets the value of the lineDirection property.

getLineDirectionList() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getLineLineIntersection(Line2D.Float, Line2D.Float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

https://stackoverflow.com/a/5185725 return intersection even if out of segment.

getLineRectangleIntersection(Line2D.Float, Rectangle2D.Float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

return between 0 and 4 points

getLineType() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getLineWidth() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getLineWidth() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.StyleInfo

getLineWrapper() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getLineWrapper() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getLink() - Method in class fr.curie.cd2sbgnml.model.LinkModel

getLink() - Method in class org.sbml._2001.ns.celldesigner.EndPointInBlockDiagram

Gets the value of the link property.

getLinkAnchor() - Method in class org.sbml._2001.ns.celldesigner.BaseProduct

Gets the value of the linkAnchor property.

getLinkAnchor() - Method in class org.sbml._2001.ns.celldesigner.BaseReactant

Gets the value of the linkAnchor property.

getLinkAnchor() - Method in class org.sbml._2001.ns.celldesigner.LinkTarget

Gets the value of the linkAnchor property.

getLinkAnchor() - Method in class org.sbml._2001.ns.celldesigner.ProductLink

Gets the value of the linkAnchor property.

getLinkAnchor() - Method in class org.sbml._2001.ns.celldesigner.ReactantLink

Gets the value of the linkAnchor property.

getLinkModels() - Method in class fr.curie.cd2sbgnml.model.GenericReactionModel

getLinkTarget() - Method in class org.sbml._2001.ns.celldesigner.Modification

Gets the value of the linkTarget property.

getListofAliasWrapper() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfAntisenseRna() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfAntisenseRNAs() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType.Extension

Gets the value of the listOfAntisenseRNAs property.

getListOfBindingRegions() - Method in class org.sbml._2001.ns.celldesigner.Protein

Gets the value of the listOfBindingRegions property.

getListOfBindingSitesInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.BlockDiagram

Gets the value of the listOfBindingSitesInBlockDiagram property.

getListOfBlockDiagrams() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType.Extension

Gets the value of the listOfBlockDiagrams property.

getListOfCatalyzedReactions() - Method in class org.sbml._2001.ns.celldesigner.Species.Annotation

Gets the value of the listOfCatalyzedReactions property.

getListOfCatalyzedReactions() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAnnotationType.Extension

Gets the value of the listOfCatalyzedReactions property.

getListOfCompartmentAliases() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfCompartmentAliases() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType.Extension

Gets the value of the listOfCompartmentAliases property.

getListOfCompartments() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfCompartments() - Method in class org.sbml.sbml.level2.version4.OriginalModel

Gets the value of the listOfCompartments property.

getListOfComplexSpeciesAliases() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfComplexSpeciesAliases() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType.Extension

Gets the value of the listOfComplexSpeciesAliases property.

getListOfEffectSitesInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.BlockDiagram

Gets the value of the listOfEffectSitesInBlockDiagram property.

getListOfEventAssignments() - Method in class org.sbml.sbml.level2.version4.Event

Gets the value of the listOfEventAssignments property.

getListOfEvents() - Method in class org.sbml.sbml.level2.version4.OriginalModel

Gets the value of the listOfEvents property.

getListOfExternalConnectionsInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ExternalNameForResidue

Gets the value of the listOfExternalConnectionsInBlockDiagram property.

getListOfExternalNamesForResidue() - Method in class org.sbml._2001.ns.celldesigner.BlockDiagram

Gets the value of the listOfExternalNamesForResidue property.

getListOfFreeLines() - Method in class org.sbml._2001.ns.celldesigner.Layer

Gets the value of the listOfFreeLines property.

getListOfFunctionDefinitions() - Method in class org.sbml.sbml.level2.version4.OriginalModel

Gets the value of the listOfFunctionDefinitions property.

getListOfGateMember() - Method in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

Gets the value of the listOfGateMember property.

getListOfGene() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfGenes() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType.Extension

Gets the value of the listOfGenes property.

getListOfGroups() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType.Extension

Gets the value of the listOfGroups property.

getListOfIncludedSpecies() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfIncludedSpecies() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType.Extension

Gets the value of the listOfIncludedSpecies property.

getListOfInternalLinksInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.BlockDiagram

Gets the value of the listOfInternalLinksInBlockDiagram property.

getListOfInternalOperatorsInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.BlockDiagram

Gets the value of the listOfInternalOperatorsInBlockDiagram property.

getListOfLayers() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfLayers() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType.Extension

Gets the value of the listOfLayers property.

getListOfLineDirection() - Method in class org.sbml._2001.ns.celldesigner.ConnectScheme

Gets the value of the listOfLineDirection property.

getListOfModification() - Method in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

Gets the value of the listOfModification property.

getListOfModificationResidues() - Method in class org.sbml._2001.ns.celldesigner.Protein

Gets the value of the listOfModificationResidues property.

getListOfModifications() - Method in class org.sbml._2001.ns.celldesigner.State

Gets the value of the listOfModifications property.

getListOfModifiers() - Method in class org.sbml.sbml.level2.version4.OriginalReaction

Gets the value of the listOfModifiers property.

getListOfParameters() - Method in class org.sbml.sbml.level2.version4.KineticLaw

Gets the value of the listOfParameters property.

getListOfParameters() - Method in class org.sbml.sbml.level2.version4.OriginalModel

Gets the value of the listOfParameters property.

getListOfProductLinks() - Method in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

Gets the value of the listOfProductLinks property.

getListOfProducts() - Method in class org.sbml.sbml.level2.version4.OriginalReaction

Gets the value of the listOfProducts property.

getListOfProtein() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfProteins() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType.Extension

Gets the value of the listOfProteins property.

getListOfReactantLinks() - Method in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

Gets the value of the listOfReactantLinks property.

getListOfReactants() - Method in class org.sbml.sbml.level2.version4.OriginalReaction

Gets the value of the listOfReactants property.

getListOfReactions() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfReactions() - Method in class org.sbml.sbml.level2.version4.OriginalModel

Gets the value of the listOfReactions property.

getListOfReactionWrapper() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfRegions() - Method in class org.sbml._2001.ns.celldesigner.AntisenseRNA

Gets the value of the listOfRegions property.

getListOfRegions() - Method in class org.sbml._2001.ns.celldesigner.Gene

Gets the value of the listOfRegions property.

getListOfRegions() - Method in class org.sbml._2001.ns.celldesigner.RNA

Gets the value of the listOfRegions property.

getListOfResiduesInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.BlockDiagram

Gets the value of the listOfResiduesInBlockDiagram property.

getListOfRna() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfRNAs() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType.Extension

Gets the value of the listOfRNAs property.

getListOfRules() - Method in class org.sbml.sbml.level2.version4.OriginalModel

Gets the value of the listOfRules property.

getListOfSpecies() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfSpecies() - Method in class org.sbml.sbml.level2.version4.OriginalModel

Gets the value of the listOfSpecies property.

getListOfSpeciesAliases() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfSpeciesAliases() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType.Extension

Gets the value of the listOfSpeciesAliases property.

getListOfSpeciesTag() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Gets the value of the listOfSpeciesTag property.

getListOfSpeciesTag() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAlias

Gets the value of the listOfSpeciesTag property.

getListOfSpeciesWrapper() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfSquares() - Method in class org.sbml._2001.ns.celldesigner.Layer

Gets the value of the listOfSquares property.

getListOfStructuralStates() - Method in class org.sbml._2001.ns.celldesigner.Protein

Gets the value of the listOfStructuralStates property.

getListOfStructuralStates() - Method in class org.sbml._2001.ns.celldesigner.State

Gets the value of the listOfStructuralStates property.

