Uses of Class
mgui.interfaces.AbstractInterfaceObject

Packages that use AbstractInterfaceObject

Package	Description
mgui.datasources	This package contains the core classes for data source functionality.
mgui.graphs.networks	Classes representing network graphs.
mgui.interfaces	This package contains all main/abstract interface objects (object which provides user interations) for ModelGUI.
mgui.interfaces.attributes	Provides a standard updatable attribute object which can fire events for all interface objects.
mgui.interfaces.graphics	Provides graphical windows for user interaction with model objects.
mgui.interfaces.graphics.util	Utility classes operating on 2D and 3D graphics objects.
mgui.interfaces.graphics.video	Provides classes to generate videos from graphics windows.
mgui.interfaces.graphs	Provides an interface for user interaction with graph objects.
mgui.interfaces.graphs.shapes	Specifies shapes for 2D and 3D graph rendering.
mgui.interfaces.layouts
mgui.interfaces.maps	Provides a set a maps for use by ModelGUI objects.
mgui.interfaces.models	Base classes for specifying dynamic models.
mgui.interfaces.neuro
mgui.interfaces.pipelines.libraries
mgui.interfaces.plots	Provides 2D and 3D plotting functionality.
mgui.interfaces.plots.sgt	Plots using the Scientific Graphics Toolkit (SGT) library.
mgui.interfaces.projects	Provides an interface for projects, which specify file/URL organization and I/O operations
mgui.interfaces.shapes	This package provides interfaces for user interaction with shapes and shape models.
mgui.interfaces.shapes.attributes
mgui.interfaces.shapes.dynamic
mgui.interfaces.shapes.graphs
mgui.interfaces.shapes.mesh
mgui.interfaces.shapes.neuro
mgui.interfaces.shapes.paths
mgui.interfaces.shapes.selection
mgui.interfaces.shapes.util
mgui.interfaces.shapes.volume
mgui.interfaces.variables
mgui.io.domestic.maps
mgui.models.dynamic.functions
mgui.models.environments
mgui.models.networks
mgui.models.networks.components
mgui.models.updaters
mgui.morph.sections
mgui.neuro.components
mgui.neuro.components.compartments
mgui.neuro.components.cortical
mgui.neuro.components.cortical.functions
mgui.neuro.components.cortical.simple
mgui.neuro.components.simple
mgui.neuro.components.types
mgui.neuro.graphs
mgui.neuro.networks
mgui.neuro.updaters
mgui.pipelines	Provides a framework for defining and running processing pipelines in the ModelGUI environment.

Uses of AbstractInterfaceObject in mgui.datasources

Subclasses of AbstractInterfaceObject in mgui.datasources

Modifier and Type	Class	Description
class	DataConnection	Specifies a basic JDBC database connection, including: JDBC driver URL Connection name File location Login Password //TODO implement security on this
class	DataField	Object to specify a field data type and length.
class	DataQuery	Represents an SQL query.
class	DataSource	Acts as a port into the JDBC interface.
class	DataTable	General data table object specifying the organization of data into fields.
class	DataTableSet	Object stores a list of DataTable objects, all representing tables in a single DataSource
class	LinkedDataStream<T extends java.lang.Comparable<T>>	Provides a link to a data source, using a unique field as the link field.

Uses of AbstractInterfaceObject in mgui.graphs.networks

Subclasses of AbstractInterfaceObject in mgui.graphs.networks

Modifier and Type	Class	Description
class	AbstractNetworkGraphConnection	Represents an edge (i.e., a connection) in a network graph.
class	AbstractNetworkGraphNode	Represents a node in a network graph.

