A B C D G H I M N O P R S T V X

A

AMINOACID - Static variable in class de.bioforscher.singa.javafx.viewer.MaterialProvider

arrangeGraph(int) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphDrawingTool

Calculates one iteration of the optimization process and returns the resulting graph.

arrangeGraph(GraphType) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

B

brightness(double) - Method in class de.bioforscher.singa.javafx.renderer.colors.ColorScale.Builder

build() - Method in class de.bioforscher.singa.javafx.renderer.colors.ColorScale.Builder

Builder(double, double) - Constructor for class de.bioforscher.singa.javafx.renderer.colors.ColorScale.Builder

C

CARBON - Static variable in class de.bioforscher.singa.javafx.viewer.MaterialProvider

circlePoint(Vector2D, double) - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

Circles the outline of a point where the Vector2D is positioned.

ColorScale - Class in de.bioforscher.singa.javafx.renderer.colors

This object provides a color scale between the given minimal and maximal values.

ColorScale.Builder - Class in de.bioforscher.singa.javafx.renderer.colors

ColorScheme - Enum in de.bioforscher.singa.javafx.viewer

colorScheme - Static variable in class de.bioforscher.singa.javafx.viewer.StructureViewer

connectPoints(Collection<Vector2D>) - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

Connects the points given in the List in order of their appearance with a line.
The line width of the point is determined by the LineWidth (set by GraphicsContext.setLineWidth(double)). The color is determined by the StrokeColor (set by GraphicsContext.setStroke(Paint)).

ConvexHullPlayground - Class in de.bioforscher.singa.javafx.geometry

Created by Christoph on 14/04/2017.

ConvexHullPlayground() - Constructor for class de.bioforscher.singa.javafx.geometry.ConvexHullPlayground

crateMaterialFromColor(Color) - Static method in class de.bioforscher.singa.javafx.viewer.MaterialProvider

D

dashLineSegment(LineSegment, double...) - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

Draws the given line segment.

de.bioforscher.singa.javafx.geometry - package de.bioforscher.singa.javafx.geometry

de.bioforscher.singa.javafx.renderer - package de.bioforscher.singa.javafx.renderer

de.bioforscher.singa.javafx.renderer.colors - package de.bioforscher.singa.javafx.renderer.colors

de.bioforscher.singa.javafx.renderer.graphs - package de.bioforscher.singa.javafx.renderer.graphs

de.bioforscher.singa.javafx.renderer.molecules - package de.bioforscher.singa.javafx.renderer.molecules

de.bioforscher.singa.javafx.viewer - package de.bioforscher.singa.javafx.viewer

drawDraggedRectangle(Vector2D, Vector2D) - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

drawEdge(EdgeType) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

drawEdge(MoleculeBond) - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeGraphRenderer

drawingHeightProperty() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

drawingWidthProperty() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

drawLine(Line) - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

Draws the given line.

drawLineSegment(LineSegment) - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

Draws the given line segment.

drawNode(NodeType) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

drawNode(MoleculeAtom) - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeGraphRenderer

drawParabola(Parabola) - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

Draws the given parabola.

drawParabola(Parabola, int) - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

Draws the given parabola.

drawPoint(Vector2D, double) - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

Draws a point (filled circle) where the Vector2D is positioned.

drawPoint(Vector2D) - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

Draws a point (filled circle) where the Vector2D is positioned.

drawRectangle(Vector2D, Vector2D) - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

drawStraight(Vector2D, Vector2D) - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

Draws a straight by connecting the given start and end points.

drawTextCenteredOnPoint(String, Vector2D) - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

Draws the given text centered on the given vector.

G

getBackgroundColor() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

getCarbonColor() - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeRendererOptions

getColor(double) - Method in class de.bioforscher.singa.javafx.renderer.colors.ColorScale

Gets the color as specified by this gradient for this value between the minimal and maximal value.

getColorForElement(String) - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeRendererOptions

getDefaultMaterialForElement(Element) - Static method in class de.bioforscher.singa.javafx.viewer.MaterialProvider

getDrawingHeight() - Method in class de.bioforscher.singa.javafx.geometry.ConvexHullPlayground

getDrawingHeight() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

Gets the value of the property drawingHeight.

getDrawingHeight() - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

getDrawingHeight() - Method in class de.bioforscher.singa.javafx.renderer.RendererExamples

getDrawingWidth() - Method in class de.bioforscher.singa.javafx.geometry.ConvexHullPlayground

getDrawingWidth() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

Gets the value of the property drawingWidth.

getDrawingWidth() - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

getDrawingWidth() - Method in class de.bioforscher.singa.javafx.renderer.RendererExamples

getEdgeColor() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

getEdgeThickness() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

getGraphicsContext() - Method in class de.bioforscher.singa.javafx.geometry.ConvexHullPlayground

getGraphicsContext() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

getGraphicsContext() - Method in interface de.bioforscher.singa.javafx.renderer.Renderer