getListOfTexts() - Method in class org.sbml._2001.ns.celldesigner.Layer

Gets the value of the listOfTexts property.

getListofTextWrapper() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getListOfUnitDefinitions() - Method in class org.sbml.sbml.level2.version4.OriginalModel

Gets the value of the listOfUnitDefinitions property.

getListOfUnits() - Method in class org.sbml.sbml.level2.version4.UnitDefinition

Gets the value of the listOfUnits property.

getLn() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the ln property.

getLog() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the log property.

getLogbase() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the logbase property.

getLogicGate() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getLogicGateModificationType() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LogicGateWrapper

getLogicGates() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getLogicGateType(GlyphClazz) - Static method in class fr.curie.cd2sbgnml.model.LogicGate

getLongState(String) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.ResidueWrapper

getLt() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the lt property.

getMapBounds(Map) - Static method in class fr.curie.cd2sbgnml.SBGNUtils

returns the size of a map

getMapOfColorDefinitions(List<StyleInfo>) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.StyleInfo

getMath() - Method in class org.sbml.sbml.level2.version4.EventAssignment

Gets the value of the math property.

getMath() - Method in class org.sbml.sbml.level2.version4.FunctionDefinition

Gets the value of the math property.

getMath() - Method in class org.sbml.sbml.level2.version4.KineticLaw

Gets the value of the math property.

getMath() - Method in class org.sbml.sbml.level2.version4.MathField

Gets the value of the math property.

getMath() - Method in class org.sbml.sbml.level2.version4.Rule

Gets the value of the math property.

getMath() - Method in class org.sbml.sbml.level2.version4.StoichiometryMath

Gets the value of the math property.

getMembers() - Method in class org.sbml._2001.ns.celldesigner.Group

Gets the value of the members property.

getMetaid() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getMetaid() - Method in class org.sbml.sbml.level2.version4.SBase

Gets the value of the metaid property.

getMiddle(Point2D.Float, Point2D.Float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

getMiddleOfPolylineSegment(List<Point2D.Float>, int) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

Given a polyline defined by a list of points, and a segment index (starting at 0 for the first segment of the polyline), returns the middle of the specified segment.

getMinus() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the minus property.

getModel() - Method in class fr.curie.cd2sbgnml.SBGNSBFCModel

getModel() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getModel() - Method in class org.sbml.sbml.level2.version4.Sbml

Gets the value of the model property.

getModelDisplay() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType.Extension

Gets the value of the modelDisplay property.

getModelVersion() - Method in class org.sbml._2001.ns.celldesigner.ModelAnnotationType.Extension

Gets the value of the modelVersion property.

getModification() - Method in class org.sbml._2001.ns.celldesigner.ListOfModification

Gets the value of the modification property.

getModification() - Method in class org.sbml._2001.ns.celldesigner.ListOfModifications

Gets the value of the modification property.

getModificationLinkType() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getModificationResidue() - Method in class org.sbml._2001.ns.celldesigner.ListOfModificationResidues

Gets the value of the modificationResidue property.

getModificationType() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LogicGateWrapper

getModificationType() - Method in class org.sbml._2001.ns.celldesigner.Modification

Gets the value of the modificationType property.

getModifiers() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LogicGateWrapper

getModifiers() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getModifiers() - Method in class org.sbml._2001.ns.celldesigner.Modification

Gets the value of the modifiers property.

getModifierSpeciesReference() - Method in class org.sbml.sbml.level2.version4.ListOfModifierSpeciesReferences

Gets the value of the modifierSpeciesReference property.

getMultimer() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getMultimerFromInfo(Glyph) - Static method in class fr.curie.cd2sbgnml.SBGNUtils

Will check the presence of a unit of information with content: "N:"+multimer count and return multimer count

getMultiplier() - Method in class org.sbml.sbml.level2.version4.Unit

Gets the value of the multiplier property.

getName() - Method in class fr.curie.cd2sbgnml.CD2SBGNML

getName() - Method in class fr.curie.cd2sbgnml.SBGNML2CD

getName() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getName() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getName() - Method in class org.sbml._2001.ns.celldesigner.AntisenseRNA

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.BindingRegion

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.BindingSiteInBlockDiagram

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.CompartmentAnnotationType.Extension

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.EffectSiteInBlockDiagram

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.ExternalNameForResidue

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.Gene

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.KeyInfo

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.Layer

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.ModificationResidue

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.Protein

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.Region

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.ResidueInBlockDiagram

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.RNA

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.Species

Gets the value of the name property.

getName() - Method in class org.sbml._2001.ns.celldesigner.SpeciesIdentity

Gets the value of the name property.

getName() - Method in class org.sbml.sbml.level2.version4.Event

Gets the value of the name property.

getName() - Method in class org.sbml.sbml.level2.version4.FunctionDefinition

Gets the value of the name property.

getName() - Method in class org.sbml.sbml.level2.version4.OriginalCompartment

Gets the value of the name property.

getName() - Method in class org.sbml.sbml.level2.version4.OriginalModel

Gets the value of the name property.

getName() - Method in class org.sbml.sbml.level2.version4.OriginalReaction

Gets the value of the name property.

getName() - Method in class org.sbml.sbml.level2.version4.OriginalSpecies

Gets the value of the name property.

getName() - Method in class org.sbml.sbml.level2.version4.Parameter

Gets the value of the name property.

getName() - Method in class org.sbml.sbml.level2.version4.UnitDefinition

Gets the value of the name property.

getNameOffsetX() - Method in class org.sbml._2001.ns.celldesigner.BindingSiteInBlockDiagram

Gets the value of the nameOffsetX property.

getNameOffsetX() - Method in class org.sbml._2001.ns.celldesigner.Block

Gets the value of the nameOffsetX property.

getNameOffsetX() - Method in class org.sbml._2001.ns.celldesigner.EffectSiteInBlockDiagram

Gets the value of the nameOffsetX property.

getNameOffsetX() - Method in class org.sbml._2001.ns.celldesigner.ExternalNameForResidue

Gets the value of the nameOffsetX property.

getNameOffsetX() - Method in class org.sbml._2001.ns.celldesigner.ResidueInBlockDiagram

Gets the value of the nameOffsetX property.

getNameOffsetY() - Method in class org.sbml._2001.ns.celldesigner.BindingSiteInBlockDiagram

Gets the value of the nameOffsetY property.

getNameOffsetY() - Method in class org.sbml._2001.ns.celldesigner.Block

Gets the value of the nameOffsetY property.

getNameOffsetY() - Method in class org.sbml._2001.ns.celldesigner.EffectSiteInBlockDiagram

Gets the value of the nameOffsetY property.

getNameOffsetY() - Method in class org.sbml._2001.ns.celldesigner.ExternalNameForResidue

Gets the value of the nameOffsetY property.

getNameOffsetY() - Method in class org.sbml._2001.ns.celldesigner.ResidueInBlockDiagram

Gets the value of the nameOffsetY property.

getNamePoint() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getNamePoint() - Method in class org.sbml._2001.ns.celldesigner.CompartmentAlias

Gets the value of the namePoint property.

getNearestAnchorPoint(Point2D.Float, Rectangle2D.Float, CdShape) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

Approximate a point on/near a shape, to a CellDesigner anchor point.

getNeq() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the neq property.

getNode() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the node property.

getNode() - Method in class org.w3._1998.math.mathml.Piece

Gets the value of the node property.

getNormalizedEndPoints(List<Point2D.Float>, Glyph, Glyph, AnchorPoint, AnchorPoint) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

Assuming the point list is definitively set in absolute coordinates, will translate the start and end points of the link, if they point to centers, to the correct perimeter point of the shape.

getNot() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the not property.

getNotanumber() - Method in class org.w3._1998.math.mathml.Lambda

Gets the value of the notanumber property.