Uses of AbstractInterfaceObject in mgui.interfaces

Subclasses of AbstractInterfaceObject in mgui.interfaces

Modifier and Type	Class	Description
class	InterfaceWorkspace	A Workspace acts as a container for all data models and graphics windows.
static class	InterfaceWorkspace.CollectionTreeNode

Uses of AbstractInterfaceObject in mgui.interfaces.attributes

Subclasses of AbstractInterfaceObject in mgui.interfaces.attributes

Modifier and Type	Class	Description
class	Attribute<V>	Class serves as a general-purpose attribute.
class	AttributeList	Stores a list of Attribute objects, and provides methods to access and modify them, as well as set methods to intersect and union with other lists.
class	AttributeSelection<V>	Extends Attribute to allow a list of options, one or none of which is the current value.
class	AttributeSelectionMap<V>	Represents an Attribute with possible values mapped with String keys.

Uses of AbstractInterfaceObject in mgui.interfaces.graphics

Subclasses of AbstractInterfaceObject in mgui.interfaces.graphics

Modifier and Type	Class	Description
class	Graphic2DGrid	Defines a 2D grid, for display in an InterfaceGraphic2D window.
class	View3D	Represents a specific 3D view, defined by a frozen Camera3D object.

Uses of AbstractInterfaceObject in mgui.interfaces.graphics.util

Subclasses of AbstractInterfaceObject in mgui.interfaces.graphics.util

Modifier and Type	Class	Description
class	Axes3D	Renders 3D axes on a 3D window.

Uses of AbstractInterfaceObject in mgui.interfaces.graphics.video

Subclasses of AbstractInterfaceObject in mgui.interfaces.graphics.video

Modifier and Type	Class	Description
class	Video	Represents a video schedule, using a list of VideoTask objects which are activated at specific time points.
class	Video3D	A Video operating on an InterfaceGraphic3D window or its associated objects.

Uses of AbstractInterfaceObject in mgui.interfaces.graphs

Subclasses of AbstractInterfaceObject in mgui.interfaces.graphs

Modifier and Type	Class	Description
class	AbstractGraphEdge	Abstract representation of a graph edge, connecting two nodes.
class	AbstractGraphNode	Abstract representation of a graph node (vertex), with a specific static 3D locations.
class	DefaultGraphEdge	Default implementation of a Graph edge.
class	DefaultGraphNode	Default implementation of a Graph in modelGUI.

Uses of AbstractInterfaceObject in mgui.interfaces.graphs.shapes

Subclasses of AbstractInterfaceObject in mgui.interfaces.graphs.shapes

Modifier and Type	Class	Description
class	GraphImage	Draws an image on a graph display.
class	GraphShape	Abstract class for objects which implement VisualizationServer.Paintable; these can be used to render shapes on a graph display window.

Uses of AbstractInterfaceObject in mgui.interfaces.layouts

Subclasses of AbstractInterfaceObject in mgui.interfaces.layouts

Modifier and Type	Class	Description
class	LayoutDocument	Implements the top-level container for a 2D layout, containing renderable items within a fixed coordinate system (document coordinates/units).
class	LayoutItem	Specifies an element to be rendered in a InterfaceLayoutDocument.

Uses of AbstractInterfaceObject in mgui.interfaces.maps

Subclasses of AbstractInterfaceObject in mgui.interfaces.maps

Modifier and Type	Class	Description
class	Camera3D	Represents a particular camera position in R3, defined by a center of rotation, line of sight vector, and a distance.
class	Camera3D.CameraLightSource
class	ColourMap	Abstract class for mapping values (instances of Comparable) to colours.
class	ContinuousColourMap	Maps colours to values based upon a set of anchors (expressed on the range [0:1]) and an interpolator.
class	DiscreteColourMap	Colour map for discrete 1-to-1 mappings (integers to colours).
class	Map	Represents a coordinate mapping from one coordinate system to another (typically a model system to screen or printer coordinates)
class	Map2D	Maps from a given coordinate system to the screen
class	Map3D	Class to provide an interface for mapping a 3D viewing platform.
class	NameMap	Associates a name with an integer.

Uses of AbstractInterfaceObject in mgui.interfaces.models

Subclasses of AbstractInterfaceObject in mgui.interfaces.models

Modifier and Type	Class	Description
class	InterfaceAbstractModel

Uses of AbstractInterfaceObject in mgui.interfaces.neuro

Subclasses of AbstractInterfaceObject in mgui.interfaces.neuro

Modifier and Type	Class	Description
class	InterfaceNeuroAtlas	Defines an atlas mapping a set of data points to integers which map in turn to atlas names (via a name map).

