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

A

absoluteCx - Variable in class org.sbml.jsbml.ext.render.Ellipse

absoluteCx - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteCy - Variable in class org.sbml.jsbml.ext.render.Ellipse

absoluteCy - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteCz - Variable in class org.sbml.jsbml.ext.render.Ellipse

absoluteCz - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteFx - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteFy - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteFz - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteHeight - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteR - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteRx - Variable in class org.sbml.jsbml.ext.render.Ellipse

absoluteRx - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteRy - Variable in class org.sbml.jsbml.ext.render.Ellipse

absoluteRy - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteWidth - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteX - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteX1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteX2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteY - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteY1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteY2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteZ - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteZ1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

absoluteZ2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

AbstractLayoutBuilder<P,NodeT,ArcT> - Class in org.sbml.jsbml.ext.render.director

This abstract class combines the interfaces LayoutBuilder and LayoutFactory.

AbstractLayoutBuilder() - Constructor for class org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder

AbstractRenderPlugin - Class in org.sbml.jsbml.ext.render

AbstractRenderPlugin(SBase) - Constructor for class org.sbml.jsbml.ext.render.AbstractRenderPlugin

Creates an AbstractRenderPlugin instance

AbstractRenderPlugin() - Constructor for class org.sbml.jsbml.ext.render.AbstractRenderPlugin

Creates a AbstractRenderPlugin instance.

AbstractRenderPlugin(AbstractRenderPlugin) - Constructor for class org.sbml.jsbml.ext.render.AbstractRenderPlugin

Clone constructor

AbstractSBGNnode<T> - Class in org.sbml.jsbml.ext.render.director

AbstractSBGNnode() - Constructor for class org.sbml.jsbml.ext.render.director.AbstractSBGNnode

AbstractSBGNNodeWithCloneMarker<T> - Class in org.sbml.jsbml.ext.render.director

AbstractSBGNNodeWithCloneMarker() - Constructor for class org.sbml.jsbml.ext.render.director.AbstractSBGNNodeWithCloneMarker

AbstractSBGNProcessNode<T> - Class in org.sbml.jsbml.ext.render.director

AbstractSBGNProcessNode() - Constructor for class org.sbml.jsbml.ext.render.director.AbstractSBGNProcessNode

addChildElement(Transformation2D) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Adds the given element to the end of the list of children elements.

addColorDefinition(ColorDefinition) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

addCurveSegment(CurveSegment) - Method in class org.sbml.jsbml.ext.render.Polygon

Adds a new CurveSegment to the Polygon.listOfCurveSegments.

addCurveSegment(int, CurveSegment) - Method in class org.sbml.jsbml.ext.render.Polygon

addCurveSegment(CurveSegment) - Method in class org.sbml.jsbml.ext.render.RenderCurve

Adds a new CurveSegment to the RenderCurve.listOfCurveSegments.

addCurveSegment(int, CurveSegment) - Method in class org.sbml.jsbml.ext.render.RenderCurve

addElement(RenderPoint) - Method in class org.sbml.jsbml.ext.render.Polygon

addElement(RenderPoint) - Method in class org.sbml.jsbml.ext.render.RenderCurve

addElement(Transformation2D) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Adds a new Transformation2D to the listOfElements.

addGlobalRenderInformation(GlobalRenderInformation) - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

addGradientBase(GradientBase) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

addGradientStop(GradientStop) - Method in class org.sbml.jsbml.ext.render.GradientBase

addLayoutedEdge(SpeciesReferenceGlyph, ReactionGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

Add a layouted edge to the input of the algorithm.

addLayoutedGlyph(GraphicalObject) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

Add a fully layouted glyph (i.e.

addLineEnding(LineEnding) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

addLocalRenderInformation(LocalRenderInformation) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

addLocalStyle(LocalStyle) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

addStrokeDash(Short) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

addStyle(Style) - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

addUnlayoutedEdge(SpeciesReferenceGlyph, ReactionGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

Add an unlayouted edge to the input of the algorithm.

addUnlayoutedGlyph(GraphicalObject) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

Add a glyph with missing layout information (i.e.

arrayToWhitespaceSeparatedString(String[]) - Static method in class org.sbml.jsbml.ext.render.XMLTools

AssociationNode<T> - Interface in org.sbml.jsbml.ext.render.director

B

backgroundColor - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

backgroundColor - Variable in class org.sbml.jsbml.ext.render.RenderInformationBase

basepoint1_x - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

basepoint1_y - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

basepoint1_z - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

basepoint2_x - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

basepoint2_y - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

basepoint2_z - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

boundingBox - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

buildCompartment(CompartmentGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method for the drawing of a compartment with the size and position of the BoundingBox of the given CompartmentGlyph

buildConnectingArc(SpeciesReferenceGlyph, ReactionGlyph, double) - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method for the drawing of a connecting arc or line with the size and position specified by the given SpeciesReferenceGlyph

buildCubicBezier(CubicBezier, double) - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method to draw an arc between the two base points of the given CubicBezier.

buildEntityPoolNode(SpeciesGlyph, boolean) - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method for the drawing of an entity pool node with the given size and position of the BoundingBox of the given SpeciesGlyph

builderEnd() - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method for actions that have to be done at the end of the builder e.g.

builderStart(Layout) - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method for preparations that have to be done at the beginning of the builder, e.g., the commands at the beginning of a LaTeX document

buildProcessNode(ReactionGlyph, double, double) - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method for the drawing of a process node with the size and position of the BoundingBox of the given ReactionGlyph

buildTextGlyph(TextGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method for drawing/writing the given TextGlyph

C

calculateAverageCurvePosition(SpeciesReferenceRole, List<SpeciesReferenceGlyph>) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

This method calculates the average position of a curve at the direction of the reaction glyph, if the role of a species reference glyph is PRODUCT, the start point of the curve is at the reaction glyph, else the start point is at the species and the end point at the reaction glyph.

calculateAverageSpeciesPosition(SpeciesReferenceRole, List<SpeciesReferenceGlyph>) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

method calculates the average position of the species glyphs belonging to the given list of species reference glyphs, the role of the species reference glyph must be of the given type

calculateCenter(GraphicalObject) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

Compute the coordinates of the central point of a GraphicalObject.

calculateCenter(GraphicalObject, int, int) - Static method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

calculateOldSpeciesGlyphDockingPosition(Point, SimpleLayoutAlgorithm.RelativePosition, SpeciesGlyph) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

Deprecated.

calculateReactionGlyphDockingPoint(ReactionGlyph, double, SpeciesReferenceGlyph) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

c

calculateReactionGlyphRotationAngle(ReactionGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

method to calculate the rotation angle of the lines from the reaction box, in degrees

calculateReactionGlyphRotationAngle(ReactionGlyph) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

calculateRotationAngle(Point, Point) - Static method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

Calculate the rotation angle for a line determined by two Points.

calculateSpeciesGlyphDockingPosition(Point, ReactionGlyph, SpeciesReferenceRole, SpeciesGlyph) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

Compute the docking Point at the species for the curve defined by the ReactionGlyph and the SpeciesGlyph.

Catalysis<T> - Interface in org.sbml.jsbml.ext.render.director

interface all the different graphical representations for catalysis arcs have to implement

center(BoundingBox) - Static method in class org.sbml.jsbml.ext.render.director.Geometry

Calculates the center of the given bounding box and returns a point representing that center.

clone() - Method in class org.sbml.jsbml.ext.render.ColorDefinition

clone() - Method in class org.sbml.jsbml.ext.render.DefaultValues

clone() - Method in class org.sbml.jsbml.ext.render.Ellipse

clone() - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

clone() - Method in class org.sbml.jsbml.ext.render.GradientBase

clone() - Method in class org.sbml.jsbml.ext.render.GradientStop

clone() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

clone() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

clone() - Method in class org.sbml.jsbml.ext.render.Image

clone() - Method in class org.sbml.jsbml.ext.render.LinearGradient

clone() - Method in class org.sbml.jsbml.ext.render.LineEnding

clone() - Method in class org.sbml.jsbml.ext.render.ListOfGlobalRenderInformation

clones this class

clone() - Method in class org.sbml.jsbml.ext.render.ListOfLocalRenderInformation

clones this class

clone() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

clone() - Method in class org.sbml.jsbml.ext.render.LocalStyle

clone() - Method in class org.sbml.jsbml.ext.render.Polygon

clone() - Method in class org.sbml.jsbml.ext.render.RadialGradient

clone() - Method in class org.sbml.jsbml.ext.render.Rectangle

clone() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

clone() - Method in class org.sbml.jsbml.ext.render.RenderCurve

clone() - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin

clone() - Method in class org.sbml.jsbml.ext.render.RenderGroup

clone() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

clone() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

clone() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

clone() - Method in class org.sbml.jsbml.ext.render.RenderPoint

clone() - Method in class org.sbml.jsbml.ext.render.Style

clone() - Method in class org.sbml.jsbml.ext.render.Text

clone() - Method in class org.sbml.jsbml.ext.render.Transformation

clone() - Method in class org.sbml.jsbml.ext.render.Transformation2D

ColorDefinition - Class in org.sbml.jsbml.ext.render

ColorDefinition() - Constructor for class org.sbml.jsbml.ext.render.ColorDefinition

Creates an ColorDefinition instance

ColorDefinition(String) - Constructor for class org.sbml.jsbml.ext.render.ColorDefinition

Creates a ColorDefinition instance with an id.

ColorDefinition(String, Color) - Constructor for class org.sbml.jsbml.ext.render.ColorDefinition

Creates a ColorDefinition instance with an id.

ColorDefinition(int, int) - Constructor for class org.sbml.jsbml.ext.render.ColorDefinition

Creates a ColorDefinition instance with a level and version.

ColorDefinition(String, int, int) - Constructor for class org.sbml.jsbml.ext.render.ColorDefinition

Creates a ColorDefinition instance with an id, level, and version.

ColorDefinition(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.render.ColorDefinition

Creates a ColorDefinition instance with an id, name, level, and version.

ColorDefinition(ColorDefinition) - Constructor for class org.sbml.jsbml.ext.render.ColorDefinition

Clone constructor

colorDefiniton - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Compartment<T> - Class in org.sbml.jsbml.ext.render.director

Compartment() - Constructor for class org.sbml.jsbml.ext.render.director.Compartment

COMPARTMENT_LINK - Static variable in class org.sbml.jsbml.ext.render.director.LayoutDirector

Constant for use as the key for compartment links, also see LayoutDirector.LAYOUT_LINK.

completeGlyphs() - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

Return the input set of unlayouted glyphs with completed layout information.

Consumption<T> - Interface in org.sbml.jsbml.ext.render.director

interface all the different graphical representations for consumption arcs have to implement

correctDimensions(GraphicalObject) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

Correct the dimensions of a GraphicalObject by changing its BoundingBox.

correctRotationAngle(double) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

Normalize a given rotation angle, i.e., express the angle in the range from 0° to 90° (excluding 90°).

create() - Method in class org.sbml.jsbml.ext.render.director.GlyphCreator

compartment, species, reactions, textglyph TODO do not create one glyph per species, instead create exactly one glyph for each species that acts as a main substrate and product and create multiple glyphs for all species that act as side-substrates or side products this produces a far more useful graph

createArc(SpeciesReferenceGlyph, ReactionGlyph) - Method in class org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder

Create a SBGNArc for the given SpeciesReferenceGlyph and ReactionGlyph.

createAssociationNode() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createBoundingBox() - Method in class org.sbml.jsbml.ext.render.LineEnding

createBoundingBoxWithLevelAndVersion() - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

Creates a BoundingBox with the level and version of this layout.

createCatalysis() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createCompartment() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createCompartmentGlyphDimension(CompartmentGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

method to create a Dimensions for a CompartmentGlyph if it was missing in the layout model

createCompartmentGlyphPosition(CompartmentGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

Deprecated.

createConsumption() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createCubicBezier() - Method in class org.sbml.jsbml.ext.render.Polygon

Creates a new CubicBezier instance and adds it to the Polygon.listOfCurveSegments list.

createCubicBezier() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Creates a new CubicBezier instance and adds it to the RenderCurve.listOfCurveSegments list.

createCurve(ReactionGlyph, SpeciesReferenceGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

method to create the Curve of a SpeciesReferenceGlyph, starting or ending at the given ReactionGlyph

createCurve() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Creates a new RenderCurve element, adds it to the ListOfElements list and returns it.

createDissociationNode() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createElement() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Deprecated.

use#createRenderPoint()

createEllipse() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Creates a new Ellipse element, adds it to the ListOfElements list and returns it.

createGlobalRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

create a new GlobalRenderInformation element and adds it to the ListOfGlobalRenderInformation list

createGlobalRenderInformation(String) - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

create a new GlobalRenderInformation element and adds it to the ListOfGlobalRenderInformation list

createGlyphBoundingBox(GraphicalObject, SpeciesReferenceGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

method to create a BoundingBox for every kind of GraphicalObject.

createGradientStop(double, String) - Method in class org.sbml.jsbml.ext.render.GradientBase

create a new GradientStop element and adds it to the ListOfGradientStops list

createImage() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Creates a new Image element, adds it to the ListOfElements list and returns it.

createInhibition() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createLayoutDimension() - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

method to create a Dimensions for the layout if it was missing in the layout model

createLineSegment() - Method in class org.sbml.jsbml.ext.render.Polygon

Creates a new LineSegment instance and adds it to the Polygon.listOfCurveSegments list.

createLineSegment() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Creates a new LineSegment instance and adds it to the RenderCurve.listOfCurveSegments list.

createLocalRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

Creates a new LocalRenderInformation element and adds it to the ListOfLocalRenderInformation list

createLocalRenderInformation(String) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