getNotanumber() - Method in class org.w3._1998.math.mathml.Math

Gets the value of the notanumber property.

getNotanumber() - Method in class org.w3._1998.math.mathml.NodeContainer

Gets the value of the notanumber property.

getNotanumber() - Method in class org.w3._1998.math.mathml.Otherwise

Gets the value of the notanumber property.

getNotanumber() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the notanumber property.

getNotes() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getNotes() - Method in interface fr.curie.cd2sbgnml.xmlcdwrappers.INotesFeature

getNotes() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getNotes() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getNotes(List<Element>) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.Utils

Get the html Element notes of a celldesigner/sbml xml element

getNotes(Notes) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.Utils

getNotes(SBase.Notes) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.Utils

getNotes() - Method in class org.sbml._2001.ns.celldesigner.AntisenseRNA

Gets the value of the notes property.

getNotes() - Method in class org.sbml._2001.ns.celldesigner.Gene

Gets the value of the notes property.

getNotes() - Method in class org.sbml._2001.ns.celldesigner.Protein

Gets the value of the notes property.

getNotes() - Method in class org.sbml._2001.ns.celldesigner.RNA

Gets the value of the notes property.

getNotes() - Method in class org.sbml._2001.ns.celldesigner.Species

Gets the value of the notes property.

getNotes() - Method in class org.sbml.sbml.level2.version4.SBase

Gets the value of the notes property.

getNum0() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getNum0() - Method in class org.sbml._2001.ns.celldesigner.EditPoints

Gets the value of the num0 property.

getNum0() - Method in class org.sbml._2001.ns.celldesigner.Modification

Gets the value of the num0 property.

getNum1() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getNum1() - Method in class org.sbml._2001.ns.celldesigner.EditPoints

Gets the value of the num1 property.

getNum1() - Method in class org.sbml._2001.ns.celldesigner.Modification

Gets the value of the num1 property.

getNum2() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getNum2() - Method in class org.sbml._2001.ns.celldesigner.EditPoints

Gets the value of the num2 property.

getNum2() - Method in class org.sbml._2001.ns.celldesigner.Modification

Gets the value of the num2 property.

getOffset() - Method in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

Gets the value of the offset property.

getOffset() - Method in class org.sbml.sbml.level2.version4.Unit

Gets the value of the offset property.

getOffsetX() - Method in class org.sbml._2001.ns.celldesigner.DegradedShapeInBlockDiagram

Gets the value of the offsetX property.

getOffsetX() - Method in class org.sbml._2001.ns.celldesigner.EffectSiteInBlockDiagram

Gets the value of the offsetX property.

getOffsetX() - Method in class org.sbml._2001.ns.celldesigner.EndPointInBlockDiagram

Gets the value of the offsetX property.

getOffsetX() - Method in class org.sbml._2001.ns.celldesigner.InternalOperatorInBlockDiagram

Gets the value of the offsetX property.

getOffsetX() - Method in class org.sbml._2001.ns.celldesigner.InternalOperatorValueInBlockDiagram

Gets the value of the offsetX property.

getOffsetX() - Method in class org.sbml._2001.ns.celldesigner.Modification

Gets the value of the offsetX property.

getOffsetX() - Method in class org.sbml._2001.ns.celldesigner.ResidueInBlockDiagram

Gets the value of the offsetX property.

getOffsetX() - Method in class org.sbml._2001.ns.celldesigner.StartingPointInBlockDiagram

Gets the value of the offsetX property.

getOffsetY() - Method in class org.sbml._2001.ns.celldesigner.BindingSiteInBlockDiagram

Gets the value of the offsetY property.

getOffsetY() - Method in class org.sbml._2001.ns.celldesigner.DegradedInBlockDiagram

Gets the value of the offsetY property.

getOffsetY() - Method in class org.sbml._2001.ns.celldesigner.DegradedShapeInBlockDiagram

Gets the value of the offsetY property.

getOffsetY() - Method in class org.sbml._2001.ns.celldesigner.EffectSiteInBlockDiagram

Gets the value of the offsetY property.

getOffsetY() - Method in class org.sbml._2001.ns.celldesigner.EndPointInBlockDiagram

Gets the value of the offsetY property.

getOffsetY() - Method in class org.sbml._2001.ns.celldesigner.ExternalNameForResidue

Gets the value of the offsetY property.

getOffsetY() - Method in class org.sbml._2001.ns.celldesigner.InternalOperatorInBlockDiagram

Gets the value of the offsetY property.

getOffsetY() - Method in class org.sbml._2001.ns.celldesigner.InternalOperatorValueInBlockDiagram

Gets the value of the offsetY property.

getOffsetY() - Method in class org.sbml._2001.ns.celldesigner.Modification

Gets the value of the offsetY property.

getOffsetY() - Method in class org.sbml._2001.ns.celldesigner.StartingPointInBlockDiagram

Gets the value of the offsetY property.

getOmittedShapeIndex() - Method in class org.sbml._2001.ns.celldesigner.EditPoints

Gets the value of the omittedShapeIndex property.

getOperator() - Method in class org.sbml._2001.ns.celldesigner.EndPointInBlockDiagram

Gets the value of the operator property.

getOperator() - Method in class org.sbml._2001.ns.celldesigner.StartingPointInBlockDiagram

Gets the value of the operator property.

getOr() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the or property.

getOrientation() - Method in class fr.curie.cd2sbgnml.model.ReactionNodeModel

getOtherwise() - Method in class org.w3._1998.math.mathml.Piecewise

Gets the value of the otherwise property.

getOuterWidth() - Method in class org.sbml._2001.ns.celldesigner.DoubleLine

Gets the value of the outerWidth property.

getOutside() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getOutside() - Method in class org.sbml.sbml.level2.version4.OriginalCompartment

Gets the value of the outside property.

getPaint() - Method in class org.sbml._2001.ns.celldesigner.BriefView

Gets the value of the paint property.

getPaint() - Method in class org.sbml._2001.ns.celldesigner.CompartmentAlias

Gets the value of the paint property.

getPaint() - Method in class org.sbml._2001.ns.celldesigner.LayerCompartmentAlias

Gets the value of the paint property.

getPaint() - Method in class org.sbml._2001.ns.celldesigner.LayerSpeciesAlias

Gets the value of the paint property.

getPaint() - Method in class org.sbml._2001.ns.celldesigner.UsualView

Gets the value of the paint property.

getParameter() - Method in class org.sbml.sbml.level2.version4.ListOfParameters

Gets the value of the parameter property.

getParameter() - Method in class org.sbml.sbml.level2.version4.OriginalModel.ListOfParameters

Gets the value of the parameter property.

getPi() - Method in class org.w3._1998.math.mathml.Lambda

Gets the value of the pi property.

getPi() - Method in class org.w3._1998.math.mathml.Math

Gets the value of the pi property.

getPi() - Method in class org.w3._1998.math.mathml.NodeContainer

Gets the value of the pi property.

getPi() - Method in class org.w3._1998.math.mathml.Otherwise

Gets the value of the pi property.

getPi() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the pi property.

getPiece() - Method in class org.w3._1998.math.mathml.Piecewise

Gets the value of the piece property.

getPiecewise() - Method in class org.w3._1998.math.mathml.Lambda

Gets the value of the piecewise property.

getPiecewise() - Method in class org.w3._1998.math.mathml.Math

Gets the value of the piecewise property.

getPiecewise() - Method in class org.w3._1998.math.mathml.NodeContainer

Gets the value of the piecewise property.

getPiecewise() - Method in class org.w3._1998.math.mathml.Otherwise

Gets the value of the piecewise property.

getPiecewise() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the piecewise property.

getPlus() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the plus property.

getPoint() - Method in class org.sbml._2001.ns.celldesigner.CompartmentAlias

Gets the value of the point property.

