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References

algorithms

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components

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V RelGraph: *

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components/gui

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V SearchBar: *

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V ObjToArray: *

model

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Coalescence model

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C Graph

The main model graph (the group with configuration options for the model viewer)

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C Group

Group (subgraph) model

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C Chain

Chain model

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Channel model

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Group template

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C Tree

Tree model

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C Logger

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The class defining common methods for all resources

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C Border

The class defining the border of a shape (lyph or region)

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C Lyph

Class that models lyphs

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C Region

Class that models regions

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C Shape

Class that specifies borders of lyphs and regions

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C Link

The class to visualize processes (edges)

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The class to model Material resources

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C Node

The class to visualize Node resources in the force-directed graphs

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The class implementing common methods for the visual resources.

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F addColor(resources: *, defaultColor: *)

Add color to the visual resources in the list that do not have color assigned yet

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F findResourceByID(eArray: *, e: *): * | void | T

Finds a resource object in the parent group given an object or an ID

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F getClassName(spec: *): *

Extracts class name from the schema definition

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F getRefs(spec: *): *

Returns a list of references in the schema type specification

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F isClassAbstract(clsName: *)

Indicates whether schema class definition is abstract

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F mergeGenResource(group: *, parentGroup: *, resource: *, prop: *)

Add a given resource to a given group and a parent group if it does not exist

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F mergeGenResources(group: *, parentGroup: *, lnk,trg, lyph: *)

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V COALESCENCE_TOPOLOGY: {"EMBEDDING": string, "CONNECTING": string}

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V LEVEL: {"INFO": string, "WARN": string, "ERROR": string}

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V STATUS: {"OK": string, "WARNING": string, "ERROR": string}

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V modelClasses: {"Resource": *, "VisualResource": *, "GroupTemplate": *, "Shape": *, "External": *, "Coalescence": *, "Channel": *, "Chain": *, "Tree": *, "Group": *, "Graph": *, "Node": *, "Link": *, "Material": *, "Region": *, "Lyph": *, "Border": *}

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V LYPH_TOPOLOGY: {"TUBE": string, "BAG": string, "BAG2": string, "CYST": string}

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JSON Path validator

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V LINK_GEOMETRY: {LINK: string, SEMICIRCLE: string, RECTANGLE: string, PATH: string, SPLINE: string, INVISIBLE: string, FORCE: string}

Supported link geometries

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V LINK_STROKE: {DASHED: string, THICK: string}

Supported link strokes

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V PROCESS_TYPE: {ADVECTIVE: string, DIFFUSIVE: string}

Process types

services

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test-app

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V TestApp: *

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three

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The class to create materials with predefined default parameters

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F align(link: {source: Vector3, target: Vector3}, obj: Object3D, reversed: boolean)

Align an object along its axis (link)

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F angle(v1: Vector3, v2: Vector3): number

Compute the angle between two 3d vectors

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F bezierSemicircle(startV: Vector3, endV: Vector3): CubicBezierCurve3

Create a cubic Bezier curve resembling a semicircle

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F boundToPolygon(link: {source: Vector2, target: Vector2}, boundaryLinks: Array)

Force link ends to stay inside of a polygon (reset coordinates to the intersection point)

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F boundToRectangle(point: Vector2, min: {x: number, y: number}, max: {x: number, y: number})

Pushes a point inside of a rectangle on a plane

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Convert color string to hex

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F commonTemplate(lyph1: *, lyph2: *): *

Determines whether two lyphs have a common supertype

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F copyCoords(target: *, source: *)

Copy coordinates from source object to target

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F createMeshWithBorder(shape: Shape, params: Object): Mesh

Create a 3d object with border

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F d3Layer(inner: *, outer: *, params: *): THREE.Mesh

Draws layer of a lyph in 3d.

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F d3Lyph(outer: *, params: *): *

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F direction(source: Vector3, target: Vector3): null

Create a vector between two 3d points

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F extractCoords(source: Object): Vector3

Create a vector from an object that contains coordinate fields x, y, and z

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F geometryDifference(smallGeom: *, largeGeom: *, params: *): *

Computes difference between two geometries

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F getBoundingBox(mesh: Mesh): Box3

Get bounding box for a mesh geometry

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F getCenterOfMass(points: Array<Vector3>): Vector3

Return the center of mass given a set of control points

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F getCenterPoint(mesh: Mesh): Vector3

Find coordinates of the central point of the given mesh

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F getPoint(curve: *, s: *, t: *, offset: *): *

Get a point on a curve

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F isInRange(from: *, to: *, angle: *): boolean

Checks that the angle is between given angles

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F layerShape(inner: Array, outer: Array): Shape

Create lyph layer shape

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F lyphShape(params: Array): Shape

Create lyph shape

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F mergedGeometry(tube: *, cupTop: *, cupBottom: *, offset: *): Geometry | SEA3D.Geometry | * | THREE.Geometry

Helper function to produce a merged layer geometry given a tube shape and two cups representing open or closed borders

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F rectangleCurve(startV: Vector3, endV: Vector3): CurvePath<Vector> | CurvePath

Create a curve path resembling a semi-rectangle with rounded corners

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V THREE: *