Returns the assigned GraphicContext.

getGraphicsContext() - Method in class de.bioforscher.singa.javafx.renderer.RendererExamples

getGraphQueue() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

getHydrogenColor() - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeRendererOptions

getIdentifierTextColor() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

getMaterialForType(StructuralFamily) - Static method in class de.bioforscher.singa.javafx.viewer.MaterialProvider

getNitrogenColor() - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeRendererOptions

getNodeColor() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

getNodeDiameter() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

getOxygenColor() - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeRendererOptions

getPhosphorusColor() - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeRendererOptions

getRenderingOptions() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

getSulfurColor() - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeRendererOptions

graph - Static variable in class de.bioforscher.singa.javafx.renderer.graphs.GraphDisplayApplication

GraphDisplayApplication - Class in de.bioforscher.singa.javafx.renderer.graphs

GraphDisplayApplication() - Constructor for class de.bioforscher.singa.javafx.renderer.graphs.GraphDisplayApplication

GraphDrawingTool<NodeType extends Node<NodeType,Vector2D,IdentifierType>,EdgeType extends Edge<NodeType>,IdentifierType,GraphType extends Graph<NodeType,EdgeType,IdentifierType>> - Class in de.bioforscher.singa.javafx.renderer.graphs

This class tries to arrange a graph using force directed placement.

GraphDrawingTool(GraphType, DoubleProperty, DoubleProperty, int) - Constructor for class de.bioforscher.singa.javafx.renderer.graphs.GraphDrawingTool

Creates a new GraphDrawingTool.

GraphProducer<NodeType extends Node<NodeType,Vector2D,IdentifierType>,EdgeType extends Edge<NodeType>,IdentifierType,GraphType extends Graph<NodeType,EdgeType,IdentifierType>> - Class in de.bioforscher.singa.javafx.renderer.graphs

GraphProducer(GraphRenderer<NodeType, EdgeType, IdentifierType, GraphType>, GraphType, int) - Constructor for class de.bioforscher.singa.javafx.renderer.graphs.GraphProducer

GraphRenderer<NodeType extends Node<NodeType,Vector2D,IdentifierType>,EdgeType extends Edge<NodeType>,IdentifierType,GraphType extends Graph<NodeType,EdgeType,IdentifierType>> - Class in de.bioforscher.singa.javafx.renderer.graphs

GraphRenderer() - Constructor for class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

GraphRenderOptions - Class in de.bioforscher.singa.javafx.renderer.graphs

The default rendering options for any graph.

GraphRenderOptions() - Constructor for class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

GraphViewerPlayground - Class in de.bioforscher.singa.javafx.renderer.graphs

GraphViewerPlayground() - Constructor for class de.bioforscher.singa.javafx.renderer.graphs.GraphViewerPlayground

H

handle(long) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

HYDROGEN - Static variable in class de.bioforscher.singa.javafx.viewer.MaterialProvider

I

init() - Method in class de.bioforscher.singa.javafx.geometry.ConvexHullPlayground

ip - Variable in class de.bioforscher.singa.javafx.viewer.XForm

isDisplayingEdges() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

isDisplayingIdentifierText() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

isDisplayingNodes() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

M

main(String[]) - Static method in class de.bioforscher.singa.javafx.geometry.ConvexHullPlayground

main(String[]) - Static method in class de.bioforscher.singa.javafx.renderer.graphs.GraphDisplayApplication

main(String[]) - Static method in class de.bioforscher.singa.javafx.renderer.graphs.GraphViewerPlayground

main(String[]) - Static method in class de.bioforscher.singa.javafx.renderer.RendererExamples

main(String[]) - Static method in class de.bioforscher.singa.javafx.viewer.StructureViewer

main(String[]) - Static method in class de.bioforscher.singa.javafx.viewer.StructureViewerPlayground

MaterialProvider - Class in de.bioforscher.singa.javafx.viewer

MaterialProvider() - Constructor for class de.bioforscher.singa.javafx.viewer.MaterialProvider

maximalHue(double) - Method in class de.bioforscher.singa.javafx.renderer.colors.ColorScale.Builder

maximalHue(Color) - Method in class de.bioforscher.singa.javafx.renderer.colors.ColorScale.Builder

minimalHue(double) - Method in class de.bioforscher.singa.javafx.renderer.colors.ColorScale.Builder

minimalHue(Color) - Method in class de.bioforscher.singa.javafx.renderer.colors.ColorScale.Builder

MoleculeGraphRenderer - Class in de.bioforscher.singa.javafx.renderer.molecules

MoleculeGraphRenderer() - Constructor for class de.bioforscher.singa.javafx.renderer.molecules.MoleculeGraphRenderer

MoleculeRendererOptions - Class in de.bioforscher.singa.javafx.renderer.molecules