getPoints(Arc) - Static method in class fr.curie.cd2sbgnml.SBGNUtils

Return a list of the start, intermediate and end points of an arc.

getPortDistanceRatio() - Method in class fr.curie.cd2sbgnml.model.ReactionNodeModel

getPortIn() - Method in class fr.curie.cd2sbgnml.model.ReactionNodeModel

getPortOut() - Method in class fr.curie.cd2sbgnml.model.ReactionNodeModel

getPos() - Method in class org.sbml._2001.ns.celldesigner.Region

Gets the value of the pos property.

getPosition() - Method in class org.sbml._2001.ns.celldesigner.LinkAnchor

Gets the value of the position property.

getPositionFromAngle(Rectangle2D.Float, float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

result returned in relative coordinates from rectangle center

getPositionIndex() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getPositionToCompartment() - Method in class org.sbml._2001.ns.celldesigner.Species.Annotation

Gets the value of the positionToCompartment property.

getPositionToCompartment() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAnnotationType.Extension

Gets the value of the positionToCompartment property.

getPower() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the power property.

getPreferredPrefix(String, String, boolean) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.Utils.DefaultNamespacePrefixMapper

getPrefix() - Method in class org.sbml._2001.ns.celldesigner.Info

Gets the value of the prefix property.

getProcess() - Method in class fr.curie.cd2sbgnml.model.GenericReactionModel

getProcessAnchorIndex(Modification) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getProcessAnchorIndex() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getProcessLine(Link, Point2D, SBGNML2CD.ReactionFeatures) - Method in class fr.curie.cd2sbgnml.SBGNML2CD

getProcessSegment(Reaction) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

Get the segment index on which the process glyph of a reaction is located.

getProcessSegmentIndex() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getProduct() - Method in class org.sbml._2001.ns.celldesigner.ProductLink

Gets the value of the product property.

getProductLink() - Method in class org.sbml._2001.ns.celldesigner.ListOfProductLinks

Gets the value of the productLink property.

getProtein(String) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getProtein() - Method in class org.sbml._2001.ns.celldesigner.BindingSiteInBlockDiagram

Gets the value of the protein property.

getProtein() - Method in class org.sbml._2001.ns.celldesigner.BlockDiagram

Gets the value of the protein property.

getProtein() - Method in class org.sbml._2001.ns.celldesigner.EffectTargetInBlockDiagram

Gets the value of the protein property.

getProtein() - Method in class org.sbml._2001.ns.celldesigner.ExternalNameForResidue

Gets the value of the protein property.

getProtein() - Method in class org.sbml._2001.ns.celldesigner.ListOfProteins

Gets the value of the protein property.

getProteinReference() - Method in class org.sbml._2001.ns.celldesigner.SpeciesIdentity

Gets the value of the proteinReference property.

getRDFAnnotations(List<Element>) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.Utils

Get the RDF element from an annotation element, if present

getReactant() - Method in class org.sbml._2001.ns.celldesigner.ReactantLink

Gets the value of the reactant property.

getReactantLink() - Method in class org.sbml._2001.ns.celldesigner.ListOfReactantLinks

Gets the value of the reactantLink property.

getReactantList() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getReactantModels() - Method in class fr.curie.cd2sbgnml.model.GenericReactionModel

getReactantType() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getReactantTypes(List<Arc>, boolean) - Static method in class fr.curie.cd2sbgnml.SBGNUtils

Returns a list of 3 lists containing: 0 - the reactants consumed by the reaction 1 - the products of the reaction 2 - all other types of interactions (catalysis, stimulation...) If the reaction is reversible, then no consumption arc is present.

getReaction() - Method in class org.sbml._2001.ns.celldesigner.Catalyzed

Gets the value of the reaction property.

getReaction() - Method in class org.sbml._2001.ns.celldesigner.EffectSiteInBlockDiagram

Gets the value of the reaction property.

getReaction() - Method in class org.sbml.sbml.level2.version4.OriginalModel.ListOfReactions

Gets the value of the reaction property.

getReactionNodeModels() - Method in class fr.curie.cd2sbgnml.model.GenericReactionModel

getReactionType() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

getReactionType() - Method in class org.sbml._2001.ns.celldesigner.ReactionAnnotationType.Extension

Gets the value of the reactionType property.

getReactionWrapperFor(String) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getReactionWrappersForAlias(String) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getRectangleFromGlyph(Glyph) - Static method in class fr.curie.cd2sbgnml.SBGNUtils

Converts an SBGN glyph's bbox to a Rectangle2D

getRectangleIndex() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getRectangleIndex() - Method in class org.sbml._2001.ns.celldesigner.ConnectScheme

Gets the value of the rectangleIndex property.

getReducedCdClass(ArcClazz) - Static method in class fr.curie.cd2sbgnml.model.LinkModel

getReferenceId() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getReferenceNotes() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getRefId() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.StyleInfo

getRefPoint() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.TextWrapper

getRegion() - Method in class org.sbml._2001.ns.celldesigner.ListOfRegions

Gets the value of the region property.

getRelativeAnchorCoordinate(CdShape, float, float, AnchorPoint) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

Get relative coordinate of an anchor point from center of the shape

getRelativeAnchorCoordinate(AnchorPoint) - Method in class fr.curie.cd2sbgnml.model.ReactantModel

Get relative coordinate of an anchor point from center of the shape

getRelativeAnchorCoords(int) - Method in class fr.curie.cd2sbgnml.model.Process

Take a celldesigner index representing the possible anchor points on a process glyph, and return the corresponding coordinates, relative to the center of the process, with center at origin.

getRelativeLeftParallelogramAnchorPosition(AnchorPoint, float, float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

getRelativePhenotypeAnchorPosition(AnchorPoint, float, float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

angle of the right and left "arrows" of the phenotype are fixed (45°) the diagonals on the left and right are the diagonals of 4 squares of side h/2

getRelativePositionOfAuxUnit(Rectangle2D, Rectangle2D) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

Relative position of center of auxiliary unit from center of its parent glyph.

getRelativeReceptorAnchorPosition(AnchorPoint, float, float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

getRelativeRectangleAnchorPosition(AnchorPoint, float, float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

getRelativeRightParallelogramAnchorPosition(AnchorPoint, float, float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

right and left side also have 45° slope

getResidue() - Method in class org.sbml._2001.ns.celldesigner.EndPointInBlockDiagram

Gets the value of the residue property.

getResidue() - Method in class org.sbml._2001.ns.celldesigner.ExternalConnectionInBlockDiagram

Gets the value of the residue property.

getResidue() - Method in class org.sbml._2001.ns.celldesigner.ListOfModifications.Modification

Gets the value of the residue property.

getResidue() - Method in class org.sbml._2001.ns.celldesigner.ResidueInBlockDiagram

Gets the value of the residue property.

getResidue() - Method in class org.sbml._2001.ns.celldesigner.StartingPointInBlockDiagram

Gets the value of the residue property.

getResidueInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.ListOfResiduesInBlockDiagram

Gets the value of the residueInBlockDiagram property.

getResidues() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getResultExtension() - Method in class fr.curie.cd2sbgnml.CD2SBGNML

getResultExtension() - Method in class fr.curie.cd2sbgnml.SBGNML2CD

getRNA(String) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getRNA() - Method in class org.sbml._2001.ns.celldesigner.ListOfRNAs

Gets the value of the rna property.

getRnaReference() - Method in class org.sbml._2001.ns.celldesigner.SpeciesIdentity

Gets the value of the rnaReference property.

getRoot() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the root property.

getSBGNAnnotation(Element, String) - Method in class fr.curie.cd2sbgnml.CD2SBGNML

Convert a rdf element to an SBGN extension, with an annotation element inside wrapping the rdf.