Creates a new LocalRenderInformation element and adds it to the ListOfLocalRenderInformation list

createMacromolecule() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createModulation() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createNecessaryStimulation() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createNucleicAcidFeature() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createOmittedProcessNode() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createPerturbingAgent() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.RenderParser

createPluginFor(ASTNode) - Method in class org.sbml.jsbml.xml.parsers.RenderParser

createPolygon() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Creates a new Polygon element, adds it to the ListOfElements list and returns it.

createProcessNode() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createProduction() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createReactionGlyphDimension(ReactionGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

method to create a Dimensions for a ReactionGlyph if it was missing in the layout model

createReactionGlyphDimension(ReactionGlyph) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

createReactionGlyphPosition(ReactionGlyph) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

createReactionGlyphPositionNew(ReactionGlyph) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

createRectangle() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Creates a new Rectangle element, adds it to the ListOfElements list and returns it.

createRenderCubicBezier() - Method in class org.sbml.jsbml.ext.render.Polygon

Creates a new RenderCubicBezier instance and adds it to the ListOfElements list

createRenderCubicBezier() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Creates a new RenderCubicBezier instance and adds it to the ListOfElements list

createRenderGroup() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Creates a new RenderGroup element, adds it to the ListOfElements list and returns it.

createRenderPoint() - Method in class org.sbml.jsbml.ext.render.Polygon

Creates a new RenderPoint instance and adds it to the ListOfElements list

createRenderPoint() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Creates a new RenderPoint instance and adds it to the ListOfElements list

createReversibleConsumption() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createSimpleChemical() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createSourceSink() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createSpeciesGlyphDimension() - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

method to create a Dimensions for a SpeciesGlyph if it was missing in the layout model

createSpeciesReferenceGlyphDimension(ReactionGlyph, SpeciesReferenceGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

method to create a Dimensions for a SpeciesReferenceGlyph if it was missing in the layout model

createSpeciesReferenceGlyphPosition(ReactionGlyph, SpeciesReferenceGlyph) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

createStimulation() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createText() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Creates a new Text element, adds it to the ListOfElements list and returns it.

createTextGlyphDimension(TextGlyph) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

method to create a Dimensions for a TextGlyph if it was missing in the layout model

createUncertainProcessNode() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

createUnspecifiedNode() - Method in interface org.sbml.jsbml.ext.render.director.LayoutFactory

cx - Variable in class org.sbml.jsbml.ext.render.Ellipse

cx - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

cy - Variable in class org.sbml.jsbml.ext.render.Ellipse

cy - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

cz - Variable in class org.sbml.jsbml.ext.render.Ellipse

cz - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

D

decodeStringToArrayDouble(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools

decodeStringToArrayShort(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools

decodeStringToColor(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools

DefaultValues - Class in org.sbml.jsbml.ext.render

Encodes default values within the containing ListOfGlobalRenderInformation or ListOfLocalRenderInformation.

DefaultValues() - Constructor for class org.sbml.jsbml.ext.render.DefaultValues

Creates an DefaultValues instance

DefaultValues(int, int) - Constructor for class org.sbml.jsbml.ext.render.DefaultValues

Creates a DefaultValues instance with a level and version.

DefaultValues(DefaultValues) - Constructor for class org.sbml.jsbml.ext.render.DefaultValues

Clone constructor

defaultValues - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

determineRole(SpeciesReferenceGlyph) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector

DissociationNode<T> - Interface in org.sbml.jsbml.ext.render.director

draw(double, double, double, double, double, double) - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNNodeWithCloneMarker

draw(Curve, double, Point) - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNProcessNode

draw(CurveSegment, double) - Method in interface org.sbml.jsbml.ext.render.director.SBGNArc

Method for drawing the connecting arc, with appropriate line ending and the given line width

draw(Curve, double) - Method in interface org.sbml.jsbml.ext.render.director.SBGNArc

Draw a whole curve consisting of multiple curve segments with the given line width.

draw(Curve) - Method in interface org.sbml.jsbml.ext.render.director.SBGNArc

Draw a whole curve consisting of multiple curve segments.

draw(double, double, double, double, double, double) - Method in interface org.sbml.jsbml.ext.render.director.SBGNNode

Method for drawing an entity pool node with the specified position and size of a BoundingBox

draw(Curve, double, Point) - Method in interface org.sbml.jsbml.ext.render.director.SBGNProcessNode

Draw a whole curve consisting of multiple curve segments with the given line width.

draw(double, double, double, double, double, double, double, Point) - Method in interface org.sbml.jsbml.ext.render.director.SBGNProcessNode

drawCurveSegment(CurveSegment, double, Point) - Method in interface org.sbml.jsbml.ext.render.director.SBGNProcessNode

E

edgeIsLayouted(ReactionGlyph, SpeciesReferenceGlyph) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Check if the incoming edge is layouted, i.e.

element - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Ellipse - Class in org.sbml.jsbml.ext.render

Encodes an ellipse.

Ellipse() - Constructor for class org.sbml.jsbml.ext.render.Ellipse

Creates a new Ellipse instance.

Ellipse(Ellipse) - Constructor for class org.sbml.jsbml.ext.render.Ellipse

Creates a new Ellipse instance, copied from the given ellipse.

Ellipse(int, int) - Constructor for class org.sbml.jsbml.ext.render.Ellipse

Creates a new Ellipse instance.

ellipse - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

enableRotationMapping - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

encodeArrayDoubleToString(Double[]) - Static method in class org.sbml.jsbml.ext.render.XMLTools

encodeArrayShortToString(Short[]) - Static method in class org.sbml.jsbml.ext.render.XMLTools

encodeColorToString(Color) - Static method in class org.sbml.jsbml.ext.render.XMLTools

endHead - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

endHead - Variable in class org.sbml.jsbml.ext.render.RenderCurve

equals(Object) - Method in class org.sbml.jsbml.ext.render.ColorDefinition

equals(Object) - Method in class org.sbml.jsbml.ext.render.Ellipse

equals(Object) - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

equals(Object) - Method in class org.sbml.jsbml.ext.render.GradientBase

equals(Object) - Method in class org.sbml.jsbml.ext.render.GradientStop

equals(Object) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

equals(Object) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

equals(Object) - Method in class org.sbml.jsbml.ext.render.Image

equals(Object) - Method in class org.sbml.jsbml.ext.render.LinearGradient

equals(Object) - Method in class org.sbml.jsbml.ext.render.LineEnding

equals(Object) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

equals(Object) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

equals(Object) - Method in class org.sbml.jsbml.ext.render.LocalStyle

equals(Object) - Method in class org.sbml.jsbml.ext.render.Polygon

equals(Object) - Method in class org.sbml.jsbml.ext.render.RadialGradient

equals(Object) - Method in class org.sbml.jsbml.ext.render.Rectangle

equals(Object) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

equals(Object) - Method in class org.sbml.jsbml.ext.render.RenderCurve

equals(Object) - Method in class org.sbml.jsbml.ext.render.RenderCurveSegment

equals(Object) - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.render.RenderGroup

equals(Object) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

equals(Object) - Method in class org.sbml.jsbml.ext.render.RenderPoint

equals(Object) - Method in class org.sbml.jsbml.ext.render.Style

equals(Object) - Method in class org.sbml.jsbml.ext.render.Text

equals(Object) - Method in class org.sbml.jsbml.ext.render.Transformation

equals(Object) - Method in class org.sbml.jsbml.ext.render.Transformation2D

euclideanDistance(Point, Point) - Static method in class org.sbml.jsbml.ext.render.director.Geometry

Calculates the Eucledian distance between two points a and b.

F

fill - Variable in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

fill - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

fillRule - Variable in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

fillRule - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

findLayout(GraphicalObject) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

Find the Layout to which the given GraphicalObject belongs.

findSpeciesGlyphByRole(List<SpeciesReferenceGlyph>, SpeciesReferenceRole) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

Return the first SpeciesGlyph from a list of SpeciesReferenceGlyphs which has the given SpeciesReferenceRole.

FontFamily - Enum in org.sbml.jsbml.ext.render

The FontFamily enumeration gives a hint as to which font is to be used when rendering Text elements.

fontFamily - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

FontRenderStyle - Interface in org.sbml.jsbml.ext.render

fontSize - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

fontStyleItalic - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

fontStyleItalicFalse - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

fontStyleItalicToString(boolean) - Static method in class org.sbml.jsbml.ext.render.XMLTools

fontStyleItalicTrue - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

fontWeightBold - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

fontWeightBoldFalse - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

fontWeightBoldToString(boolean) - Static method in class org.sbml.jsbml.ext.render.XMLTools

fontWeightBoldTrue - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

fromString(String) - Static method in enum org.sbml.jsbml.ext.render.RenderCurveSegment.Type

Returns the Type corresponding to the given String.

fx - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

fy - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

fz - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

G

Geometry - Class in org.sbml.jsbml.ext.render.director

Geometry() - Constructor for class org.sbml.jsbml.ext.render.director.Geometry

getAddWhiskers() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Returns the value of addWhiskers

getAlgorithm() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.GradientBase

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.GradientStop

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.Image

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.LineEnding

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.Polygon

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.Rectangle

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.RenderCurve

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.render.Style

getBackgroundColor() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getBoundingBox() - Method in class org.sbml.jsbml.ext.render.LineEnding

getBuilder() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.GradientBase

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.GradientStop

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.Image

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.LineEnding

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.Polygon

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.Rectangle

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.RenderCurve

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.RenderGroup

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.render.Style

getChildCount() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

getChildCount() - Method in class org.sbml.jsbml.ext.render.GradientBase

getChildCount() - Method in class org.sbml.jsbml.ext.render.GradientStop

getChildCount() - Method in class org.sbml.jsbml.ext.render.Image

getChildCount() - Method in class org.sbml.jsbml.ext.render.LineEnding

getChildCount() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

getChildCount() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

getChildCount() - Method in class org.sbml.jsbml.ext.render.Polygon

getChildCount() - Method in class org.sbml.jsbml.ext.render.Rectangle

getChildCount() - Method in class org.sbml.jsbml.ext.render.RenderCurve

getChildCount() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getChildCount() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getChildCount() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.render.Style

getColorDefinition(String) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

getColorDefinitionCount() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

getCurveSegment(int) - Method in class org.sbml.jsbml.ext.render.Polygon

Gets an element from the Polygon.listOfCurveSegments at the given index.

getCurveSegment(int) - Method in class org.sbml.jsbml.ext.render.RenderCurve

Gets an element from the RenderCurve.listOfCurveSegments at the given index.

getCurveSegmentCount() - Method in class org.sbml.jsbml.ext.render.Polygon

Returns the number of CurveSegments in this RenderCurve.

getCurveSegmentCount() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Returns the number of CurveSegments in this RenderCurve.

getCx() - Method in class org.sbml.jsbml.ext.render.Ellipse

getCx() - Method in class org.sbml.jsbml.ext.render.RadialGradient

getCy() - Method in class org.sbml.jsbml.ext.render.Ellipse

getCy() - Method in class org.sbml.jsbml.ext.render.RadialGradient

getCz() - Method in class org.sbml.jsbml.ext.render.Ellipse

getCz() - Method in class org.sbml.jsbml.ext.render.RadialGradient

getDefaultValue(String) - Method in class org.sbml.jsbml.ext.render.DefaultValues

getDefaultValues() - Method in class org.sbml.jsbml.ext.render.DefaultValues

getDefaultValues() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Returns the value of ListOfRenderInformation.defaultValues.

getElement(int) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Gets an element from the listOfElements at the given index.

getElement(String) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Gets an element from the listOfElements, with the given id.

getElementCount() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns the number of Transformation2Ds in this RenderGroup.

getElementName() - Method in class org.sbml.jsbml.ext.render.GradientStop

getElementName() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

getElementName() - Method in class org.sbml.jsbml.ext.render.LocalStyle

getElementName() - Method in class org.sbml.jsbml.ext.render.RenderCurve

getElementName() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getElementName() - Method in class org.sbml.jsbml.ext.render.RenderPoint

getEndHead() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Returns the value of endHead

getEndHead() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getFill() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

getFillRule() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

getFontFamily() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

getFontFamily() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getFontFamily() - Method in class org.sbml.jsbml.ext.render.Text

getFontSize() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

getFontSize() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getFontSize() - Method in class org.sbml.jsbml.ext.render.Text

getFontStyleItalic() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns the value of fontStyleItalic

getFontWeightBold() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns the value of fontWeightBold

getFx() - Method in class org.sbml.jsbml.ext.render.RadialGradient

getFy() - Method in class org.sbml.jsbml.ext.render.RadialGradient

getFz() - Method in class org.sbml.jsbml.ext.render.RadialGradient

getGroup() - Method in class org.sbml.jsbml.ext.render.LineEnding

getGroup() - Method in class org.sbml.jsbml.ext.render.Style

getHeight() - Method in class org.sbml.jsbml.ext.render.Image

getHeight() - Method in class org.sbml.jsbml.ext.render.Rectangle

getHref() - Method in class org.sbml.jsbml.ext.render.Image

getIDList() - Method in class org.sbml.jsbml.ext.render.LocalStyle

getLayout() - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

getLayout() - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

getLayoutIndex() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

getLineWidth() - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNnode

getLineWidth() - Method in interface org.sbml.jsbml.ext.render.director.SBGNNode

getListOfColorDefinitions() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getListOfCurveSegments() - Method in class org.sbml.jsbml.ext.render.Polygon

Returns the Polygon.listOfCurveSegments.

getListOfCurveSegments() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Returns the RenderCurve.listOfCurveSegments.

getListOfElements() - Method in class org.sbml.jsbml.ext.render.Polygon

getListOfElements() - Method in class org.sbml.jsbml.ext.render.RenderCurve

getListOfElements() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns the listOfElements.

getListOfGlobalRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

getListOfGradientDefinitions() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getListOfGradientStops() - Method in class org.sbml.jsbml.ext.render.GradientBase

getListOfLineEndings() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getListOfLocalRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

getListOfLocalStyles() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

getListOfStyles() - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

getLocalRenderInformation(int) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

getLocalStyleCount() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.RenderParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.RenderParser

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.render.RenderConstants

Returns the namespace URI corresponding to the given level and version.