Uses of AbstractInterfaceObject in mgui.interfaces.pipelines.libraries

Subclasses of AbstractInterfaceObject in mgui.interfaces.pipelines.libraries

Modifier and Type	Class	Description
class	PipelineProcessLibrary	Represents a collection of PipelineProcesses, typically referring to the same underlying software library.

Uses of AbstractInterfaceObject in mgui.interfaces.plots

Subclasses of AbstractInterfaceObject in mgui.interfaces.plots

Modifier and Type	Class	Description
class	InterfacePlotObject	Abstract representation of a plottable object; allows objects to be represented generically as interface objects.

Uses of AbstractInterfaceObject in mgui.interfaces.plots.sgt

Subclasses of AbstractInterfaceObject in mgui.interfaces.plots.sgt

Modifier and Type	Class	Description
class	SgtAxis<A extends gov.noaa.pmel.sgt.Axis>	Interface for displaying an axis on a plot.
class	SgtLine	A plotted line in a Scientific Graphics Toolkit (SGT) plot.
class	SgtPlotObject<T extends gov.noaa.pmel.sgt.dm.SGTData>	A plottable object for a Scientific Graphics Toolkit (SGT) plot.
class	SgtPointSet	Represents a set of points for an Scientific Graphics Toolkit (SGT) plot.

Uses of AbstractInterfaceObject in mgui.interfaces.projects

Subclasses of AbstractInterfaceObject in mgui.interfaces.projects

Modifier and Type	Class	Description
class	InterfaceProject	Represents a modelGUI project, which specifies an organizational structure for persistent data related to a common project.
class	ProjectDataItem	Specifies a data item in a modelGUI project, including its name, its I/O classes, and its filename form (a pattern identifying the location or URL of the item).
class	ProjectDirectory	Specifies a project directory, including its subdirectories and all prespecified data items that it contains.
class	ProjectInstance	Specifies an element instance in a project (e.g., a subject).
class	ProjectInstanceGroup	Represents a group partition in a project, which refers to a set of subdirectories within the instances directory, each representing a different level of the group.

Uses of AbstractInterfaceObject in mgui.interfaces.shapes

Subclasses of AbstractInterfaceObject in mgui.interfaces.shapes

Modifier and Type	Class	Description
class	BoolPolygon2DInt
class	Box3DInt
class	Circle2DInt
class	Ellipse2DInt	Interface for a Ellipse2D shape.
class	Image2DInt	Displays an image inside a Rect2D shape.
class	Image3DInt	Draws a rectangular planar image in R3.
class	InterfaceShape	Abstract base class for all shape interfaces (ShapeInts).
class	InterfaceShape.VertexDataSet
class	IntPolygon2DInt
class	Line2DInt
class	LPolygon2DInt	Light 2D polygon with no attributes (attributes are assignable)
class	LPolygon3DInt
class	Mesh2DInt	A 2D representation of a Mesh3DInt object.
class	Mesh3DInt	Interface for a Mesh3D shape.
class	Plane3DInt
class	Point2DInt
class	PointSet2DInt	Shape interface for a set of 2D vertices.
class	PointSet3DInt	Shape interface for a set of 3D points.
class	Polygon2DInt	Interface for a 2D polygon.
class	Polygon3DInt	Interface for a 3D polygon object.
class	PolygonSet3DInt	Interface for a set of 3D polygons.
class	Rect2DInt	Represents a 2D rectangle.
class	Rect3DInt
class	SectionSet2DInt	Provides a 2D representation of a 3D section set, where it intersects a particular plane.
class	SectionSet3DInt	Represents a set of parallel sections, based upon a reference plane (thisShape), and a spacing value.
class	Shape2DInt	Base class for all interfaces to 2D geometrical shapes.
class	Shape2DSelectionSet
class	Shape3DInt	Base class for all Shape3D interface objects.
class	ShapeModel3D	The top container for all shape interfaces.
class	ShapeSet2DInt	Represents a set of Shape2DInt objects.
class	ShapeSet3DInt	Represents a set of Shape3DInt objects.
class	TensorVolume3DInt
class	TestTextureInt
class	Text2DInt
class	Text2DIntMouseCoords
class	Vector2DInt
class	Vector3DInt
class	VectorSet3DInt
class	VertexDataColumn	Encapsulates a column of vertex-wise numerical data.
class	Volume2DInt	2D sectional representation of a Volume3DInt.
class	Volume3DInt	Class acting as interface to a volume shape, as defined by the Grid3D geometry class.
class	VolumeSet3DInt	A set of Volume3DInt objects which render as an overlay image.
class	X3DScene3DInt