getSbgnClass(String) - Static method in class fr.curie.cd2sbgnml.model.LinkModel

getSbgnClass() - Method in class fr.curie.cd2sbgnml.model.LinkModel

getSbgnClass(LogicGateWrapper.LogicGateType) - Static method in class fr.curie.cd2sbgnml.model.LogicGate

getSbgnClass(String) - Static method in class fr.curie.cd2sbgnml.model.Process

getSbgnClass(String) - Static method in class fr.curie.cd2sbgnml.model.ReactantModel

getSBGNNotes(Element) - Method in class fr.curie.cd2sbgnml.CD2SBGNML

Convert html Element into an SBGN notes object

getSbgnShape() - Method in class fr.curie.cd2sbgnml.graphics.Glyph

getSbgnShape(String) - Static method in class fr.curie.cd2sbgnml.model.ReactantModel

getSbgnText() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasInfoWrapper

getSbgnText() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ResidueWrapper

getSbml() - Method in class fr.curie.cd2sbgnml.CellDesignerSBFCModel

getScale() - Method in class org.sbml.sbml.level2.version4.Unit

Gets the value of the scale property.

getScheme() - Method in class org.sbml._2001.ns.celldesigner.Paint

Gets the value of the scheme property.

getSec() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the sec property.

getSech() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the sech property.

getSemantics() - Method in class org.w3._1998.math.mathml.Lambda

Gets the value of the semantics property.

getSemantics() - Method in class org.w3._1998.math.mathml.Math

Gets the value of the semantics property.

getSemantics() - Method in class org.w3._1998.math.mathml.NodeContainer

Gets the value of the semantics property.

getSemantics() - Method in class org.w3._1998.math.mathml.Otherwise

Gets the value of the semantics property.

getSemantics() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the semantics property.

getShortState(String) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.ResidueWrapper

getSide() - Method in class org.sbml._2001.ns.celldesigner.ModificationResidue

Gets the value of the side property.

getSin() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the sin property.

getSingleLine() - Method in class org.sbml._2001.ns.celldesigner.BriefView

Gets the value of the singleLine property.

getSingleLine() - Method in class org.sbml._2001.ns.celldesigner.UsualView

Gets the value of the singleLine property.

getSinh() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the sinh property.

getSize() - Method in class fr.curie.cd2sbgnml.model.ReactionNodeModel

getSize() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getSize() - Method in class org.sbml._2001.ns.celldesigner.BindingRegion

Gets the value of the size property.

getSize() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias.Font

Gets the value of the size property.

getSize() - Method in class org.sbml._2001.ns.celldesigner.LayerSpeciesAlias.Font

Gets the value of the size property.

getSize() - Method in class org.sbml._2001.ns.celldesigner.Region

Gets the value of the size property.

getSize() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAlias.Font

Gets the value of the size property.

getSize() - Method in class org.sbml.sbml.level2.version4.OriginalCompartment

Gets the value of the size property.

getSizeX() - Method in class org.sbml._2001.ns.celldesigner.ModelDisplay

Gets the value of the sizeX property.

getSizeY() - Method in class org.sbml._2001.ns.celldesigner.ModelDisplay

Gets the value of the sizeY property.

getSpatialDimensions() - Method in class org.sbml.sbml.level2.version4.OriginalCompartment

Gets the value of the spatialDimensions property.

getSpatialSizeUnits() - Method in class org.sbml._2001.ns.celldesigner.Species

Gets the value of the spatialSizeUnits property.

getSpatialSizeUnits() - Method in class org.sbml.sbml.level2.version4.OriginalSpecies

Gets the value of the spatialSizeUnits property.

getSpecies(String) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getSpecies() - Method in class org.sbml._2001.ns.celldesigner.BaseProduct

Gets the value of the species property.

getSpecies() - Method in class org.sbml._2001.ns.celldesigner.BaseReactant

Gets the value of the species property.

getSpecies() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Gets the value of the species property.

getSpecies() - Method in class org.sbml._2001.ns.celldesigner.EffectSiteInBlockDiagram

Gets the value of the species property.

getSpecies() - Method in class org.sbml._2001.ns.celldesigner.LinkTarget

Gets the value of the species property.

getSpecies() - Method in class org.sbml._2001.ns.celldesigner.ListOfIncludedSpecies

Gets the value of the species property.

getSpecies() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAlias

Gets the value of the species property.

getSpecies() - Method in class org.sbml.sbml.level2.version4.OriginalModel.ListOfSpecies

Gets the value of the species property.

getSpecies() - Method in class org.sbml.sbml.level2.version4.SimpleSpeciesReference

Gets the value of the species property.

getSpeciesAlias() - Method in class org.sbml._2001.ns.celldesigner.ListOfSpeciesAliases

Gets the value of the speciesAlias property.

getSpeciesAliasFor(String) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getSpeciesId() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

getSpeciesIdentity() - Method in class org.sbml._2001.ns.celldesigner.Species.Annotation

Gets the value of the speciesIdentity property.

getSpeciesIdentity() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAnnotationType.Extension

Gets the value of the speciesIdentity property.

getSpeciesReference() - Method in class org.sbml.sbml.level2.version4.ListOfSpeciesReferences

Gets the value of the speciesReference property.

getSpeciesTag() - Method in class org.sbml._2001.ns.celldesigner.ListOfSpeciesTag

Gets the value of the speciesTag property.

getSpeciesW() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

getSpeciesWrapperFor(String) - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ModelWrapper

getStart() - Method in class fr.curie.cd2sbgnml.graphics.Link

getStart() - Method in class fr.curie.cd2sbgnml.model.LinkModel

getStartingPointInBlockDiagram() - Method in class org.sbml._2001.ns.celldesigner.InternalLinkInBlockDiagram

Gets the value of the startingPointInBlockDiagram property.

getState() - Method in class org.sbml._2001.ns.celldesigner.Info

Gets the value of the state property.

getState() - Method in class org.sbml._2001.ns.celldesigner.ListOfModifications.Modification

Gets the value of the state property.

getState() - Method in class org.sbml._2001.ns.celldesigner.SpeciesIdentity

Gets the value of the state property.

getState() - Method in class org.sbml._2001.ns.celldesigner.View

Gets the value of the state property.

getStateVariable(String, String, Rectangle2D.Float, float) - Method in class fr.curie.cd2sbgnml.CD2SBGNML

getStateVariableFromResidueWrapper(ResidueWrapper, Rectangle2D.Float) - Method in class fr.curie.cd2sbgnml.CD2SBGNML

getStateVariables(Glyph) - Static method in class fr.curie.cd2sbgnml.SBGNUtils

getStoichiometry() - Method in class org.sbml.sbml.level2.version4.OriginalSpeciesReference

Gets the value of the stoichiometry property.

getStoichiometryMath() - Method in class org.sbml.sbml.level2.version4.OriginalSpeciesReference

Gets the value of the stoichiometryMath property.

getStructuralState() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getStructuralState() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Gets the value of the structuralState property.

getStructuralState() - Method in class org.sbml._2001.ns.celldesigner.ListOfStructuralStates

Gets the value of the structuralState property.

getStructuralState() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAlias

Gets the value of the structuralState property.

getStructuralState() - Method in class org.sbml._2001.ns.celldesigner.StructuralStates

Gets the value of the structuralState property.

getStyle() - Method in class org.w3._1998.math.mathml.Annotation

Gets the value of the style property.

getStyle() - Method in class org.w3._1998.math.mathml.AnnotationXml

Gets the value of the style property.

getStyle() - Method in class org.w3._1998.math.mathml.Ci

Gets the value of the style property.

getStyle() - Method in class org.w3._1998.math.mathml.Cn

Gets the value of the style property.

getStyle() - Method in class org.w3._1998.math.mathml.Csymbol

Gets the value of the style property.