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.RenderParser

getNumCurveSegments() - Method in class org.sbml.jsbml.ext.render.Polygon

Returns the number of CurveSegments in this RenderCurve.

getNumCurveSegments() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Returns the number of CurveSegments in this RenderCurve.

getNumElements() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns the number of Transformation2Ds in this RenderGroup.

getObjectRole() - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin

Returns the value of RenderGraphicalObjectPlugin.objectRole.

getOffset() - Method in class org.sbml.jsbml.ext.render.GradientStop

getPackageName() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.RenderParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.RenderParser

getPointOfContactToProduct() - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNProcessNode

getPointOfContactToProduct() - Method in interface org.sbml.jsbml.ext.render.director.SBGNProcessNode

getPointOfContactToSubstrate() - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNProcessNode

getPointOfContactToSubstrate() - Method in interface org.sbml.jsbml.ext.render.director.SBGNProcessNode

getPrefix() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

getProduct() - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

getProduct() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Return the product of the building process.

getProgramName() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getProgramVersion() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getR() - Method in class org.sbml.jsbml.ext.render.RadialGradient

getReferenceRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

getRelativePosition(Point, Point) - Static method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

method calculates the relative position of the second bounding box with respect to the first bounding box ABOVE: middle of the second bounding box is directly above the middle of the first bounding box BELOW: middle of the second bounding box is directly below the middle of the first bounding box LEFT: middle of the second bounding box is directly left of the middle of the first bounding box RIGHT: middle of the second bounding box is directly right of the middle of the first bounding box

getRenderFillColor(SpeciesGlyph) - Static method in class org.sbml.jsbml.ext.render.director.RenderProcessor

getRenderInformation() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

getRoleList() - Method in class org.sbml.jsbml.ext.render.Style

getRx() - Method in class org.sbml.jsbml.ext.render.Ellipse

getRx() - Method in class org.sbml.jsbml.ext.render.Rectangle

getRy() - Method in class org.sbml.jsbml.ext.render.Ellipse

getRy() - Method in class org.sbml.jsbml.ext.render.Rectangle

getSBGNArc(int) - Method in class org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder

Creates the correct SBGNArc according to the given SBO term.

getSBGNArc(SpeciesReferenceRole) - Method in class org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder

Creates the correct SBGNArc according to the given SpeciesReferenceRole.

getSBGNNode(int) - Method in class org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder

Create the correct SBGNNode according to the given SBO term.

getSBGNReactionNode(int) - Method in class org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder

Create the correct process node according to the SBO term of the reaction.

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.RenderParser

getSpreadMethod() - Method in class org.sbml.jsbml.ext.render.GradientBase

getStartHead() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Returns the value of startHead

getStartHead() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getStopColor() - Method in class org.sbml.jsbml.ext.render.GradientStop

getStroke() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

getStrokeDash(int) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

getStrokeDashArray() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

getStrokeWidth() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

getTextAnchor() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

getTextAnchor() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getTextAnchor() - Method in class org.sbml.jsbml.ext.render.Text

getTransform() - Method in class org.sbml.jsbml.ext.render.Transformation2D

getType() - Method in class org.sbml.jsbml.ext.render.RenderCurveSegment

Returns the type.

getTypeList() - Method in class org.sbml.jsbml.ext.render.Style

getURI() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

getValue() - Method in class org.sbml.jsbml.ext.render.ColorDefinition

getVersionMajor() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Returns the value of versionMajor

getVersionMinor() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Returns the value of versionMinor

getVTextAnchor() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

getVTextAnchor() - Method in class org.sbml.jsbml.ext.render.RenderGroup

getVTextAnchor() - Method in class org.sbml.jsbml.ext.render.Text

getWidth() - Method in class org.sbml.jsbml.ext.render.Image

getWidth() - Method in class org.sbml.jsbml.ext.render.Rectangle

getX() - Method in class org.sbml.jsbml.ext.render.Image

getX() - Method in interface org.sbml.jsbml.ext.render.Point3D

getX() - Method in class org.sbml.jsbml.ext.render.Rectangle

getX() - Method in class org.sbml.jsbml.ext.render.RenderPoint

getX() - Method in class org.sbml.jsbml.ext.render.Text

getX1() - Method in class org.sbml.jsbml.ext.render.LinearGradient

getX1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

getX2() - Method in class org.sbml.jsbml.ext.render.LinearGradient

getX2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

getXmlString() - Method in enum org.sbml.jsbml.ext.render.RenderCurveSegment.Type

Returns the String that will be written to XML.

getY() - Method in class org.sbml.jsbml.ext.render.Image

getY() - Method in interface org.sbml.jsbml.ext.render.Point3D

getY() - Method in class org.sbml.jsbml.ext.render.Rectangle

getY() - Method in class org.sbml.jsbml.ext.render.RenderPoint

getY() - Method in class org.sbml.jsbml.ext.render.Text

getY1() - Method in class org.sbml.jsbml.ext.render.LinearGradient

getY1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

getY2() - Method in class org.sbml.jsbml.ext.render.LinearGradient

getY2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

getZ() - Method in class org.sbml.jsbml.ext.render.Image

getZ() - Method in interface org.sbml.jsbml.ext.render.Point3D

getZ() - Method in class org.sbml.jsbml.ext.render.Rectangle

getZ() - Method in class org.sbml.jsbml.ext.render.RenderPoint

getZ() - Method in class org.sbml.jsbml.ext.render.Text

getZ1() - Method in class org.sbml.jsbml.ext.render.LinearGradient

getZ1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

getZ2() - Method in class org.sbml.jsbml.ext.render.LinearGradient

getZ2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

GlobalRenderInformation - Class in org.sbml.jsbml.ext.render

GlobalRenderInformation() - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation

Creates an GlobalRenderInformation instance

GlobalRenderInformation(GlobalRenderInformation) - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation

Clone constructor

GlobalRenderInformation(int, int) - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation

Creates a GlobalRenderInformation instance with a level and version.

GlobalRenderInformation(String) - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation

Creates a GlobalRenderInformation instance with an id.

GlobalRenderInformation(String, int, int) - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation

Creates a GlobalRenderInformation instance with an id, level, and version.

GlobalRenderInformation(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.render.GlobalRenderInformation

Creates a GlobalRenderInformation instance with an id, name, level, and version.

globalRenderInformation - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

GlyphCreator - Class in org.sbml.jsbml.ext.render.director

This class creates a SBML layout for a model without layout information.

GlyphCreator(Model) - Constructor for class org.sbml.jsbml.ext.render.director.GlyphCreator

glyphHasDimensions(GraphicalObject) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Check if a glyph has dimensions.

glyphHasPosition(GraphicalObject) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Check if a glyph has a position.

glyphIsLayouted(GraphicalObject) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Check if a glyph as complete layout information (i.e.

GradientBase - Class in org.sbml.jsbml.ext.render

GradientBase() - Constructor for class org.sbml.jsbml.ext.render.GradientBase

Creates an GradientBase instance

GradientBase(String, GradientStop) - Constructor for class org.sbml.jsbml.ext.render.GradientBase

Creates a GradientBase instance with an id.

GradientBase(String, GradientStop, int, int) - Constructor for class org.sbml.jsbml.ext.render.GradientBase

Creates a GradientBase instance with an id, name, level, and version.

GradientBase(GradientBase) - Constructor for class org.sbml.jsbml.ext.render.GradientBase

Clone constructor

gradientBase - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

GradientBase.Spread - Enum in org.sbml.jsbml.ext.render

The type GradientSpreadMethod is being used by GradientBase elements to decide how gradients propagate over the whole element they are applied to.

GradientStop - Class in org.sbml.jsbml.ext.render

GradientStop(Double, String) - Constructor for class org.sbml.jsbml.ext.render.GradientStop

Creates a GradientStop instance with an offset and a color.

GradientStop(Double, String, int, int) - Constructor for class org.sbml.jsbml.ext.render.GradientStop

Creates a GradientStop instance with an offset, color, level, and version.

GradientStop(GradientStop) - Constructor for class org.sbml.jsbml.ext.render.GradientStop

Clone constructor

GradientStop() - Constructor for class org.sbml.jsbml.ext.render.GradientStop

gradientStop - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

GraphicalPrimitive1D - Class in org.sbml.jsbml.ext.render

GraphicalPrimitive1D() - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

Creates an GraphicalPrimitive1D instance

GraphicalPrimitive1D(int, int) - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

Creates an GraphicalPrimitive1D instance

GraphicalPrimitive1D(GraphicalPrimitive1D) - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

Clone constructor

GraphicalPrimitive2D - Class in org.sbml.jsbml.ext.render

GraphicalPrimitive2D() - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

Creates an GraphicalPrimitive2D instance

GraphicalPrimitive2D(int, int) - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

Creates an GraphicalPrimitive2D instance

GraphicalPrimitive2D(GraphicalPrimitive2D) - Constructor for class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

Clone constructor

GraphicalPrimitive2D.FillRule - Enum in org.sbml.jsbml.ext.render

The type FillRule enumeration describes how a surface created by connecting points on a Polygon are to be filled when rendered.

group - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

group - Variable in class org.sbml.jsbml.ext.render.Style

H

hasCloneMarker() - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNNodeWithCloneMarker

hasCloneMarker() - Method in interface org.sbml.jsbml.ext.render.director.SBGNNodeWithCloneMarker

hashCode() - Method in class org.sbml.jsbml.ext.render.ColorDefinition

hashCode() - Method in class org.sbml.jsbml.ext.render.Ellipse

hashCode() - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

hashCode() - Method in class org.sbml.jsbml.ext.render.GradientBase

hashCode() - Method in class org.sbml.jsbml.ext.render.GradientStop

hashCode() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

hashCode() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

hashCode() - Method in class org.sbml.jsbml.ext.render.Image

hashCode() - Method in class org.sbml.jsbml.ext.render.LinearGradient

hashCode() - Method in class org.sbml.jsbml.ext.render.LineEnding

hashCode() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

hashCode() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

hashCode() - Method in class org.sbml.jsbml.ext.render.LocalStyle

hashCode() - Method in class org.sbml.jsbml.ext.render.Polygon

hashCode() - Method in class org.sbml.jsbml.ext.render.RadialGradient

hashCode() - Method in class org.sbml.jsbml.ext.render.Rectangle

hashCode() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

hashCode() - Method in class org.sbml.jsbml.ext.render.RenderCurve

hashCode() - Method in class org.sbml.jsbml.ext.render.RenderCurveSegment

hashCode() - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin

hashCode() - Method in class org.sbml.jsbml.ext.render.RenderGroup

hashCode() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

hashCode() - Method in class org.sbml.jsbml.ext.render.RenderPoint

hashCode() - Method in class org.sbml.jsbml.ext.render.Style

hashCode() - Method in class org.sbml.jsbml.ext.render.Text

hashCode() - Method in class org.sbml.jsbml.ext.render.Transformation

hashCode() - Method in class org.sbml.jsbml.ext.render.Transformation2D

height - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

href - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

HTextAnchor - Enum in org.sbml.jsbml.ext.render

The enumeration HTextAnchor defines the horizontal alignment of text elements.

I

id - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

idList - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Image - Class in org.sbml.jsbml.ext.render

Image() - Constructor for class org.sbml.jsbml.ext.render.Image

Creates an Image instance

Image(String) - Constructor for class org.sbml.jsbml.ext.render.Image

Creates a Image instance with an id.