Uses of AbstractInterfaceObject in mgui.interfaces.shapes.attributes

Subclasses of AbstractInterfaceObject in mgui.interfaces.shapes.attributes

Modifier and Type	Class	Description
class	ShapeAttribute<V>	Extends Attribute to indicate shape-specific parameters (e.g., whether a change to the value requires a redraw.

Uses of AbstractInterfaceObject in mgui.interfaces.shapes.dynamic

Subclasses of AbstractInterfaceObject in mgui.interfaces.shapes.dynamic

Modifier and Type	Class	Description
class	Volume4DInt	Volume with 3 space and 1 time dimension.

Uses of AbstractInterfaceObject in mgui.interfaces.shapes.graphs

Subclasses of AbstractInterfaceObject in mgui.interfaces.shapes.graphs

Modifier and Type	Class	Description
class	Graph2DInt	Graph shape represented in R2.
class	Graph3DInt	Represents a graph as a 3D shape.

Uses of AbstractInterfaceObject in mgui.interfaces.shapes.mesh

Subclasses of AbstractInterfaceObject in mgui.interfaces.shapes.mesh

Modifier and Type	Class	Description
class	VertexSelection	Defines a selection of nodes for a shape object.

Uses of AbstractInterfaceObject in mgui.interfaces.shapes.neuro

Subclasses of AbstractInterfaceObject in mgui.interfaces.shapes.neuro

Modifier and Type	Class	Description
class	CorticalHemisphereSet3DInt
class	CorticalSurfaceSet3DInt	Representation of a set of cortical surfaces, including grey matter (GM) interfaces with white matter (WM) and cerebrospinal fluid (CSF).

Uses of AbstractInterfaceObject in mgui.interfaces.shapes.paths

Subclasses of AbstractInterfaceObject in mgui.interfaces.shapes.paths

Modifier and Type	Class	Description
class	PathDataRenderer	Specifies how data attached to a path is to be rendered.

Uses of AbstractInterfaceObject in mgui.interfaces.shapes.selection

Subclasses of AbstractInterfaceObject in mgui.interfaces.shapes.selection

Modifier and Type	Class	Description
class	ShapeSelectionSet

Uses of AbstractInterfaceObject in mgui.interfaces.shapes.util

Subclasses of AbstractInterfaceObject in mgui.interfaces.shapes.util

Modifier and Type	Class	Description
class	ClipPlane	Class specifies a clipping region around a plane, with back and front clip distances.

Uses of AbstractInterfaceObject in mgui.interfaces.shapes.volume

Subclasses of AbstractInterfaceObject in mgui.interfaces.shapes.volume

Modifier and Type	Class	Description
class	GridVertexDataColumn	Vertex data column defined for a Volume3DInt.

Uses of AbstractInterfaceObject in mgui.interfaces.variables

Subclasses of AbstractInterfaceObject in mgui.interfaces.variables

Modifier and Type	Class	Description
class	MatrixInt	Interface for a 2D matrix, represented internally as a Jama matrix of doubles.
class	StringVectorInt	Stores an array of String objects as a variable.
class	VariableInt<T>	An interface to a variable object.
class	VectorInt<T extends MguiNumber>	Represents an array of numeric values.