getStyle() - Method in class org.w3._1998.math.mathml.MathBase

Gets the value of the style property.

getStyleInfo() - Method in class fr.curie.cd2sbgnml.model.LinkModel

getStyleInfo() - Method in class fr.curie.cd2sbgnml.model.ReactionNodeModel

getStyleInfo() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

getStyleInfo() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getSub() - Method in class org.sbml._2001.ns.celldesigner.InternalOperatorInBlockDiagram

Gets the value of the sub property.

getSubstanceUnits() - Method in class org.sbml._2001.ns.celldesigner.Species

Gets the value of the substanceUnits property.

getSubstanceUnits() - Method in class org.sbml.sbml.level2.version4.KineticLaw

Gets the value of the substanceUnits property.

getSubstanceUnits() - Method in class org.sbml.sbml.level2.version4.OriginalSpecies

Gets the value of the substanceUnits property.

getSx() - Method in class org.sbml._2001.ns.celldesigner.LayerLineBounds

Gets the value of the sx property.

getSy() - Method in class org.sbml._2001.ns.celldesigner.LayerLineBounds

Gets the value of the sy property.

getTagBounds() - Method in class org.sbml._2001.ns.celldesigner.SpeciesTag

Gets the value of the tagBounds property.

getTagEdgeLine() - Method in class org.sbml._2001.ns.celldesigner.SpeciesTag

Gets the value of the tagEdgeLine property.

getTagFramePaint() - Method in class org.sbml._2001.ns.celldesigner.SpeciesTag

Gets the value of the tagFramePaint property.

getTan() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the tan property.

getTanh() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the tanh property.

getTarget() - Method in class org.sbml._2001.ns.celldesigner.LayerSpeciesAlias

Gets the value of the target property.

getTargetId() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.TextWrapper

getTargetId() - Method in class org.sbml._2001.ns.celldesigner.LayerSpeciesAlias

Gets the value of the targetId property.

getTargetLineIndex() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getTargetLineIndex() - Method in class org.sbml._2001.ns.celldesigner.Modification

Gets the value of the targetLineIndex property.

getTargetLineIndex() - Method in class org.sbml._2001.ns.celldesigner.ProductLink

Gets the value of the targetLineIndex property.

getTargetLineIndex() - Method in class org.sbml._2001.ns.celldesigner.ReactantLink

Gets the value of the targetLineIndex property.

getTargetType() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.TextWrapper

getText() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.TextWrapper

getThickness() - Method in class org.sbml._2001.ns.celldesigner.DoubleLine

Gets the value of the thickness property.

getTimes() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the times property.

getTimeUnits() - Method in class org.sbml.sbml.level2.version4.Event

Gets the value of the timeUnits property.

getTimeUnits() - Method in class org.sbml.sbml.level2.version4.KineticLaw

Gets the value of the timeUnits property.

getTopLevelParent() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

getTopPositionFromRatio(Rectangle2D.Float, float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

For genes modification residues, CD uses a % of the glyph width as location.

getTopRatioOfAuxUnit(Rectangle2D, Rectangle2D) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

getTransformsToGlobalCoords(Point2D, Point2D) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

Given 2 points in global map coordinate, defining an origin and a unit vector, returns a list of transforms that can be applied to convert local coordinates (in the space defined by those 2 points) to global coordinates (same system the 2 points are provided with).

getTransformsToGlobalCoords(Point2D, Point2D, Point2D) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

Given 3 points in global map coordinate, defining an origin and 2 unit vectors, returns a list of transforms that can be applied to convert local coordinates (in the space defined by those 3 points) to global coordinates (same system the 3 points are provided with).

getTransformsToLocalCoords(Point2D, Point2D) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

just reverse the order and invert each transform

getTransformsToLocalCoords(Point2D, Point2D, Point2D) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

getTrigger() - Method in class org.sbml.sbml.level2.version4.Event

Gets the value of the trigger property.

getTrue() - Method in class org.w3._1998.math.mathml.Lambda

Gets the value of the true property.

getTrue() - Method in class org.w3._1998.math.mathml.Math

Gets the value of the true property.

getTrue() - Method in class org.w3._1998.math.mathml.NodeContainer

Gets the value of the true property.

getTrue() - Method in class org.w3._1998.math.mathml.Otherwise

Gets the value of the true property.

getTrue() - Method in class org.w3._1998.math.mathml.Semantics

Gets the value of the true property.

gettShapeIndex() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LineWrapper

getTShapeIndex() - Method in class org.sbml._2001.ns.celldesigner.EditPoints

Gets the value of the tShapeIndex property.

getType() - Method in class fr.curie.cd2sbgnml.model.LogicGate

getType() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.LogicGateWrapper

getType() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getType() - Method in class org.sbml._2001.ns.celldesigner.AntisenseRNA

Gets the value of the type property.

getType() - Method in class org.sbml._2001.ns.celldesigner.EffectInBlockDiagram

Gets the value of the type property.

getType() - Method in class org.sbml._2001.ns.celldesigner.ExternalConnectionInBlockDiagram

Gets the value of the type property.

getType() - Method in class org.sbml._2001.ns.celldesigner.Gene

Gets the value of the type property.

getType() - Method in class org.sbml._2001.ns.celldesigner.InternalLinkInBlockDiagram

Gets the value of the type property.

getType() - Method in class org.sbml._2001.ns.celldesigner.InternalOperatorInBlockDiagram

Gets the value of the type property.

getType() - Method in class org.sbml._2001.ns.celldesigner.LayerCompartmentAlias

Gets the value of the type property.

getType() - Method in class org.sbml._2001.ns.celldesigner.LineType2

Gets the value of the type property.

getType() - Method in class org.sbml._2001.ns.celldesigner.Modification

Gets the value of the type property.

getType() - Method in class org.sbml._2001.ns.celldesigner.Protein

Gets the value of the type property.

getType() - Method in class org.sbml._2001.ns.celldesigner.Region

Gets the value of the type property.

getType() - Method in class org.sbml._2001.ns.celldesigner.ResidueInBlockDiagram

Gets the value of the type property.

getType() - Method in class org.sbml._2001.ns.celldesigner.RNA

Gets the value of the type property.

getType() - Method in class org.w3._1998.math.mathml.Cn

Gets the value of the type property.

getTypeFromString(String) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

getUnit() - Method in class org.sbml.sbml.level2.version4.ListOfUnits

Gets the value of the unit property.

getUnitDefinition() - Method in class org.sbml.sbml.level2.version4.OriginalModel.ListOfUnitDefinitions

Gets the value of the unitDefinition property.

getUnitOfInfo(String, Rectangle2D.Float, float) - Method in class fr.curie.cd2sbgnml.CD2SBGNML

getUnitOfInfo(Glyph, String) - Static method in class fr.curie.cd2sbgnml.SBGNUtils

getUnits() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.CompartmentWrapper

getUnits() - Method in class org.sbml.sbml.level2.version4.OriginalCompartment

Gets the value of the units property.

getUnits() - Method in class org.sbml.sbml.level2.version4.Parameter

Gets the value of the units property.

getURI() - Method in class fr.curie.cd2sbgnml.CellDesignerSBFCModel

getUsualView() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Gets the value of the usualView property.

getUsualView() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAlias

Gets the value of the usualView property.

getValue() - Method in class org.sbml._2001.ns.celldesigner.EditPoints

List of coordinate values.Gets the value of the value property.

getValue() - Method in class org.sbml._2001.ns.celldesigner.InternalOperatorValueInBlockDiagram

Gets the value of the value property.

getValue() - Method in class org.sbml._2001.ns.celldesigner.LineDirection

Gets the value of the value property.

getValue() - Method in class org.sbml.sbml.level2.version4.Parameter

Gets the value of the value property.