Image(Image) - Constructor for class org.sbml.jsbml.ext.render.Image

Clone constructor

image - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Inhibition<T> - Interface in org.sbml.jsbml.ext.render.director

interface all the different graphical representations for inhibition arcs have to implement

initDefaults() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.render.ColorDefinition

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.render.DefaultValues

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

initDefaults() - Method in class org.sbml.jsbml.ext.render.GradientBase

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.render.GradientStop

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

initDefaults() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

initDefaults() - Method in class org.sbml.jsbml.ext.render.Image

initDefaults() - Method in class org.sbml.jsbml.ext.render.LinearGradient

initDefaults() - Method in class org.sbml.jsbml.ext.render.LineEnding

initDefaults() - Method in class org.sbml.jsbml.ext.render.ListOfGlobalRenderInformation

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.render.ListOfLocalRenderInformation

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

initDefaults() - Method in class org.sbml.jsbml.ext.render.Polygon

initDefaults() - Method in class org.sbml.jsbml.ext.render.RadialGradient

initDefaults() - Method in class org.sbml.jsbml.ext.render.Rectangle

initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderCurve

initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin

initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderGroup

initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

initDefaults() - Method in class org.sbml.jsbml.ext.render.RenderPoint

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.render.Style

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.render.Text

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.render.Transformation

Initializes the default values using the namespace.

initDefaults() - Method in class org.sbml.jsbml.ext.render.Transformation2D

isAbsoluteCx() - Method in class org.sbml.jsbml.ext.render.Ellipse

isAbsoluteCx() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isAbsoluteCy() - Method in class org.sbml.jsbml.ext.render.Ellipse

isAbsoluteCy() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isAbsoluteCz() - Method in class org.sbml.jsbml.ext.render.Ellipse

isAbsoluteCz() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isAbsoluteFx() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isAbsoluteFy() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isAbsoluteFz() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isAbsoluteHeight() - Method in class org.sbml.jsbml.ext.render.Image

isAbsoluteHeight() - Method in class org.sbml.jsbml.ext.render.Rectangle

isAbsolutePosition(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools

isAbsoluteR() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isAbsoluteRx() - Method in class org.sbml.jsbml.ext.render.Ellipse

isAbsoluteRx() - Method in class org.sbml.jsbml.ext.render.Rectangle

isAbsoluteRy() - Method in class org.sbml.jsbml.ext.render.Ellipse

isAbsoluteRy() - Method in class org.sbml.jsbml.ext.render.Rectangle

isAbsoluteWidth() - Method in class org.sbml.jsbml.ext.render.Image

isAbsoluteWidth() - Method in class org.sbml.jsbml.ext.render.Rectangle

isAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Image

isAbsoluteX() - Method in interface org.sbml.jsbml.ext.render.Point3D

isAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Rectangle

isAbsoluteX() - Method in class org.sbml.jsbml.ext.render.RenderPoint

isAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Text

isAbsoluteX1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isAbsoluteX2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Image

isAbsoluteY() - Method in interface org.sbml.jsbml.ext.render.Point3D

isAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Rectangle

isAbsoluteY() - Method in class org.sbml.jsbml.ext.render.RenderPoint

isAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Text

isAbsoluteY1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isAbsoluteY2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Image

isAbsoluteZ() - Method in interface org.sbml.jsbml.ext.render.Point3D

isAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Rectangle

isAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.RenderPoint

isAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Text

isAbsoluteZ1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isAbsoluteZ2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isEnableRotationMapping() - Method in class org.sbml.jsbml.ext.render.LineEnding

isFontStyleItalic() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

isFontStyleItalic() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns the value of fontStyleItalic

isFontStyleItalic() - Method in class org.sbml.jsbml.ext.render.Text

isFontWeightBold() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

isFontWeightBold() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns the value of fontWeightBold

isFontWeightBold() - Method in class org.sbml.jsbml.ext.render.Text

isIdMandatory() - Method in class org.sbml.jsbml.ext.render.ColorDefinition

isIdMandatory() - Method in class org.sbml.jsbml.ext.render.GradientBase

isIdMandatory() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

isIdMandatory() - Method in class org.sbml.jsbml.ext.render.Style

isModifier(SpeciesReferenceGlyph) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Check if a species reference glyph can be interpreted as an activator, inhibitor, or generic modifier.

isProduct(SpeciesReferenceGlyph) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Check if a species reference glyph is a product.

isProductReady() - Method in class org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder

isProductReady() - Method in interface org.sbml.jsbml.ext.render.director.LayoutBuilder

method to check if the builder has produced a complete product

isRenderCubicBezier() - Method in class org.sbml.jsbml.ext.render.RenderCurveSegment

Returns true if the type is equals to RenderCurveSegment.Type.RENDER_CUBIC_BEZIER.

isRenderPoint() - Method in class org.sbml.jsbml.ext.render.RenderCurveSegment

Returns true if the type is equals to RenderCurveSegment.Type.RENDER_POINT.

isRequired() - Method in class org.sbml.jsbml.xml.parsers.RenderParser

isSetAbsoluteCx() - Method in class org.sbml.jsbml.ext.render.Ellipse

isSetAbsoluteCx() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isSetAbsoluteCy() - Method in class org.sbml.jsbml.ext.render.Ellipse

isSetAbsoluteCy() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isSetAbsoluteCz() - Method in class org.sbml.jsbml.ext.render.Ellipse

isSetAbsoluteCz() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isSetAbsoluteFx() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isSetAbsoluteFy() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isSetAbsoluteFz() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isSetAbsoluteHeight() - Method in class org.sbml.jsbml.ext.render.Image

isSetAbsoluteHeight() - Method in class org.sbml.jsbml.ext.render.Rectangle

isSetAbsoluteR() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isSetAbsoluteRx() - Method in class org.sbml.jsbml.ext.render.Ellipse

isSetAbsoluteRx() - Method in class org.sbml.jsbml.ext.render.Rectangle

isSetAbsoluteRy() - Method in class org.sbml.jsbml.ext.render.Ellipse

isSetAbsoluteRy() - Method in class org.sbml.jsbml.ext.render.Rectangle

isSetAbsoluteWidth() - Method in class org.sbml.jsbml.ext.render.Image

isSetAbsoluteWidth() - Method in class org.sbml.jsbml.ext.render.Rectangle

isSetAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Image

isSetAbsoluteX() - Method in interface org.sbml.jsbml.ext.render.Point3D

isSetAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Rectangle

isSetAbsoluteX() - Method in class org.sbml.jsbml.ext.render.RenderPoint

isSetAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Text

isSetAbsoluteX1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isSetAbsoluteX2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isSetAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Image

isSetAbsoluteY() - Method in interface org.sbml.jsbml.ext.render.Point3D

isSetAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Rectangle

isSetAbsoluteY() - Method in class org.sbml.jsbml.ext.render.RenderPoint

isSetAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Text

isSetAbsoluteY1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isSetAbsoluteY2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isSetAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Image

isSetAbsoluteZ() - Method in interface org.sbml.jsbml.ext.render.Point3D

isSetAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Rectangle

isSetAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.RenderPoint

isSetAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Text

isSetAbsoluteZ1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isSetAbsoluteZ2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isSetAddWhiskers() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Returns whether addWhiskers is set

isSetBackgroundColor() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

isSetBoundingBox() - Method in class org.sbml.jsbml.ext.render.LineEnding

isSetCloneMarker() - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNNodeWithCloneMarker

isSetCloneMarker() - Method in interface org.sbml.jsbml.ext.render.director.SBGNNodeWithCloneMarker

isSetCx() - Method in class org.sbml.jsbml.ext.render.Ellipse

isSetCx() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isSetCy() - Method in class org.sbml.jsbml.ext.render.Ellipse

isSetCy() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isSetCz() - Method in class org.sbml.jsbml.ext.render.Ellipse

isSetCz() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isSetDefaultValues() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Returns whether ListOfRenderInformation.defaultValues is set.

isSetEnableRotationMapping() - Method in class org.sbml.jsbml.ext.render.LineEnding

isSetEndHead() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Returns true if endHead is set.

isSetEndHead() - Method in class org.sbml.jsbml.ext.render.RenderGroup

isSetFill() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

isSetFillRule() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

isSetFontFamily() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

isSetFontFamily() - Method in class org.sbml.jsbml.ext.render.RenderGroup

isSetFontFamily() - Method in class org.sbml.jsbml.ext.render.Text

isSetFontSize() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

isSetFontSize() - Method in class org.sbml.jsbml.ext.render.RenderGroup

isSetFontSize() - Method in class org.sbml.jsbml.ext.render.Text

isSetFontStyleItalic() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

isSetFontStyleItalic() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns whether fontStyleItalic is set

isSetFontStyleItalic() - Method in class org.sbml.jsbml.ext.render.Text

isSetFontWeightBold() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

isSetFontWeightBold() - Method in class org.sbml.jsbml.ext.render.RenderGroup

isSetFontWeightBold() - Method in class org.sbml.jsbml.ext.render.Text

isSetFx() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isSetFy() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isSetFz() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isSetGroup() - Method in class org.sbml.jsbml.ext.render.LineEnding

isSetGroup() - Method in class org.sbml.jsbml.ext.render.Style

isSetHeight() - Method in class org.sbml.jsbml.ext.render.Image

isSetHeight() - Method in class org.sbml.jsbml.ext.render.Rectangle

isSetHref() - Method in class org.sbml.jsbml.ext.render.Image

isSetIDList() - Method in class org.sbml.jsbml.ext.render.LocalStyle

isSetLayout() - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

isSetLayout() - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

isSetListOfColorDefinitions() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

isSetListOfCurveSegments() - Method in class org.sbml.jsbml.ext.render.Polygon

Returns true if Polygon.listOfCurveSegments contains at least one element.

isSetListOfCurveSegments() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Returns true if RenderCurve.listOfCurveSegments contains at least one element.

isSetListOfElements() - Method in class org.sbml.jsbml.ext.render.Polygon

isSetListOfElements() - Method in class org.sbml.jsbml.ext.render.RenderCurve

isSetListOfElements() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns true, if listOfElements contains at least one element.

isSetListOfGlobalRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

isSetListOfGradientDefinitions() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

isSetListOfGradientStops() - Method in class org.sbml.jsbml.ext.render.GradientBase

isSetListOfLineEndings() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

isSetListOfLocalRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

isSetListOfLocalStyles() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

isSetListOfStyles() - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

isSetObjectRole() - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin

Returns whether RenderGraphicalObjectPlugin.objectRole is set.

isSetOffset() - Method in class org.sbml.jsbml.ext.render.GradientStop

isSetProgramName() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

isSetProgramVersion() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

isSetR() - Method in class org.sbml.jsbml.ext.render.RadialGradient

isSetReferenceRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

isSetRenderInformation() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

isSetRoleList() - Method in class org.sbml.jsbml.ext.render.Style

isSetRx() - Method in class org.sbml.jsbml.ext.render.Ellipse

isSetRx() - Method in class org.sbml.jsbml.ext.render.Rectangle

isSetRy() - Method in class org.sbml.jsbml.ext.render.Ellipse

isSetRy() - Method in class org.sbml.jsbml.ext.render.Rectangle

isSetSpreadMethod() - Method in class org.sbml.jsbml.ext.render.GradientBase

isSetStartHead() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Returns true if startHead is set

isSetStartHead() - Method in class org.sbml.jsbml.ext.render.RenderGroup

isSetStopColor() - Method in class org.sbml.jsbml.ext.render.GradientStop

isSetStroke() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

isSetStrokeDashArray() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

isSetStrokeWidth() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

isSetTextAnchor() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

isSetTextAnchor() - Method in class org.sbml.jsbml.ext.render.RenderGroup

isSetTextAnchor() - Method in class org.sbml.jsbml.ext.render.Text

isSetTransform() - Method in class org.sbml.jsbml.ext.render.Transformation2D

isSetType() - Method in class org.sbml.jsbml.ext.render.RenderCurveSegment

Returns true if the type is set.

isSetTypeList() - Method in class org.sbml.jsbml.ext.render.Style

isSetValue() - Method in class org.sbml.jsbml.ext.render.ColorDefinition

isSetVersionMajor() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Returns true if versionMajor is set.

isSetVersionMinor() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Returns true if versionMinor is set.

isSetVTextAnchor() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

isSetVTextAnchor() - Method in class org.sbml.jsbml.ext.render.RenderGroup

isSetVTextAnchor() - Method in class org.sbml.jsbml.ext.render.Text

isSetWidth() - Method in class org.sbml.jsbml.ext.render.Image

isSetWidth() - Method in class org.sbml.jsbml.ext.render.Rectangle

isSetX() - Method in class org.sbml.jsbml.ext.render.Image

isSetX() - Method in interface org.sbml.jsbml.ext.render.Point3D

isSetX() - Method in class org.sbml.jsbml.ext.render.Rectangle

isSetX() - Method in class org.sbml.jsbml.ext.render.RenderPoint

isSetX() - Method in class org.sbml.jsbml.ext.render.Text

isSetX1() - Method in class org.sbml.jsbml.ext.render.LinearGradient

isSetX1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isSetX2() - Method in class org.sbml.jsbml.ext.render.LinearGradient

isSetX2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isSetY() - Method in class org.sbml.jsbml.ext.render.Image

isSetY() - Method in interface org.sbml.jsbml.ext.render.Point3D

isSetY() - Method in class org.sbml.jsbml.ext.render.Rectangle

isSetY() - Method in class org.sbml.jsbml.ext.render.RenderPoint

isSetY() - Method in class org.sbml.jsbml.ext.render.Text

isSetY1() - Method in class org.sbml.jsbml.ext.render.LinearGradient

isSetY1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isSetY2() - Method in class org.sbml.jsbml.ext.render.LinearGradient

isSetY2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isSetZ() - Method in class org.sbml.jsbml.ext.render.Image

isSetZ() - Method in interface org.sbml.jsbml.ext.render.Point3D

isSetZ() - Method in class org.sbml.jsbml.ext.render.Rectangle

isSetZ() - Method in class org.sbml.jsbml.ext.render.RenderPoint

isSetZ() - Method in class org.sbml.jsbml.ext.render.Text

isSetZ1() - Method in class org.sbml.jsbml.ext.render.LinearGradient

isSetZ1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isSetZ2() - Method in class org.sbml.jsbml.ext.render.LinearGradient

isSetZ2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

isSubstrate(SpeciesReferenceGlyph) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Check if a species reference glyph is a substrate.

K

KEY_FOR_FLUX_VALUES - Static variable in class org.sbml.jsbml.ext.render.director.LayoutDirector

Constant for use as the key for flux values.

L

layout - Variable in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

The Layout object of the SBML Model.

LAYOUT_LINK - Static variable in class org.sbml.jsbml.ext.render.director.GlyphCreator

LAYOUT_LINK - Static variable in class org.sbml.jsbml.ext.render.director.LayoutDirector

Constant for use as the key for layout links.

LayoutAlgorithm - Interface in org.sbml.jsbml.ext.render.director

Interface for defining an algorithm to create bounding boxes, dimensions and points missing in the layout.

LayoutBuilder<P> - Interface in org.sbml.jsbml.ext.render.director

LayoutBuilder provides methods to build graphical representations for all glyph types.

LayoutDirector<P> - Class in org.sbml.jsbml.ext.render.director

LayoutDirector produces a graphical representation of a layout of an SBMLDocument.