Uses of AbstractInterfaceObject in mgui.io.domestic.maps

Subclasses of AbstractInterfaceObject in mgui.io.domestic.maps

Modifier and Type	Class	Description
class	Vector3ColourMap	Provides a colour mapping for a vector of size three, such that each element of the vector has a colour assignment, and the resulting colour is a weighting of these colours by x, y, z components:

Uses of AbstractInterfaceObject in mgui.models.dynamic.functions

Subclasses of AbstractInterfaceObject in mgui.models.dynamic.functions

Modifier and Type	Class	Description
class	DecayFunction
class	Function	Abstract class for all model functions.
class	HardLimitFunction
class	ODEFunction
class	SigmoidFunction	As the name suggests...

Uses of AbstractInterfaceObject in mgui.models.environments

Subclasses of AbstractInterfaceObject in mgui.models.environments

Modifier and Type	Class	Description
class	AbstractEnvironmentDataSource<T extends MguiNumber>	Serves as a data source updated by a DynamicModelEnvironment.
class	SimpleEnvironment<T extends MguiNumber>	Represents a simple environment, with a set of named observable scalar state variables.
class	SimpleEnvironmentInputDataSource<T extends MguiNumber>	Represents a simple input source for dynamic model environment.
class	SimpleEnvironmentObservableDataSource<T extends MguiNumber>	Simple data source which updates in response to changes in an environment's state variables.

Uses of AbstractInterfaceObject in mgui.models.networks

Subclasses of AbstractInterfaceObject in mgui.models.networks

Modifier and Type	Class	Description
class	AbstractNetwork
class	AbstractNetworkModel	Abstract class for all neuronal models to inherit.

Uses of AbstractInterfaceObject in mgui.models.networks.components

Subclasses of AbstractInterfaceObject in mgui.models.networks.components

Modifier and Type	Class	Description
class	AbstractNetworkComponent	Abstract generic class for neuro model components to inherit.

Uses of AbstractInterfaceObject in mgui.models.updaters

Subclasses of AbstractInterfaceObject in mgui.models.updaters

Modifier and Type	Class	Description
class	LinearUpdater
class	PulseTrainUpdater
class	PulseTrainUpdater.CurrentPulse
class	SimpleEnvironmentUpdater	Default super class for environment updaters.

Uses of AbstractInterfaceObject in mgui.morph.sections

Subclasses of AbstractInterfaceObject in mgui.morph.sections

Modifier and Type	Class	Description
class	MorphSections3DInt	Class representing a set of intermediate sections (subsections), such that each subsection holds an iterative morphing representation from some source shape to some target shape.
class	RadialRep2DInt

Uses of AbstractInterfaceObject in mgui.neuro.components

Subclasses of AbstractInterfaceObject in mgui.neuro.components

Modifier and Type	Class	Description
class	AbstractAxon	Default class for an axon.
class	AbstractDendrite
class	AbstractDendrites	Default class for dendrites.
class	AbstractMotorNeuron	Abstract class for a motor (output) neuron.
class	AbstractNeuroComponent	Abstract generic class for neuro model components to inherit.
class	AbstractNeuron
class	AbstractNeuronalComponent	Abstract class for all neuronal components (i.e., components of instances of Neuron) to inherit.
class	AbstractSensoryNeuron
class	AbstractSoma
class	AbstractSynapse
class	CorticalRegion	Represents a component at the resolution of a cortical region.
class	CorticalVolume	A Volume3D-based representation of a cortical region.