getValue() - Method in class org.w3._1998.math.mathml.Annotation

Gets the value of the value property.

getValue() - Method in class org.w3._1998.math.mathml.Ci

Gets the value of the value property.

getValue() - Method in class org.w3._1998.math.mathml.Csymbol

Gets the value of the value property.

getVariable() - Method in class org.sbml.sbml.level2.version4.AssignmentRule

Gets the value of the variable property.

getVariable() - Method in class org.sbml.sbml.level2.version4.EventAssignment

Gets the value of the variable property.

getVariable() - Method in class org.sbml.sbml.level2.version4.RateRule

Gets the value of the variable property.

getVersion() - Method in class org.sbml.sbml.level2.version4.Sbml

Gets the value of the version property.

getView() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Gets the value of the view property.

getView() - Method in class org.sbml._2001.ns.celldesigner.SpeciesAlias

Gets the value of the view property.

getW() - Method in class org.sbml._2001.ns.celldesigner.Bounds

Gets the value of the w property.

getW() - Method in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias.BackupSize

Gets the value of the w property.

getW() - Method in class org.sbml._2001.ns.celldesigner.TagBounds

Gets the value of the w property.

getWidth() - Method in class fr.curie.cd2sbgnml.graphics.Glyph

getWidth() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

getWidth() - Method in class org.sbml._2001.ns.celldesigner.Block

Gets the value of the width property.

getWidth() - Method in class org.sbml._2001.ns.celldesigner.BoxSize

Gets the value of the width property.

getWidth() - Method in class org.sbml._2001.ns.celldesigner.Canvas

Gets the value of the width property.

getWidth() - Method in class org.sbml._2001.ns.celldesigner.DegradedShapeInBlockDiagram

Gets the value of the width property.

getWidth() - Method in class org.sbml._2001.ns.celldesigner.Halo

Gets the value of the width property.

getWidth() - Method in class org.sbml._2001.ns.celldesigner.Line

Gets the value of the width property.

getWidth() - Method in class org.sbml._2001.ns.celldesigner.LineType2

Gets the value of the width property.

getWidth() - Method in class org.sbml._2001.ns.celldesigner.SingleLine

Gets the value of the width property.

getWidth() - Method in class org.sbml._2001.ns.celldesigner.TagEdgeLine

Gets the value of the width property.

getX() - Method in class org.sbml._2001.ns.celldesigner.Block

Gets the value of the x property.

getX() - Method in class org.sbml._2001.ns.celldesigner.Bounds

Gets the value of the x property.

getX() - Method in class org.sbml._2001.ns.celldesigner.Halo

Gets the value of the x property.

getX() - Method in class org.sbml._2001.ns.celldesigner.InnerPosition

Gets the value of the x property.

getX() - Method in class org.sbml._2001.ns.celldesigner.LayerSpeciesAlias

Gets the value of the x property.

getX() - Method in class org.sbml._2001.ns.celldesigner.Offset

Gets the value of the x property.

getX() - Method in class org.sbml._2001.ns.celldesigner.Point

Gets the value of the x property.

getX() - Method in class org.sbml._2001.ns.celldesigner.TagBounds

Gets the value of the x property.

getXor() - Method in class org.w3._1998.math.mathml.Apply

Gets the value of the xor property.

getY() - Method in class org.sbml._2001.ns.celldesigner.Block

Gets the value of the y property.

getY() - Method in class org.sbml._2001.ns.celldesigner.Bounds

Gets the value of the y property.

getY() - Method in class org.sbml._2001.ns.celldesigner.Halo

Gets the value of the y property.

getY() - Method in class org.sbml._2001.ns.celldesigner.InnerPosition

Gets the value of the y property.

getY() - Method in class org.sbml._2001.ns.celldesigner.LayerSpeciesAlias

Gets the value of the y property.

getY() - Method in class org.sbml._2001.ns.celldesigner.Offset

Gets the value of the y property.

getY() - Method in class org.sbml._2001.ns.celldesigner.Point

Gets the value of the y property.

getY() - Method in class org.sbml._2001.ns.celldesigner.TagBounds

Gets the value of the y property.

Glyph - Class in fr.curie.cd2sbgnml.graphics

Something that can be placed on a map, that is not a link.

Glyph(Point2D.Float, float, float, CdShape, SbgnShape) - Constructor for class fr.curie.cd2sbgnml.graphics.Glyph

Group - Class in org.sbml._2001.ns.celldesigner

Group of speciesAliases.

Group() - Constructor for class org.sbml._2001.ns.celldesigner.Group

group - Variable in class org.sbml._2001.ns.celldesigner.ListOfGroups

gt - Variable in class org.w3._1998.math.mathml.Apply

H

h - Variable in class org.sbml._2001.ns.celldesigner.Bounds

h - Variable in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias.BackupSize

h - Variable in class org.sbml._2001.ns.celldesigner.TagBounds

halo - Variable in class org.sbml._2001.ns.celldesigner.BlockDiagram

Halo - Class in org.sbml._2001.ns.celldesigner

Halo around a block(protein).

Halo() - Constructor for class org.sbml._2001.ns.celldesigner.Halo

hasOnlySubstanceUnits - Variable in class org.sbml._2001.ns.celldesigner.Species

hasOnlySubstanceUnits - Variable in class org.sbml.sbml.level2.version4.OriginalSpecies

hasProcess() - Method in class fr.curie.cd2sbgnml.model.GenericReactionModel

hasProcess(Reaction) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

hasProcess() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

hasUnitOfInfo(Glyph, String) - Static method in class fr.curie.cd2sbgnml.SBGNUtils

Return wether the glyph has at least one unit of information with label matching regexp.

height - Variable in class org.sbml._2001.ns.celldesigner.Block

height - Variable in class org.sbml._2001.ns.celldesigner.BoxSize

height - Variable in class org.sbml._2001.ns.celldesigner.Canvas

height - Variable in class org.sbml._2001.ns.celldesigner.DegradedShapeInBlockDiagram

height - Variable in class org.sbml._2001.ns.celldesigner.Halo

homodimer - Variable in class org.sbml._2001.ns.celldesigner.State

hypothetical - Variable in class org.sbml._2001.ns.celldesigner.SpeciesIdentity

I

IAnnotationsFeature - Interface in fr.curie.cd2sbgnml.xmlcdwrappers

id - Variable in class fr.curie.cd2sbgnml.xmlcdwrappers.ResidueWrapper

id - Variable in class org.sbml._2001.ns.celldesigner.AntisenseRNA

id - Variable in class org.sbml._2001.ns.celldesigner.BindingRegion

id - Variable in class org.sbml._2001.ns.celldesigner.BindingSiteInBlockDiagram

id - Variable in class org.sbml._2001.ns.celldesigner.CompartmentAlias

id - Variable in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

id - Variable in class org.sbml._2001.ns.celldesigner.DegradedInBlockDiagram

id - Variable in class org.sbml._2001.ns.celldesigner.EffectSiteInBlockDiagram

id - Variable in class org.sbml._2001.ns.celldesigner.ExternalNameForResidue

id - Variable in class org.sbml._2001.ns.celldesigner.Gene

id - Variable in class org.sbml._2001.ns.celldesigner.Group

id - Variable in class org.sbml._2001.ns.celldesigner.InternalLinkInBlockDiagram

id - Variable in class org.sbml._2001.ns.celldesigner.InternalOperatorInBlockDiagram