LayoutDirector(File, LayoutBuilder<P>, LayoutAlgorithm) - Constructor for class org.sbml.jsbml.ext.render.director.LayoutDirector

LayoutDirector(SBMLDocument, LayoutBuilder<P>, LayoutAlgorithm) - Constructor for class org.sbml.jsbml.ext.render.director.LayoutDirector

LayoutDirector(SBMLDocument, LayoutBuilder<P>, LayoutAlgorithm, int) - Constructor for class org.sbml.jsbml.ext.render.director.LayoutDirector

LayoutDirector(Layout, LayoutBuilder<P>, LayoutAlgorithm) - Constructor for class org.sbml.jsbml.ext.render.director.LayoutDirector

LayoutFactory<NodeT,ArcT> - Interface in org.sbml.jsbml.ext.render.director

Interface that defines methods to create and return the different types of nodes and arcs.

level - Variable in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

SBML level

LinearGradient - Class in org.sbml.jsbml.ext.render

LinearGradient() - Constructor for class org.sbml.jsbml.ext.render.LinearGradient

Creates an LinearGradient instance

LinearGradient(LinearGradient) - Constructor for class org.sbml.jsbml.ext.render.LinearGradient

Clone constructor

linearGradient - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

LineEnding - Class in org.sbml.jsbml.ext.render

LineEnding() - Constructor for class org.sbml.jsbml.ext.render.LineEnding

Creates an LineEnding instance

LineEnding(LineEnding) - Constructor for class org.sbml.jsbml.ext.render.LineEnding

Clone constructor

lineEnding - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

linkObjectRoleToStyle(Map<String, LocalStyle>, GraphicalObject) - Static method in class org.sbml.jsbml.ext.render.director.RenderProcessor

list_of_elements - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

listOfColorDefinitions - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

listOfColorDefinitions - Variable in class org.sbml.jsbml.ext.render.RenderInformationBase

listOfCurveSegments - Variable in class org.sbml.jsbml.ext.render.RenderCurve

listOfElements - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

listOfElements - Variable in class org.sbml.jsbml.ext.render.RenderCurve

ListOfGlobalRenderInformation - Class in org.sbml.jsbml.ext.render

Derives from the ListOf class and contains one or more objects of type GlobalRenderInformation.

ListOfGlobalRenderInformation() - Constructor for class org.sbml.jsbml.ext.render.ListOfGlobalRenderInformation

Creates a new ListOfGlobalRenderInformation instance

ListOfGlobalRenderInformation(int, int) - Constructor for class org.sbml.jsbml.ext.render.ListOfGlobalRenderInformation

Creates a new ListOfGlobalRenderInformation instance with a level and version.

ListOfGlobalRenderInformation(ListOfGlobalRenderInformation) - Constructor for class org.sbml.jsbml.ext.render.ListOfGlobalRenderInformation

Clone constructor

listOfGlobalRenderInformation - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

listOfGradientDefinitions - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

listOfGradientDefinitions - Variable in class org.sbml.jsbml.ext.render.RenderInformationBase

listOfGradientStops - Variable in class org.sbml.jsbml.ext.render.GradientBase

listOfGradientStops - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

listOfLineEndings - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

listOfLineEndings - Variable in class org.sbml.jsbml.ext.render.RenderInformationBase

ListOfLocalRenderInformation - Class in org.sbml.jsbml.ext.render

Derives from the ListOf class and contains one or more objects of type LocalRenderInformation.

ListOfLocalRenderInformation() - Constructor for class org.sbml.jsbml.ext.render.ListOfLocalRenderInformation

Creates a new ListOfLocalRenderInformation instance.

ListOfLocalRenderInformation(int, int) - Constructor for class org.sbml.jsbml.ext.render.ListOfLocalRenderInformation

Creates a new ListOfLocalRenderInformation instance with a level and version.

ListOfLocalRenderInformation(ListOfLocalRenderInformation) - Constructor for class org.sbml.jsbml.ext.render.ListOfLocalRenderInformation

Clone constructor

listOfLocalRenderInformation - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

listOfLocalStyles - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

ListOfRenderInformation<T extends RenderInformationBase> - Class in org.sbml.jsbml.ext.render

Derives from the ListOf class and contains one or more objects of type RenderInformationBase.

ListOfRenderInformation() - Constructor for class org.sbml.jsbml.ext.render.ListOfRenderInformation

Creates a new ListOfRenderInformation instance

ListOfRenderInformation(int, int) - Constructor for class org.sbml.jsbml.ext.render.ListOfRenderInformation

Creates a new ListOfRenderInformation instance with a level and version.

ListOfRenderInformation(ListOfRenderInformation<?>) - Constructor for class org.sbml.jsbml.ext.render.ListOfRenderInformation

Clone constructor

listOfStyles - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

LocalRenderInformation - Class in org.sbml.jsbml.ext.render

LocalRenderInformation() - Constructor for class org.sbml.jsbml.ext.render.LocalRenderInformation

Creates an LocalRenderInformation instance

LocalRenderInformation(String) - Constructor for class org.sbml.jsbml.ext.render.LocalRenderInformation

Creates a LocalRenderInformation instance with an id.

LocalRenderInformation(int, int) - Constructor for class org.sbml.jsbml.ext.render.LocalRenderInformation

Creates a LocalRenderInformation instance with a level and version.

LocalRenderInformation(String, int, int) - Constructor for class org.sbml.jsbml.ext.render.LocalRenderInformation

Creates a LocalRenderInformation instance with an id, level, and version.

LocalRenderInformation(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.render.LocalRenderInformation

Creates a LocalRenderInformation instance with an id, name, level, and version.

LocalRenderInformation(LocalRenderInformation) - Constructor for class org.sbml.jsbml.ext.render.LocalRenderInformation

Clone constructor

localRenderInformation - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

LocalStyle - Class in org.sbml.jsbml.ext.render

LocalStyle() - Constructor for class org.sbml.jsbml.ext.render.LocalStyle

Creates a new LocalStyle instance

LocalStyle(RenderGroup) - Constructor for class org.sbml.jsbml.ext.render.LocalStyle

Creates a LocalStyle instance with a group

LocalStyle(int, int, RenderGroup) - Constructor for class org.sbml.jsbml.ext.render.LocalStyle

Creates a LocalStyle instance with a level and version.

LocalStyle(String, int, int, RenderGroup) - Constructor for class org.sbml.jsbml.ext.render.LocalStyle

Creates a LocalStyle instance with an id, name, level, and version.

LocalStyle(LocalStyle) - Constructor for class org.sbml.jsbml.ext.render.LocalStyle

Creates a new LocalStyle instance, cloned from the given object.

localStyle - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

M

Macromolecule<T> - Class in org.sbml.jsbml.ext.render.director

interface all the different graphical representations for macromolecule nodes have to implement

Macromolecule() - Constructor for class org.sbml.jsbml.ext.render.director.Macromolecule

MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Modulation<T> - Interface in org.sbml.jsbml.ext.render.director

Interface for the SBGN specified modulation arc.

N

namespaces_L2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

namespaces_L3 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

namespaceURI - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

The latest namespace URI of this parser, this value can change between releases.

namespaceURI_L2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

NecessaryStimulation<T> - Interface in org.sbml.jsbml.ext.render.director

Interface for the SBGN specified necessary stimulation arc.

NO_WHISKERS - Static variable in class org.sbml.jsbml.ext.render.director.LayoutDirector

normalize(GeneralPath) - Static method in class org.sbml.jsbml.ext.render.director.Geometry

NucleicAcidFeature<T> - Class in org.sbml.jsbml.ext.render.director

NucleicAcidFeature() - Constructor for class org.sbml.jsbml.ext.render.director.NucleicAcidFeature

O

objectRole - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

offset - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

OmittedProcessNode<T> - Interface in org.sbml.jsbml.ext.render.director

org.sbml.jsbml.ext.render - package org.sbml.jsbml.ext.render

Provides classes for the render package, see the specification at sbml.org.

org.sbml.jsbml.ext.render.director - package org.sbml.jsbml.ext.render.director

This package contains interfaces and classes to create an implementation to create a graphical representation of the Layout of a SBML document.

org.sbml.jsbml.xml.parsers - package org.sbml.jsbml.xml.parsers

P

packageName - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

parseFontStyleItalic(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools

parseFontWeightBold(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools

parsePosition(String) - Static method in class org.sbml.jsbml.ext.render.XMLTools

PerturbingAgent<T> - Class in org.sbml.jsbml.ext.render.director

PerturbingAgent() - Constructor for class org.sbml.jsbml.ext.render.director.PerturbingAgent

PN_RELATIVE_DOCKING_POINT - Static variable in class org.sbml.jsbml.ext.render.director.LayoutDirector

Constant for use as the key for relative docking points.

Point3D - Interface in org.sbml.jsbml.ext.render

Polygon - Class in org.sbml.jsbml.ext.render

Polygon() - Constructor for class org.sbml.jsbml.ext.render.Polygon

Creates an Polygon instance

Polygon(Polygon) - Constructor for class org.sbml.jsbml.ext.render.Polygon

Clone constructor

polygon - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

positioningToString(double, boolean) - Static method in class org.sbml.jsbml.ext.render.XMLTools

preprocess(Layout) - Static method in class org.sbml.jsbml.ext.render.director.RenderProcessor

processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.RenderParser

processEndDocument(SBMLDocument) - Method in class org.sbml.jsbml.xml.parsers.RenderParser

ProcessNode<T> - Interface in org.sbml.jsbml.ext.render.director

processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.RenderParser

Production<T> - Interface in org.sbml.jsbml.ext.render.director

interface all the different graphical representations for production arcs have to implement

programName - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

programName - Variable in class org.sbml.jsbml.ext.render.RenderInformationBase

programVersion - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

programVersion - Variable in class org.sbml.jsbml.ext.render.RenderInformationBase

R

r - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

RadialGradient - Class in org.sbml.jsbml.ext.render

RadialGradient() - Constructor for class org.sbml.jsbml.ext.render.RadialGradient

Creates an RadialGradient instance

RadialGradient(RadialGradient) - Constructor for class org.sbml.jsbml.ext.render.RadialGradient

Clone constructor

radialGradient - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.ColorDefinition

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.DefaultValues

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.Ellipse

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.GradientBase

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.GradientStop

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.Image

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.LinearGradient

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.LineEnding

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.LocalStyle

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.RadialGradient

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.Rectangle

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.RenderCurve

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.RenderCurveSegment

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.RenderGroup

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.RenderPoint

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.Style

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.Text

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.render.Transformation

Rectangle - Class in org.sbml.jsbml.ext.render

Rectangle() - Constructor for class org.sbml.jsbml.ext.render.Rectangle

Creates a new Rectangle instance.

Rectangle(Rectangle) - Constructor for class org.sbml.jsbml.ext.render.Rectangle

Clone constructor

rectangle - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

referenceRenderInformation - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

referenceRenderInformation - Variable in class org.sbml.jsbml.ext.render.RenderInformationBase

removeColorDefinition(ColorDefinition) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

removeColorDefinition(int) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

removeColorDefinition(String) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

removeCurveSegment(CurveSegment) - Method in class org.sbml.jsbml.ext.render.Polygon

Removes an element from the Polygon.listOfCurveSegments.

removeCurveSegment(int) - Method in class org.sbml.jsbml.ext.render.Polygon

Removes an element from the Polygon.listOfCurveSegments at the given index.

removeCurveSegment(CurveSegment) - Method in class org.sbml.jsbml.ext.render.RenderCurve

Removes an element from the RenderCurve.listOfCurveSegments.

removeCurveSegment(int) - Method in class org.sbml.jsbml.ext.render.RenderCurve

Removes an element from the RenderCurve.listOfCurveSegments at the given index.

removeElement(RenderPoint) - Method in class org.sbml.jsbml.ext.render.Polygon

removeElement(int) - Method in class org.sbml.jsbml.ext.render.Polygon

removeElement(RenderPoint) - Method in class org.sbml.jsbml.ext.render.RenderCurve

removeElement(int) - Method in class org.sbml.jsbml.ext.render.RenderCurve

removeElement(Transformation2D) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Removes an element from the listOfElements.

removeElement(String) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Removes an element from the listOfElements.

removeElement(int) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Removes an element from the listOfElements at the given index.

removeGlobalRenderInformation(GlobalRenderInformation) - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

removeGlobalRenderInformation(int) - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

removeGlobalRenderInformation(String) - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

removeGradientBase(GradientBase) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

removeGradientBase(int) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

removeGradientStop(GradientStop) - Method in class org.sbml.jsbml.ext.render.GradientBase

removeGradientStop(int) - Method in class org.sbml.jsbml.ext.render.GradientBase

removeLineEnding(LineEnding) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

removeLineEnding(int) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

removeLocalRenderInformation(LocalRenderInformation) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

removeLocalRenderInformation(int) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

removeLocalRenderInformation(String) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

removeLocalStyle(LocalStyle) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

removeLocalStyle(int) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

removeStyle(Style) - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

removeStyle(int) - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

RENDER_LINK - Static variable in class org.sbml.jsbml.ext.render.director.RenderProcessor

RenderConstants - Class in org.sbml.jsbml.ext.render

Contains some constants related to the render package.

RenderConstants() - Constructor for class org.sbml.jsbml.ext.render.RenderConstants

renderCubicBezier - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

RenderCubicBezier - Class in org.sbml.jsbml.ext.render

RenderCubicBezier() - Constructor for class org.sbml.jsbml.ext.render.RenderCubicBezier

Creates an RenderCubicBezier instance

RenderCubicBezier(RenderCubicBezier) - Constructor for class org.sbml.jsbml.ext.render.RenderCubicBezier

Clone constructor

renderCurve - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

RenderCurve - Class in org.sbml.jsbml.ext.render

Implements the curve concept from the SBML render extension.