Uses of AbstractInterfaceObject in mgui.neuro.components.compartments

Subclasses of AbstractInterfaceObject in mgui.neuro.components.compartments

Modifier and Type	Class	Description
class	AbstractCompartment	Basic compartment for compartmental model components.
class	CompartmentalComponent	Base abstract class for all components using a compartmental model.
class	CompartmentalDendrite	Represents a dendrite whose activity is determined by the cable model (see Rawl etc.) and a compartmental discrete (numerical) approximation of its differential functions.
class	CompartmentalNeuron
class	CompartmentalSoma
class	NeuronalCompartmentalComponent
class	SimpleCompartment

Uses of AbstractInterfaceObject in mgui.neuro.components.cortical

Subclasses of AbstractInterfaceObject in mgui.neuro.components.cortical

Modifier and Type	Class	Description
class	AbstractCorticalConnection	Abstract class serving as a base for all cortical connections.
class	AbstractCorticalInput
class	AbstractCorticalOutput
class	AbstractCorticalRegion	Represents a component at the resolution of a cortical region.
class	CorticalVolume	A Volume3D-based representation of a cortical region.

Uses of AbstractInterfaceObject in mgui.neuro.components.cortical.functions

Subclasses of AbstractInterfaceObject in mgui.neuro.components.cortical.functions

Modifier and Type	Class	Description
class	BiexponentialFunction	Simplistic bi-exponential representation of population activity in a cortical region, which responds to input events.
class	CorticalFunction
class	MorrisLecarFunction	Regional cortical model based upon Morris and Lecar (1981), and Breakspear et al.

Uses of AbstractInterfaceObject in mgui.neuro.components.cortical.simple

Subclasses of AbstractInterfaceObject in mgui.neuro.components.cortical.simple

Modifier and Type	Class	Description
class	SimpleCorticalConnection
class	SimpleCorticalInput
class	SimpleCorticalOutput
class	SimpleCorticalRegion

Uses of AbstractInterfaceObject in mgui.neuro.components.simple

Subclasses of AbstractInterfaceObject in mgui.neuro.components.simple

Modifier and Type	Class	Description
class	SimpleAxon
class	SimpleDendrite	Simple dendrite, e.g., for SimpleNeuron.
class	SimpleDendrites	Basic input unit for, e.g., SimpleNeuron.
class	SimpleMotorNeuron	Simple implementation of a motor (output) neuron.
class	SimpleNeuron	Simple McCulloch-Pitts model of an artificial neuron.
class	SimpleSensoryNeuron	A simple input (i.e., sensory) neuron.
class	SimpleSoma	Simple soma for, e.g., SimpleNeuron.
class	SimpleSynapse	Simple synapse for, e.g., SimpleNeuron

Uses of AbstractInterfaceObject in mgui.neuro.components.types

Subclasses of AbstractInterfaceObject in mgui.neuro.components.types

Modifier and Type	Class	Description
class	ConnectableNeuron

Uses of AbstractInterfaceObject in mgui.neuro.graphs

Subclasses of AbstractInterfaceObject in mgui.neuro.graphs

Modifier and Type	Class	Description
class	CorticalNetworkGraphConnection
class	CorticalNetworkGraphNode
class	NeuralNetConnection
class	NeuralNetNode	Extension of DirectedSparseVertex to specifically represent nodes in neural networks, i.e., containing references to instances of Neuron.

Uses of AbstractInterfaceObject in mgui.neuro.networks

Subclasses of AbstractInterfaceObject in mgui.neuro.networks

Modifier and Type	Class	Description
class	AbstractNeuralNet	Abstract class for all neural net classes to inherit.
class	CorticalNetwork
class	KohonenNet
class	PerceptronNet

Uses of AbstractInterfaceObject in mgui.neuro.updaters

Subclasses of AbstractInterfaceObject in mgui.neuro.updaters

Modifier and Type	Class	Description
class	PulseTrainUpdater
class	PulseTrainUpdater.CurrentPulse

Uses of AbstractInterfaceObject in mgui.pipelines

Subclasses of AbstractInterfaceObject in mgui.pipelines

Modifier and Type	Class	Description
class	InterfacePipeline	Represents a series of Tasks that are to be run sequentially, such that the output of a task becomes the input of the subsequent one.
class	PipelineFork	Represents a fork in a pipeline; i.e., a branching point, where the output of the previous process becomes the input of two or more independent pipelines.
class	PipelineProcessInstance	Represents a specific instance of a Java process.
class	PipelineTask	A task is a launchable component of a pipeline.