id - Variable in class org.sbml._2001.ns.celldesigner.Layer

id - Variable in class org.sbml._2001.ns.celldesigner.ModificationResidue

id - Variable in class org.sbml._2001.ns.celldesigner.Protein

id - Variable in class org.sbml._2001.ns.celldesigner.Region

id - Variable in class org.sbml._2001.ns.celldesigner.ResidueInBlockDiagram

id - Variable in class org.sbml._2001.ns.celldesigner.RNA

id - Variable in class org.sbml._2001.ns.celldesigner.Species

id - Variable in class org.sbml._2001.ns.celldesigner.SpeciesAlias

id - Variable in class org.sbml.sbml.level2.version4.Event

id - Variable in class org.sbml.sbml.level2.version4.FunctionDefinition

id - Variable in class org.sbml.sbml.level2.version4.OriginalCompartment

id - Variable in class org.sbml.sbml.level2.version4.OriginalModel

id - Variable in class org.sbml.sbml.level2.version4.OriginalReaction

id - Variable in class org.sbml.sbml.level2.version4.OriginalSpecies

id - Variable in class org.sbml.sbml.level2.version4.Parameter

id - Variable in class org.sbml.sbml.level2.version4.UnitDefinition

id - Variable in class org.w3._1998.math.mathml.Annotation

id - Variable in class org.w3._1998.math.mathml.AnnotationXml

id - Variable in class org.w3._1998.math.mathml.Ci

id - Variable in class org.w3._1998.math.mathml.Cn

id - Variable in class org.w3._1998.math.mathml.Csymbol

id - Variable in class org.w3._1998.math.mathml.MathBase

index - Variable in class org.sbml._2001.ns.celldesigner.LineDirection

inferAnchorPoint(Point2D.Float, ReactantWrapper, Rectangle2D.Float) - Static method in class fr.curie.cd2sbgnml.SBGNML2CD

inferProcessAnchorPoint(Point2D.Float, Process) - Static method in class fr.curie.cd2sbgnml.SBGNML2CD

infinity - Variable in class org.w3._1998.math.mathml.Lambda

infinity - Variable in class org.w3._1998.math.mathml.Math

infinity - Variable in class org.w3._1998.math.mathml.NodeContainer

infinity - Variable in class org.w3._1998.math.mathml.Otherwise

infinity - Variable in class org.w3._1998.math.mathml.Semantics

info - Variable in class org.sbml._2001.ns.celldesigner.CompartmentAlias

info - Variable in class org.sbml._2001.ns.celldesigner.ComplexSpeciesAlias

Info - Class in org.sbml._2001.ns.celldesigner

Java class for info complex type.

Info() - Constructor for class org.sbml._2001.ns.celldesigner.Info

info - Variable in class org.sbml._2001.ns.celldesigner.SpeciesAlias

initialAmount - Variable in class org.sbml._2001.ns.celldesigner.Species

initialAmount - Variable in class org.sbml.sbml.level2.version4.OriginalSpecies

initialConcentration - Variable in class org.sbml._2001.ns.celldesigner.Species

initialConcentration - Variable in class org.sbml.sbml.level2.version4.OriginalSpecies

innerPosition - Variable in class org.sbml._2001.ns.celldesigner.BriefView

InnerPosition - Class in org.sbml._2001.ns.celldesigner

Innerposition relative to a surrounding object.

InnerPosition() - Constructor for class org.sbml._2001.ns.celldesigner.InnerPosition

innerPosition - Variable in class org.sbml._2001.ns.celldesigner.UsualView

innerWidth - Variable in class org.sbml._2001.ns.celldesigner.DoubleLine

INotesFeature - Interface in fr.curie.cd2sbgnml.xmlcdwrappers

InternalLinkInBlockDiagram - Class in org.sbml._2001.ns.celldesigner

Link between operators, residues, binding sites, effect sites.

InternalLinkInBlockDiagram() - Constructor for class org.sbml._2001.ns.celldesigner.InternalLinkInBlockDiagram

internalLinkInBlockDiagram - Variable in class org.sbml._2001.ns.celldesigner.ListOfInternalLinksInBlockDiagram

InternalOperatorInBlockDiagram - Class in org.sbml._2001.ns.celldesigner

Operator inside of a block(protein) describing logic.

InternalOperatorInBlockDiagram() - Constructor for class org.sbml._2001.ns.celldesigner.InternalOperatorInBlockDiagram

internalOperatorInBlockDiagram - Variable in class org.sbml._2001.ns.celldesigner.ListOfInternalOperatorsInBlockDiagram

internalOperatorValueInBlockDiagram - Variable in class org.sbml._2001.ns.celldesigner.InternalOperatorInBlockDiagram

InternalOperatorValueInBlockDiagram - Class in org.sbml._2001.ns.celldesigner

Assigned value to the operator.

InternalOperatorValueInBlockDiagram() - Constructor for class org.sbml._2001.ns.celldesigner.InternalOperatorValueInBlockDiagram

interpolationByDistance(Point2D.Float, Point2D.Float, float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

see https://stackoverflow.com/a/9343170 return a point on the line defined by p1 and p2 that as away from p1 by d units

interpolationByRatio(Point2D.Float, Point2D.Float, float) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

see https://stackoverflow.com/a/9343170 return a point on the line defined by p1 and p2 that is ratio% away from p1

interpretToUTF8(String) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.Utils

Resolve some special encoded strings in CellDesigner as UTF8 chars.

isActive() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.AliasWrapper

isActive() - Method in class org.sbml._2001.ns.celldesigner.Region

Gets the value of the active property.

isArrow - Variable in class org.sbml._2001.ns.celldesigner.LayerFreeLine

isBoundaryCondition() - Method in class org.sbml._2001.ns.celldesigner.Species

Gets the value of the boundaryCondition property.

isBoundaryCondition() - Method in class org.sbml.sbml.level2.version4.OriginalSpecies

Gets the value of the boundaryCondition property.

isBranchType() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

isBranchTypeLeft() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

isBranchTypeRight() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactionWrapper

isComplex() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

isConstant() - Method in class org.sbml._2001.ns.celldesigner.Species

Gets the value of the constant property.

isConstant() - Method in class org.sbml.sbml.level2.version4.OriginalCompartment

Gets the value of the constant property.

isConstant() - Method in class org.sbml.sbml.level2.version4.OriginalSpecies

Gets the value of the constant property.

isConstant() - Method in class org.sbml.sbml.level2.version4.Parameter

Gets the value of the constant property.

isCorrectType(File) - Method in class fr.curie.cd2sbgnml.CellDesignerSBFCModel

isDefinedAndFinite(double) - Static method in class fr.curie.cd2sbgnml.graphics.GeometryUtils

isDotted - Variable in class org.sbml._2001.ns.celldesigner.LayerFreeLine

isFast() - Method in class org.sbml.sbml.level2.version4.OriginalReaction

Gets the value of the fast property.

isHasOnlySubstanceUnits() - Method in class org.sbml._2001.ns.celldesigner.Species

Gets the value of the hasOnlySubstanceUnits property.

isHasOnlySubstanceUnits() - Method in class org.sbml.sbml.level2.version4.OriginalSpecies

Gets the value of the hasOnlySubstanceUnits property.

isHypothetical() - Method in class org.sbml._2001.ns.celldesigner.SpeciesIdentity

Gets the value of the hypothetical property.

isIncludedSpecies() - Method in class fr.curie.cd2sbgnml.xmlcdwrappers.SpeciesWrapper

isIsArrow() - Method in class org.sbml._2001.ns.celldesigner.LayerFreeLine

Gets the value of the isArrow property.

isIsDotted() - Method in class org.sbml._2001.ns.celldesigner.LayerFreeLine

Gets the value of the isDotted property.

isLocked() - Method in class org.sbml._2001.ns.celldesigner.Layer

Gets the value of the locked property.

isLogicGate(Glyph) - Static method in class fr.curie.cd2sbgnml.SBGNUtils

isLogicGate(Modification) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.ReactantWrapper

isNoteEmpty(Element) - Static method in class fr.curie.cd2sbgnml.xmlcdwrappers.Utils

Celldesigner saves empty notes of the form