RenderCurve() - Constructor for class org.sbml.jsbml.ext.render.RenderCurve

Creates an Curve instance

RenderCurve(RenderCurve) - Constructor for class org.sbml.jsbml.ext.render.RenderCurve

Clone constructor

RenderCurveSegment - Class in org.sbml.jsbml.ext.render

Parent class to RenderPoint and RenderCubicBezier.

RenderCurveSegment() - Constructor for class org.sbml.jsbml.ext.render.RenderCurveSegment

Creates a new RenderCurveSegment instance.

RenderCurveSegment(RenderCurveSegment) - Constructor for class org.sbml.jsbml.ext.render.RenderCurveSegment

Creates a new RenderCurveSegment instance cloned from the given RenderCurveSegment.

RenderCurveSegment(int, int) - Constructor for class org.sbml.jsbml.ext.render.RenderCurveSegment

Creates a new RenderCurveSegment instance.

RenderCurveSegment.Type - Enum in org.sbml.jsbml.ext.render

RenderGraphicalObjectPlugin - Class in org.sbml.jsbml.ext.render

Extends the GraphicalObject class with an extra attribute.

RenderGraphicalObjectPlugin(GraphicalObject) - Constructor for class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin

Creates a new RenderGraphicalObjectPlugin instance.

RenderGraphicalObjectPlugin(RenderGraphicalObjectPlugin) - Constructor for class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin

Clone constructor

RenderGroup - Class in org.sbml.jsbml.ext.render

The RenderGroup class from the SBML render extension is used to group graphical primitives together to create composite representations from simple primitives.

RenderGroup() - Constructor for class org.sbml.jsbml.ext.render.RenderGroup

Creates an Group instance

RenderGroup(String) - Constructor for class org.sbml.jsbml.ext.render.RenderGroup

Creates a Group instance with an id.

RenderGroup(int, int) - Constructor for class org.sbml.jsbml.ext.render.RenderGroup

Creates a Group instance with a level and version.

RenderGroup(String, int, int) - Constructor for class org.sbml.jsbml.ext.render.RenderGroup

Creates a Group instance with an id, level, and version.

RenderGroup(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.render.RenderGroup

Creates a Group instance with an id, name, level, and version.

RenderGroup(RenderGroup) - Constructor for class org.sbml.jsbml.ext.render.RenderGroup

Clone constructor

renderInformation - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

RenderInformationBase - Class in org.sbml.jsbml.ext.render

RenderInformationBase() - Constructor for class org.sbml.jsbml.ext.render.RenderInformationBase

Creates an RenderInformationBase instance

RenderInformationBase(String) - Constructor for class org.sbml.jsbml.ext.render.RenderInformationBase

Creates a RenderInformationBase instance with an id.

RenderInformationBase(int, int) - Constructor for class org.sbml.jsbml.ext.render.RenderInformationBase

Creates a RenderInformationBase instance with a level and version.

RenderInformationBase(String, int, int) - Constructor for class org.sbml.jsbml.ext.render.RenderInformationBase

Creates a RenderInformationBase instance with an id, level, and version.

RenderInformationBase(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.render.RenderInformationBase

Creates a RenderInformationBase instance with an id, name, level, and version.

RenderInformationBase(RenderInformationBase) - Constructor for class org.sbml.jsbml.ext.render.RenderInformationBase

Clone constructor

RenderLayoutPlugin - Class in org.sbml.jsbml.ext.render

RenderLayoutPlugin(Layout) - Constructor for class org.sbml.jsbml.ext.render.RenderLayoutPlugin

Creates a RenderLayoutPlugin instance

RenderLayoutPlugin(RenderLayoutPlugin) - Constructor for class org.sbml.jsbml.ext.render.RenderLayoutPlugin

Clone constructor

RenderListOfLayoutsPlugin - Class in org.sbml.jsbml.ext.render

RenderListOfLayoutsPlugin(ListOf<Layout>) - Constructor for class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

Creates an RenderModelPlugin instance

RenderListOfLayoutsPlugin(RenderListOfLayoutsPlugin) - Constructor for class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

Clone constructor

RenderParser - Class in org.sbml.jsbml.xml.parsers

RenderParser() - Constructor for class org.sbml.jsbml.xml.parsers.RenderParser

renderPoint - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

RenderPoint - Class in org.sbml.jsbml.ext.render

RenderPoint() - Constructor for class org.sbml.jsbml.ext.render.RenderPoint

Creates a new RenderPoint instance

RenderPoint(RenderPoint) - Constructor for class org.sbml.jsbml.ext.render.RenderPoint

Clone constructor

RenderProcessor - Class in org.sbml.jsbml.ext.render.director

A currently very preliminary class with inaccurate interpretation of rendering information.

RenderProcessor() - Constructor for class org.sbml.jsbml.ext.render.director.RenderProcessor

ReversibleConsumption<T> - Interface in org.sbml.jsbml.ext.render.director

Interface for all reversible consumption processes.

roleList - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

roleList - Variable in class org.sbml.jsbml.ext.render.Style

run() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

rx - Variable in class org.sbml.jsbml.ext.render.Ellipse

rx - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

ry - Variable in class org.sbml.jsbml.ext.render.Ellipse

ry - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

S

SBGNArc<T> - Interface in org.sbml.jsbml.ext.render.director

interface for the different types of connecting arcs consumption reversible consumption production catalysis inhibition

SBGNNode<T> - Interface in org.sbml.jsbml.ext.render.director

interface for the different types of entity pool nodes unspecified entity simple chemical macromolecule source/sink

SBGNNodeWithCloneMarker<T> - Interface in org.sbml.jsbml.ext.render.director

SBGNProcessNode<T> - Interface in org.sbml.jsbml.ext.render.director

Interface for all SBGN specified process nodes.

setAbsoluteCx(boolean) - Method in class org.sbml.jsbml.ext.render.Ellipse

Set the value of absoluteCx

setAbsoluteCx(boolean) - Method in class org.sbml.jsbml.ext.render.RadialGradient

Set the value of absoluteCx

setAbsoluteCy(boolean) - Method in class org.sbml.jsbml.ext.render.Ellipse

Set the value of absoluteCy

setAbsoluteCy(boolean) - Method in class org.sbml.jsbml.ext.render.RadialGradient

Set the value of absoluteCy

setAbsoluteCz(boolean) - Method in class org.sbml.jsbml.ext.render.Ellipse

Set the value of absoluteCz

setAbsoluteCz(boolean) - Method in class org.sbml.jsbml.ext.render.RadialGradient

Set the value of absoluteCz

setAbsoluteFx(boolean) - Method in class org.sbml.jsbml.ext.render.RadialGradient

Set the value of absoluteFx

setAbsoluteFy(boolean) - Method in class org.sbml.jsbml.ext.render.RadialGradient

Set the value of absoluteFy

setAbsoluteFz(boolean) - Method in class org.sbml.jsbml.ext.render.RadialGradient

Set the value of absoluteFz

setAbsoluteHeight(boolean) - Method in class org.sbml.jsbml.ext.render.Image

Set the value of absoluteHeight

setAbsoluteHeight(boolean) - Method in class org.sbml.jsbml.ext.render.Rectangle

Set the value of absoluteHeight

setAbsoluteR(boolean) - Method in class org.sbml.jsbml.ext.render.RadialGradient

Set the value of absoluteR

setAbsoluteRx(boolean) - Method in class org.sbml.jsbml.ext.render.Ellipse

Set the value of absoluteRx

setAbsoluteRx(boolean) - Method in class org.sbml.jsbml.ext.render.Rectangle

Set the value of absoluteRx

setAbsoluteRy(boolean) - Method in class org.sbml.jsbml.ext.render.Ellipse

Set the value of absoluteRy

setAbsoluteRy(boolean) - Method in class org.sbml.jsbml.ext.render.Rectangle

Set the value of absoluteRy

setAbsoluteWidth(boolean) - Method in class org.sbml.jsbml.ext.render.Image

Set the value of absoluteWidth

setAbsoluteWidth(boolean) - Method in class org.sbml.jsbml.ext.render.Rectangle

Set the value of absoluteWidth

setAbsoluteX(boolean) - Method in class org.sbml.jsbml.ext.render.Image

Set the value of absoluteX

setAbsoluteX(boolean) - Method in interface org.sbml.jsbml.ext.render.Point3D

Set the value of absoluteX

setAbsoluteX(boolean) - Method in class org.sbml.jsbml.ext.render.Rectangle

setAbsoluteX(boolean) - Method in class org.sbml.jsbml.ext.render.RenderPoint

setAbsoluteX(boolean) - Method in class org.sbml.jsbml.ext.render.Text

setAbsoluteX1(boolean) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Set the value of absoluteX1

setAbsoluteX2(boolean) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Set the value of absoluteX2

setAbsoluteY(boolean) - Method in class org.sbml.jsbml.ext.render.Image

Set the value of absoluteY

setAbsoluteY(boolean) - Method in interface org.sbml.jsbml.ext.render.Point3D

Set the value of absoluteY

setAbsoluteY(boolean) - Method in class org.sbml.jsbml.ext.render.Rectangle

setAbsoluteY(boolean) - Method in class org.sbml.jsbml.ext.render.RenderPoint

setAbsoluteY(boolean) - Method in class org.sbml.jsbml.ext.render.Text

setAbsoluteY1(boolean) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Set the value of absoluteY1

setAbsoluteY2(boolean) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Set the value of absoluteY2

setAbsoluteZ(boolean) - Method in class org.sbml.jsbml.ext.render.Image

Set the value of absoluteZ

setAbsoluteZ(boolean) - Method in interface org.sbml.jsbml.ext.render.Point3D

Set the value of absoluteZ

setAbsoluteZ(boolean) - Method in class org.sbml.jsbml.ext.render.Rectangle

setAbsoluteZ(boolean) - Method in class org.sbml.jsbml.ext.render.RenderPoint

setAbsoluteZ(boolean) - Method in class org.sbml.jsbml.ext.render.Text

setAbsoluteZ1(boolean) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Set the value of absoluteZ1

setAbsoluteZ2(boolean) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Set the value of absoluteZ2

setAddWhiskers(Boolean) - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Sets the value of addWhiskers

setAlgorithm(LayoutAlgorithm) - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

setBackgroundColor(Color) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

Set the value of backgroundColor

setBoundingBox(BoundingBox) - Method in class org.sbml.jsbml.ext.render.LineEnding

Set the value of boundingBox

setBuilder(LayoutBuilder<P>) - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

setCloneMarker(boolean) - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNNodeWithCloneMarker

setCloneMarker(boolean) - Method in interface org.sbml.jsbml.ext.render.director.SBGNNodeWithCloneMarker

Method to set the boolean clone marker value if the clone marker should be drawn.

setCx(double) - Method in class org.sbml.jsbml.ext.render.Ellipse

Set the value of cx

setCx(double) - Method in class org.sbml.jsbml.ext.render.RadialGradient

Set the value of cx

setCy(Double) - Method in class org.sbml.jsbml.ext.render.Ellipse

Set the value of cy

setCy(double) - Method in class org.sbml.jsbml.ext.render.RadialGradient

Set the value of cy

setCz(Double) - Method in class org.sbml.jsbml.ext.render.Ellipse

Set the value of cz

setCz(double) - Method in class org.sbml.jsbml.ext.render.RadialGradient

Set the value of cz

setDefaultValue(String, String) - Method in class org.sbml.jsbml.ext.render.DefaultValues

setDefaultValues(DefaultValues) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Sets the value of defaultValues

setEnableRotationMapping(Boolean) - Method in class org.sbml.jsbml.ext.render.LineEnding

Sets the value of enableRotationMapping

setEndHead(String) - Method in class org.sbml.jsbml.ext.render.RenderCurve

Sets the value of endHead

setEndHead(String) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Set the value of endHead

setFill(String) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

Set the value of fill

setFillRule(GraphicalPrimitive2D.FillRule) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

Set the value of fillRule

setFontFamily(FontFamily) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

Set the value of fontFamily

setFontFamily(FontFamily) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Set the value of fontFamily

setFontFamily(FontFamily) - Method in class org.sbml.jsbml.ext.render.Text

setFontSize(short) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

Set the value of fontSize

setFontSize(Short) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Set the value of fontSize

setFontSize(short) - Method in class org.sbml.jsbml.ext.render.Text

setFontStyleItalic(boolean) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

Set the value of fontStyleItalic

setFontStyleItalic(Boolean) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Set the value of fontStyleItalic

setFontStyleItalic(boolean) - Method in class org.sbml.jsbml.ext.render.Text

setFontWeightBold(boolean) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

Set the value of fontWeightBold

setFontWeightBold(Boolean) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Set the value of fontWeightBold

setFontWeightBold(boolean) - Method in class org.sbml.jsbml.ext.render.Text

setFx(double) - Method in class org.sbml.jsbml.ext.render.RadialGradient

Set the value of fx

setFy(double) - Method in class org.sbml.jsbml.ext.render.RadialGradient

Set the value of fy

setFz(double) - Method in class org.sbml.jsbml.ext.render.RadialGradient

Set the value of fz

setGroup(RenderGroup) - Method in class org.sbml.jsbml.ext.render.LineEnding

Sets the value of group

setGroup(RenderGroup) - Method in class org.sbml.jsbml.ext.render.Style

Set the value of group

setHeight(double) - Method in class org.sbml.jsbml.ext.render.Image

Set the value of height

setHeight(double) - Method in class org.sbml.jsbml.ext.render.Rectangle

Set the value of height

setHref(String) - Method in class org.sbml.jsbml.ext.render.Image

Set the value of href

setIDList(List<String>) - Method in class org.sbml.jsbml.ext.render.LocalStyle

Set the value of idList

setLayout(Layout) - Method in interface org.sbml.jsbml.ext.render.director.LayoutAlgorithm

setLayout(Layout) - Method in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

setLayoutIndex(int) - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

setLineWidth(double) - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNnode

setLineWidth(double) - Method in interface org.sbml.jsbml.ext.render.director.SBGNNode

setListOfColorDefinitions(ListOf<ColorDefinition>) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

setListOfCurveSegments(ListOf<CurveSegment>) - Method in class org.sbml.jsbml.ext.render.Polygon