MoleculeRendererOptions() - Constructor for class de.bioforscher.singa.javafx.renderer.molecules.MoleculeRendererOptions

N

NITROGEN - Static variable in class de.bioforscher.singa.javafx.viewer.MaterialProvider

NUCLEOTIDE - Static variable in class de.bioforscher.singa.javafx.viewer.MaterialProvider

O

OTHER_ELEMENT - Static variable in class de.bioforscher.singa.javafx.viewer.MaterialProvider

OTHER_TYPE - Static variable in class de.bioforscher.singa.javafx.viewer.MaterialProvider

OXYGEN - Static variable in class de.bioforscher.singa.javafx.viewer.MaterialProvider

P

p - Variable in class de.bioforscher.singa.javafx.viewer.XForm

R

render(GraphType) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

renderer - Static variable in class de.bioforscher.singa.javafx.renderer.graphs.GraphDisplayApplication

Renderer - Interface in de.bioforscher.singa.javafx.renderer

The renderer interface supplies default methods to draw in a GraphicsContext method.

RendererExamples - Class in de.bioforscher.singa.javafx.renderer

RendererExamples() - Constructor for class de.bioforscher.singa.javafx.renderer.RendererExamples

reset() - Method in class de.bioforscher.singa.javafx.viewer.XForm

resetTSP() - Method in class de.bioforscher.singa.javafx.viewer.XForm

run() - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphProducer

rx - Variable in class de.bioforscher.singa.javafx.viewer.XForm

ry - Variable in class de.bioforscher.singa.javafx.viewer.XForm

rz - Variable in class de.bioforscher.singa.javafx.viewer.XForm

S

s - Variable in class de.bioforscher.singa.javafx.viewer.XForm

saturation(double) - Method in class de.bioforscher.singa.javafx.renderer.colors.ColorScale.Builder

setBackgroundColor(Color) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

setCarbonColor(Color) - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeRendererOptions

setDisplayingEdges(boolean) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

setDisplayingIdentifierText(boolean) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

setDisplayingNodes(boolean) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

setEdgeColor(Color) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

setEdgeThickness(double) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

setGraphicsContext(GraphicsContext) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

setHydrogenColor(Color) - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeRendererOptions

setIdentifierTextColor(Color) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

setNitrogenColor(Color) - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeRendererOptions

setNodeColor(Color) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

setNodeDiameter(double) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderOptions

setOxygenColor(Color) - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeRendererOptions

setPhosphorusColor(Color) - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeRendererOptions

setPivot(double, double, double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setRenderingOptions(GraphRenderOptions) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphRenderer

setRotate(double, double, double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setRotateX(double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setRotateY(double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setRotateZ(double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setRy(double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setRz(double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setScale(double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setSulfurColor(Color) - Method in class de.bioforscher.singa.javafx.renderer.molecules.MoleculeRendererOptions

setSx(double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setSy(double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setSz(double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setTranslate(double, double, double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setTranslate(double, double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setTx(double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setTy(double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

setTz(double) - Method in class de.bioforscher.singa.javafx.viewer.XForm

start(Stage) - Method in class de.bioforscher.singa.javafx.geometry.ConvexHullPlayground

start(Stage) - Method in class de.bioforscher.singa.javafx.renderer.graphs.GraphDisplayApplication

start(Stage) - Method in class de.bioforscher.singa.javafx.renderer.RendererExamples

start(Stage) - Method in class de.bioforscher.singa.javafx.viewer.StructureViewer

structure - Static variable in class de.bioforscher.singa.javafx.viewer.StructureViewer

StructureViewer - Class in de.bioforscher.singa.javafx.viewer

StructureViewer() - Constructor for class de.bioforscher.singa.javafx.viewer.StructureViewer

StructureViewerPlayground - Class in de.bioforscher.singa.javafx.viewer

StructureViewerPlayground() - Constructor for class de.bioforscher.singa.javafx.viewer.StructureViewerPlayground

T

translate - Variable in class de.bioforscher.singa.javafx.viewer.XForm

V

valueOf(String) - Static method in enum de.bioforscher.singa.javafx.viewer.ColorScheme

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

valueOf(String) - Static method in enum de.bioforscher.singa.javafx.viewer.XForm.RotateOrder

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

values() - Static method in enum de.bioforscher.singa.javafx.viewer.ColorScheme

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.bioforscher.singa.javafx.viewer.XForm.RotateOrder

Returns an array containing the constants of this enum type, in the order they are declared.

X

XForm - Class in de.bioforscher.singa.javafx.viewer

XForm() - Constructor for class de.bioforscher.singa.javafx.viewer.XForm

XForm(XForm.RotateOrder) - Constructor for class de.bioforscher.singa.javafx.viewer.XForm

XForm.RotateOrder - Enum in de.bioforscher.singa.javafx.viewer

A B C D G H I M N O P R S T V X