Sets the given ListOf<CurveSegment>.

setListOfCurveSegments(ListOf<CurveSegment>) - Method in class org.sbml.jsbml.ext.render.RenderCurve

Sets the given ListOf<CurveSegment>.

setListOfElements(ListOf<RenderPoint>) - Method in class org.sbml.jsbml.ext.render.Polygon

Set the value of listOfElements

setListOfElements(ListOf<RenderPoint>) - Method in class org.sbml.jsbml.ext.render.RenderCurve

setListOfElements(ListOf<Transformation2D>) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Sets the given ListOf<Transformation2D>.

setListOfGlobalRenderInformation(ListOfGlobalRenderInformation) - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

setListOfGradientDefinitions(ListOf<GradientBase>) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

setListOfGradientStops(ListOf<GradientStop>) - Method in class org.sbml.jsbml.ext.render.GradientBase

setListOfLineEndings(ListOf<LineEnding>) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

setListOfLocalRenderInformation(ListOfLocalRenderInformation) - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

setListOfLocalStyles(ListOf<LocalStyle>) - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

setListOfStyles(ListOf<Style>) - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

setObjectRole(String) - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin

Sets the value of objectRole

setOffset(double) - Method in class org.sbml.jsbml.ext.render.GradientStop

Set the value of offset

setOfLayoutedGlyphs - Variable in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

Set to hold all layouted glyphs

setOfUnlayoutedGlyphs - Variable in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

Set to hold all unlayouted glyphs

setPointOfContactToProduct(Point) - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNProcessNode

setPointOfContactToProduct(Point) - Method in interface org.sbml.jsbml.ext.render.director.SBGNProcessNode

setPointOfContactToSubstrate(Point) - Method in class org.sbml.jsbml.ext.render.director.AbstractSBGNProcessNode

setPointOfContactToSubstrate(Point) - Method in interface org.sbml.jsbml.ext.render.director.SBGNProcessNode

setProgramName(String) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

Set the value of programmName

setProgramVersion(String) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

Set the value of programVersion

setR(double) - Method in class org.sbml.jsbml.ext.render.RadialGradient

Set the value of r

setReferenceRenderInformation(String) - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

Set the value of referenceRenderInformation

setRenderInformation(GlobalRenderInformation) - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

Set the value of renderInformation

setRoleList(List<String>) - Method in class org.sbml.jsbml.ext.render.Style

Set the value of roleList

setRx(Double) - Method in class org.sbml.jsbml.ext.render.Ellipse

Set the value of rx

setRx(double) - Method in class org.sbml.jsbml.ext.render.Rectangle

Set the value of rx

setRy(Double) - Method in class org.sbml.jsbml.ext.render.Ellipse

Set the value of ry

setRy(double) - Method in class org.sbml.jsbml.ext.render.Rectangle

Set the value of ry

setSpreadMethod(GradientBase.Spread) - Method in class org.sbml.jsbml.ext.render.GradientBase

Set the value of spreadMethod

setStartHead(String) - Method in class org.sbml.jsbml.ext.render.RenderCurve

Sets the value of startHead.

setStartHead(String) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Set the value of startHead

setStopColor(String) - Method in class org.sbml.jsbml.ext.render.GradientStop

Set the value of stopColor

setStroke(String) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

Set the value of stroke

setStrokeDashArray(Short[]) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

setStrokeDashArray(List<Short>) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

Set the value of strokeDashArray

setStrokeWidth(double) - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

Set the value of strokeWidth

setTextAnchor(HTextAnchor) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

Set the value of textAnchor

setTextAnchor(HTextAnchor) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Set the value of textAnchor

setTextAnchor(HTextAnchor) - Method in class org.sbml.jsbml.ext.render.Text

setTransform(Double[]) - Method in class org.sbml.jsbml.ext.render.Transformation2D

Set the value of transform

setTypeList(List<String>) - Method in class org.sbml.jsbml.ext.render.Style

Set the value of typeList

setValue(Color) - Method in class org.sbml.jsbml.ext.render.ColorDefinition

Set the value of value

setVersionMajor(short) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Sets the value of versionMajor

setVersionMajor(int) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

setVersionMinor(short) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Sets the value of versionMinor

setVersionMinor(int) - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

setVTextAnchor(VTextAnchor) - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

Set the value of VTextAnchor

setVTextAnchor(VTextAnchor) - Method in class org.sbml.jsbml.ext.render.RenderGroup

Set the value of vTextAnchor

setVTextAnchor(VTextAnchor) - Method in class org.sbml.jsbml.ext.render.Text

setWidth(double) - Method in class org.sbml.jsbml.ext.render.Image

Set the value of width

setWidth(double) - Method in class org.sbml.jsbml.ext.render.Rectangle

Set the value of width

setX(double) - Method in class org.sbml.jsbml.ext.render.Image

Set the value of x

setX(double) - Method in interface org.sbml.jsbml.ext.render.Point3D

Set the value of x

setX(double) - Method in class org.sbml.jsbml.ext.render.Rectangle

setX(double) - Method in class org.sbml.jsbml.ext.render.RenderPoint

setX(double) - Method in class org.sbml.jsbml.ext.render.Text

setX1(String) - Method in class org.sbml.jsbml.ext.render.LinearGradient

Set the value of x1

setX1(double) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Set the value of x1

setX2(String) - Method in class org.sbml.jsbml.ext.render.LinearGradient

Set the value of x2

setX2(double) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Set the value of x2

setY(double) - Method in class org.sbml.jsbml.ext.render.Image

Set the value of y

setY(double) - Method in interface org.sbml.jsbml.ext.render.Point3D

Set the value of y

setY(double) - Method in class org.sbml.jsbml.ext.render.Rectangle

setY(double) - Method in class org.sbml.jsbml.ext.render.RenderPoint

setY(double) - Method in class org.sbml.jsbml.ext.render.Text

setY1(String) - Method in class org.sbml.jsbml.ext.render.LinearGradient

Set the value of y1

setY1(double) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Set the value of y1

setY2(String) - Method in class org.sbml.jsbml.ext.render.LinearGradient

Set the value of y2

setY2(double) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Set the value of y2

setZ(double) - Method in class org.sbml.jsbml.ext.render.Image

Set the value of z

setZ(double) - Method in interface org.sbml.jsbml.ext.render.Point3D

Set the value of z

setZ(double) - Method in class org.sbml.jsbml.ext.render.Rectangle

setZ(double) - Method in class org.sbml.jsbml.ext.render.RenderPoint

setZ(double) - Method in class org.sbml.jsbml.ext.render.Text

setZ1(String) - Method in class org.sbml.jsbml.ext.render.LinearGradient

Set the value of z1

setZ1(double) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Set the value of z1

setZ2(String) - Method in class org.sbml.jsbml.ext.render.LinearGradient

Set the value of z2

setZ2(double) - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Set the value of z2

shortLabel - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

SimpleChemical<T> - Class in org.sbml.jsbml.ext.render.director

Abstract class that all the different graphical representations for simple chemical nodes have to extend.

SimpleChemical() - Constructor for class org.sbml.jsbml.ext.render.director.SimpleChemical

SimpleLayoutAlgorithm - Class in org.sbml.jsbml.ext.render.director

SimpleLayoutAlgorithm is a partial implementation of the LayoutAlgorithm interface which collects functions which are independent of the output format of the LayoutDirector.

SimpleLayoutAlgorithm() - Constructor for class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

SimpleLayoutAlgorithm.RelativePosition - Enum in org.sbml.jsbml.ext.render.director

Enumeration types (enums) for relative positions.

SourceSink<T> - Class in org.sbml.jsbml.ext.render.director

Abstract class that all the different graphical representations for the empty set sign have to implement

SourceSink() - Constructor for class org.sbml.jsbml.ext.render.director.SourceSink

SPECIAL_ROTATION_NEEDED - Static variable in class org.sbml.jsbml.ext.render.director.LayoutDirector

SPECIES_RELATIVE_DOCKING_POINT - Static variable in class org.sbml.jsbml.ext.render.director.LayoutDirector

Constant for use as the key for relative docking points for a species, also see LayoutDirector.PN_RELATIVE_DOCKING_POINT.

spreadMethod - Variable in class org.sbml.jsbml.ext.render.GradientBase

spreadMethod - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

startHead - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

startHead - Variable in class org.sbml.jsbml.ext.render.RenderCurve

Stimulation<T> - Interface in org.sbml.jsbml.ext.render.director

Interface for the SBGN specified stimulation arc.

stop - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

stopColor - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

stroke - Variable in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

stroke - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

strokeDashArray - Variable in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

strokeDashArray - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

strokeWidth - Variable in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

strokeWidth - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

style - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Style - Class in org.sbml.jsbml.ext.render

Style() - Constructor for class org.sbml.jsbml.ext.render.Style

Creates a Style instance with a group

Style(RenderGroup) - Constructor for class org.sbml.jsbml.ext.render.Style

Creates a Style instance with a group

Style(int, int, RenderGroup) - Constructor for class org.sbml.jsbml.ext.render.Style

Creates a Style instance with a level and version.

Style(String, int, int, RenderGroup) - Constructor for class org.sbml.jsbml.ext.render.Style

Creates a Style instance with an id, name, level, and version.

Style(Style) - Constructor for class org.sbml.jsbml.ext.render.Style

Clone constructor

Style.Type - Enum in org.sbml.jsbml.ext.render

The type StyleType is used by LocalStyle and GlobalStyle elements, in order to apply a particular style to a GraphicalObject.

T

terminated - Variable in class org.sbml.jsbml.ext.render.director.AbstractLayoutBuilder

Indicates whether graph generation has finished or not.

text - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Text - Class in org.sbml.jsbml.ext.render

Text() - Constructor for class org.sbml.jsbml.ext.render.Text

Text(int, int) - Constructor for class org.sbml.jsbml.ext.render.Text

Text(Text) - Constructor for class org.sbml.jsbml.ext.render.Text

textAnchor - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

textGlyphIsIndependent(TextGlyph) - Static method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Check whether a text glyph represents an independent text (i.e.

toGeneralPath(Curve) - Static method in class org.sbml.jsbml.ext.render.director.Geometry

toString() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

toString() - Method in enum org.sbml.jsbml.ext.render.RenderCurveSegment.Type

toString() - Method in class org.sbml.jsbml.ext.render.RenderGroup

transform - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

transform - Variable in class org.sbml.jsbml.ext.render.Transformation

transform - Variable in class org.sbml.jsbml.ext.render.Transformation2D

Transformation - Class in org.sbml.jsbml.ext.render

Transformation() - Constructor for class org.sbml.jsbml.ext.render.Transformation

Creates an Transformation instance

Transformation(int, int) - Constructor for class org.sbml.jsbml.ext.render.Transformation

Creates an Transformation instance

Transformation(Transformation) - Constructor for class org.sbml.jsbml.ext.render.Transformation

Clone constructor

Transformation2D - Class in org.sbml.jsbml.ext.render

Transformation2D() - Constructor for class org.sbml.jsbml.ext.render.Transformation2D

Creates an Transformation2D instance

Transformation2D(int, int) - Constructor for class org.sbml.jsbml.ext.render.Transformation2D

Transformation2D(Transformation2D) - Constructor for class org.sbml.jsbml.ext.render.Transformation2D

Clone constructor

type - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

typeList - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

typeList - Variable in class org.sbml.jsbml.ext.render.Style

U

UncertainProcessNode<T> - Interface in org.sbml.jsbml.ext.render.director

unsetAbsoluteCx() - Method in class org.sbml.jsbml.ext.render.Ellipse

Unsets the variable absoluteCx

unsetAbsoluteCx() - Method in class org.sbml.jsbml.ext.render.RadialGradient

Unsets the variable absoluteCx

unsetAbsoluteCy() - Method in class org.sbml.jsbml.ext.render.Ellipse

Unsets the variable absoluteCy

unsetAbsoluteCy() - Method in class org.sbml.jsbml.ext.render.RadialGradient

Unsets the variable absoluteCy

unsetAbsoluteCz() - Method in class org.sbml.jsbml.ext.render.Ellipse

Unsets the variable absoluteCz

unsetAbsoluteCz() - Method in class org.sbml.jsbml.ext.render.RadialGradient

Unsets the variable absoluteCz

unsetAbsoluteFx() - Method in class org.sbml.jsbml.ext.render.RadialGradient

Unsets the variable absoluteFx

unsetAbsoluteFy() - Method in class org.sbml.jsbml.ext.render.RadialGradient

Unsets the variable absoluteFy

unsetAbsoluteFz() - Method in class org.sbml.jsbml.ext.render.RadialGradient

Unsets the variable absoluteFz

unsetAbsoluteHeight() - Method in class org.sbml.jsbml.ext.render.Image

Unsets the variable absoluteHeight

unsetAbsoluteHeight() - Method in class org.sbml.jsbml.ext.render.Rectangle

Unsets the variable absoluteHeight

unsetAbsoluteR() - Method in class org.sbml.jsbml.ext.render.RadialGradient

Unsets the variable absoluteR

unsetAbsoluteRx() - Method in class org.sbml.jsbml.ext.render.Ellipse

Unsets the variable absoluteRx

unsetAbsoluteRx() - Method in class org.sbml.jsbml.ext.render.Rectangle

Unsets the variable absoluteRx

unsetAbsoluteRy() - Method in class org.sbml.jsbml.ext.render.Ellipse

Unsets the variable absoluteRy

unsetAbsoluteRy() - Method in class org.sbml.jsbml.ext.render.Rectangle

Unsets the variable absoluteRy

unsetAbsoluteWidth() - Method in class org.sbml.jsbml.ext.render.Image

Unsets the variable absoluteWidth

unsetAbsoluteWidth() - Method in class org.sbml.jsbml.ext.render.Rectangle

Unsets the variable absoluteWidth

unsetAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Image

Unsets the variable absoluteX

unsetAbsoluteX() - Method in interface org.sbml.jsbml.ext.render.Point3D

Unsets the variable absoluteX

unsetAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Rectangle

Unsets the variable absoluteX

unsetAbsoluteX() - Method in class org.sbml.jsbml.ext.render.RenderPoint

unsetAbsoluteX() - Method in class org.sbml.jsbml.ext.render.Text

unsetAbsoluteX1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Unsets the variable absoluteX1

unsetAbsoluteX2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Unsets the variable absoluteX2

unsetAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Image

Unsets the variable absoluteY

unsetAbsoluteY() - Method in interface org.sbml.jsbml.ext.render.Point3D

Unsets the variable absoluteY

unsetAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Rectangle

Unsets the variable absoluteY

unsetAbsoluteY() - Method in class org.sbml.jsbml.ext.render.RenderPoint

unsetAbsoluteY() - Method in class org.sbml.jsbml.ext.render.Text

unsetAbsoluteY1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Unsets the variable absoluteY1

unsetAbsoluteY2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Unsets the variable absoluteY2

unsetAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Image

Unsets the variable absoluteZ

unsetAbsoluteZ() - Method in interface org.sbml.jsbml.ext.render.Point3D

Unsets the variable absoluteZ

unsetAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Rectangle

Unsets the variable absoluteZ

unsetAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.RenderPoint

unsetAbsoluteZ() - Method in class org.sbml.jsbml.ext.render.Text

unsetAbsoluteZ1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Unsets the variable absoluteZ1

unsetAbsoluteZ2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Unsets the variable absoluteZ2

unsetAddWhiskers() - Method in class org.sbml.jsbml.ext.render.director.LayoutDirector

Unsets the variable addWhiskers

unsetBackgroundColor() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

Unsets the variable backgroundColor

unsetBoundingBox() - Method in class org.sbml.jsbml.ext.render.LineEnding

Unsets the variable boundingBox

unsetCx() - Method in class org.sbml.jsbml.ext.render.Ellipse

Unsets the variable cx

unsetCx() - Method in class org.sbml.jsbml.ext.render.RadialGradient

Unsets the variable cx

unsetCy() - Method in class org.sbml.jsbml.ext.render.Ellipse

Unsets the variable cy

unsetCy() - Method in class org.sbml.jsbml.ext.render.RadialGradient

Unsets the variable cy

unsetCz() - Method in class org.sbml.jsbml.ext.render.Ellipse

Unsets the variable cz

unsetCz() - Method in class org.sbml.jsbml.ext.render.RadialGradient

Unsets the variable cz

unsetDefaultValues() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Unsets the variable defaultValues.

unsetEnableRotationMapping() - Method in class org.sbml.jsbml.ext.render.LineEnding

Unsets the variable LineEnding.enableRotationMapping

unsetEndHead() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Unsets the variable endHead

unsetEndHead() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Unsets the variable endHead

unsetFill() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

Unsets the variable fill

unsetFillRule() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

Unsets the variable fillRule

unsetFontFamily() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

Unsets the variable fontFamily

unsetFontFamily() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Unsets the variable fontFamily

unsetFontFamily() - Method in class org.sbml.jsbml.ext.render.Text

unsetFontSize() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

Unsets the variable fontSize

unsetFontSize() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Unsets the variable fontSize

unsetFontSize() - Method in class org.sbml.jsbml.ext.render.Text

unsetFontStyleItalic() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

Unsets the variable fontStyleItalic

unsetFontStyleItalic() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Unsets the variable fontStyleItalic

unsetFontStyleItalic() - Method in class org.sbml.jsbml.ext.render.Text

unsetFontWeightBold() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

Unsets the variable fontWeightBold

unsetFontWeightBold() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Unsets the variable fontWeightBold

unsetFontWeightBold() - Method in class org.sbml.jsbml.ext.render.Text

unsetFx() - Method in class org.sbml.jsbml.ext.render.RadialGradient

Unsets the variable fx

unsetFy() - Method in class org.sbml.jsbml.ext.render.RadialGradient

Unsets the variable fy

unsetFz() - Method in class org.sbml.jsbml.ext.render.RadialGradient

Unsets the variable fz

unsetGroup() - Method in class org.sbml.jsbml.ext.render.LineEnding

Unsets the variable group

unsetGroup() - Method in class org.sbml.jsbml.ext.render.Style

Unsets the variable group

unsetHeight() - Method in class org.sbml.jsbml.ext.render.Image

Unsets the variable height

unsetHeight() - Method in class org.sbml.jsbml.ext.render.Rectangle

Unsets the variable height

unsetHref() - Method in class org.sbml.jsbml.ext.render.Image

Unsets the variable href

unsetIDList() - Method in class org.sbml.jsbml.ext.render.LocalStyle

Unsets the variable idList

unsetListOfColorDefinitions() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

unsetListOfCurveSegments() - Method in class org.sbml.jsbml.ext.render.Polygon

Returns true if Polygon.listOfCurveSegments contains at least one element, otherwise false.

unsetListOfCurveSegments() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Returns true if RenderCurve.listOfCurveSegments contains at least one element, otherwise false.

unsetListOfElements() - Method in class org.sbml.jsbml.ext.render.Polygon

Unsets the variable listOfElements

unsetListOfElements() - Method in class org.sbml.jsbml.ext.render.RenderCurve

unsetListOfElements() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Returns true, if listOfElements contain at least one element, otherwise false.

unsetListOfGlobalRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderListOfLayoutsPlugin

unsetListOfGradientDefinitions() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

unsetListOfGradientStops() - Method in class org.sbml.jsbml.ext.render.GradientBase

unsetListOfLineEndings() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

unsetListOfLocalRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderLayoutPlugin

unsetListOfLocalStyles() - Method in class org.sbml.jsbml.ext.render.LocalRenderInformation

unsetListOfStyles() - Method in class org.sbml.jsbml.ext.render.GlobalRenderInformation

unsetObjectRole() - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin

Unsets the variable objectRole.

unsetOffset() - Method in class org.sbml.jsbml.ext.render.GradientStop

Unsets the variable offset

unsetProgramName() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

Unsets the variable programmName

unsetProgramVersion() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

Unsets the variable programVersion

unsetR() - Method in class org.sbml.jsbml.ext.render.RadialGradient

Unsets the variable r

unsetReferenceRenderInformation() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

Unsets the variable referenceRenderInformation

unsetRenderInformation() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

Unsets the variable renderInformation

unsetRoleList() - Method in class org.sbml.jsbml.ext.render.Style

Unsets the variable roleList

unsetRx() - Method in class org.sbml.jsbml.ext.render.Ellipse

Unsets the variable rx

unsetRx() - Method in class org.sbml.jsbml.ext.render.Rectangle

Unsets the variable rx

unsetRy() - Method in class org.sbml.jsbml.ext.render.Ellipse

Unsets the variable ry

unsetRy() - Method in class org.sbml.jsbml.ext.render.Rectangle

Unsets the variable ry

unsetSpreadMethod() - Method in class org.sbml.jsbml.ext.render.GradientBase

Unsets the variable spreadMethod

unsetStartHead() - Method in class org.sbml.jsbml.ext.render.RenderCurve

Unsets the variable startHead

unsetStartHead() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Unsets the variable startHead

unsetStopColor() - Method in class org.sbml.jsbml.ext.render.GradientStop

Unsets the variable stopColor

unsetStroke() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

Unsets the variable stroke

unsetStrokeDashArray() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

Unsets the variable strokeDashArray

unsetStrokeWidth() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

Unsets the variable strokeWidth

unsetTextAnchor() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

Unsets the variable textAnchor

unsetTextAnchor() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Unsets the variable textAnchor

unsetTextAnchor() - Method in class org.sbml.jsbml.ext.render.Text

unsetTransform() - Method in class org.sbml.jsbml.ext.render.Transformation2D

Unsets the variable transform

unsetTypeList() - Method in class org.sbml.jsbml.ext.render.Style

Unsets the variable typeList

unsetValue() - Method in class org.sbml.jsbml.ext.render.ColorDefinition

Unsets the variable value

unsetVersionMajor() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Unsets the variable versionMajor

unsetVersionMinor() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

Unsets the variable versionMinor

unsetVTextAnchor() - Method in interface org.sbml.jsbml.ext.render.FontRenderStyle

Unsets the variable VTextAnchor

unsetVTextAnchor() - Method in class org.sbml.jsbml.ext.render.RenderGroup

Unsets the variable vTextAnchor

unsetVTextAnchor() - Method in class org.sbml.jsbml.ext.render.Text

unsetWidth() - Method in class org.sbml.jsbml.ext.render.Image

Unsets the variable width

unsetWidth() - Method in class org.sbml.jsbml.ext.render.Rectangle

Unsets the variable width

unsetX() - Method in class org.sbml.jsbml.ext.render.Image

Unsets the variable x

unsetX() - Method in interface org.sbml.jsbml.ext.render.Point3D

Unsets the variable x

unsetX() - Method in class org.sbml.jsbml.ext.render.Rectangle

Unsets the variable x

unsetX() - Method in class org.sbml.jsbml.ext.render.RenderPoint

unsetX() - Method in class org.sbml.jsbml.ext.render.Text

unsetX1() - Method in class org.sbml.jsbml.ext.render.LinearGradient

Unsets the variable x1

unsetX1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Unsets the variable x1

unsetX2() - Method in class org.sbml.jsbml.ext.render.LinearGradient

Unsets the variable x2

unsetX2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Unsets the variable x2

unsetY() - Method in class org.sbml.jsbml.ext.render.Image

Unsets the variable y

unsetY() - Method in interface org.sbml.jsbml.ext.render.Point3D

Unsets the variable y

unsetY() - Method in class org.sbml.jsbml.ext.render.Rectangle

Unsets the variable y

unsetY() - Method in class org.sbml.jsbml.ext.render.RenderPoint

unsetY() - Method in class org.sbml.jsbml.ext.render.Text

unsetY1() - Method in class org.sbml.jsbml.ext.render.LinearGradient

Unsets the variable y1

unsetY1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Unsets the variable y1

unsetY2() - Method in class org.sbml.jsbml.ext.render.LinearGradient

Unsets the variable y2

unsetY2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Unsets the variable y2

unsetZ() - Method in class org.sbml.jsbml.ext.render.Image

Unsets the variable z

unsetZ() - Method in interface org.sbml.jsbml.ext.render.Point3D

Unsets the variable z

unsetZ() - Method in class org.sbml.jsbml.ext.render.Rectangle

Unsets the variable z

unsetZ() - Method in class org.sbml.jsbml.ext.render.RenderPoint

unsetZ() - Method in class org.sbml.jsbml.ext.render.Text

unsetZ1() - Method in class org.sbml.jsbml.ext.render.LinearGradient

Unsets the variable z1

unsetZ1() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Unsets the variable z1

unsetZ2() - Method in class org.sbml.jsbml.ext.render.LinearGradient

Unsets the variable z2

unsetZ2() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

Unsets the variable z2

UnspecifiedNode<T> - Class in org.sbml.jsbml.ext.render.director

Abstract class that all the different graphical representations for unspecified entity pool nodes have to implement

UnspecifiedNode() - Constructor for class org.sbml.jsbml.ext.render.director.UnspecifiedNode

V

value - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm.RelativePosition

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

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.FontFamily

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

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.GradientBase.Spread

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

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.GraphicalPrimitive2D.FillRule

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

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.HTextAnchor

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

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.RenderCurveSegment.Type

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

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.Style.Type

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

valueOf(String) - Static method in enum org.sbml.jsbml.ext.render.VTextAnchor

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

values() - Static method in enum org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm.RelativePosition

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.FontFamily

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.GradientBase.Spread

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.GraphicalPrimitive2D.FillRule

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.HTextAnchor

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.RenderCurveSegment.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.Style.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.sbml.jsbml.ext.render.VTextAnchor

Returns an array containing the constants of this enum type, in the order they are declared.

version - Variable in class org.sbml.jsbml.ext.render.director.SimpleLayoutAlgorithm

SBML version

versionMajor - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

versionMinor - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

vTextAnchor - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

VTextAnchor - Enum in org.sbml.jsbml.ext.render

The VTextAnchor enumeration allows models to specify how text elements are to be vertically aligned within their BoundingBox.

W

width - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.AbstractRenderPlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.ColorDefinition

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.DefaultValues

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.Ellipse

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.GradientBase

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.GradientStop

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive1D

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.GraphicalPrimitive2D

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.Image

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.LinearGradient

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.LineEnding

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.ListOfRenderInformation

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.LocalStyle

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.RadialGradient

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.Rectangle

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.RenderCubicBezier

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.RenderCurve

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.RenderCurveSegment

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.RenderGroup

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.RenderInformationBase

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.RenderPoint

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.Style

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.Text

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.render.Transformation

X

x - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

x1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

x2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

XMLTools - Class in org.sbml.jsbml.ext.render

Utility class to help write the XML

XMLTools() - Constructor for class org.sbml.jsbml.ext.render.XMLTools

xsiShortLabel - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Y

y - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

y1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

y2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

Z

z - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

z1 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

z2 - Static variable in class org.sbml.jsbml.ext.render.RenderConstants

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