Uses of Interface
mgui.interfaces.trees.TreeObject

Packages that use TreeObject

Package	Description
mgui.datasources	This package contains the core classes for data source functionality.
mgui.geometry.neuro.mesh
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.attributes.video	Classes allowing video tasks to read/modify object attributes.
mgui.interfaces.cocomac	Provides interfaces with the CoCoMac database.
mgui.interfaces.console	Provides an interactive system console (currently view only).
mgui.interfaces.datasources	This package provides interface objects which allow the user to interface with the core data source classes.
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.io	This package contains all classes which perform input/output functions.
mgui.interfaces.layouts
mgui.interfaces.maps	Provides a set a maps for use by ModelGUI objects.
mgui.interfaces.math	Provides an abstract interface allowing arithmetic functions to be applied to object data (e.g., vertex data for shapes).
mgui.interfaces.models	Base classes for specifying dynamic models.
mgui.interfaces.neuro
mgui.interfaces.neuro.imaging.camino
mgui.interfaces.pipelines	This package provides interfaces for user interaction with pipelines.
mgui.interfaces.pipelines.libraries
mgui.interfaces.plots	Provides 2D and 3D plotting functionality.
mgui.interfaces.plots.mgui
mgui.interfaces.plots.osp	Plots using the Open Source Physics (OSP) library.
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.projects.util	Utility classes operating on projects.
mgui.interfaces.queries	Provides querying functionality for interface objects.
mgui.interfaces.shapes	This package provides interfaces for user interaction with shapes and shape models.
mgui.interfaces.shapes.attributes
mgui.interfaces.shapes.datasources
mgui.interfaces.shapes.dynamic
mgui.interfaces.shapes.graphs
mgui.interfaces.shapes.mesh
mgui.interfaces.shapes.neuro
mgui.interfaces.shapes.paths
mgui.interfaces.shapes.queries
mgui.interfaces.shapes.selection
mgui.interfaces.shapes.util
mgui.interfaces.shapes.video
mgui.interfaces.shapes.volume
mgui.interfaces.tables	Provides object interaction via a JTable.
mgui.interfaces.tools	Provides a framework for "tool" objects, which allow the user to modify or interrogate model objects.
mgui.interfaces.tools.shapes
mgui.interfaces.trees	Provides object interaction via a JTree
mgui.interfaces.variables
mgui.interfaces.variables.tables
mgui.io	This package contains all classes which perform input/output functions.
mgui.io.domestic	Input/output operations for "domestic" (mgui-specific) data formats.
mgui.io.domestic.datasources
mgui.io.domestic.graphs
mgui.io.domestic.maps
mgui.io.domestic.network
mgui.io.domestic.pipelines
mgui.io.domestic.printing
mgui.io.domestic.shapes
mgui.io.domestic.variables
mgui.io.domestic.videos
mgui.io.domestic.views
mgui.io.foreign.caret
mgui.io.foreign.freesurfer
mgui.io.foreign.minc
mgui.io.foreign.pajek
mgui.io.foreign.vol
mgui.io.standard.gifti
mgui.io.standard.xml
mgui.io.standard.xml.x3d
mgui.models.dynamic	Provides a framework for dynamic modelling (4D) functionality in ModelGUI.
mgui.models.dynamic.functions
mgui.models.dynamic.ode
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 TreeObject in mgui.datasources

Subinterfaces of TreeObject in mgui.datasources

Modifier and Type	Interface	Description
interface	DataSourceItem	An item (i.e., table or query) in a DataSource.

Classes in mgui.datasources that implement TreeObject

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 TreeObject in mgui.geometry.neuro.mesh

Classes in mgui.geometry.neuro.mesh that implement TreeObject

Modifier and Type	Class	Description
class	ScalpAndSkullModelOptions	Parameters for skull and scalp surface approximation.

Uses of TreeObject in mgui.graphs.networks

Classes in mgui.graphs.networks that implement TreeObject

Modifier and Type	Class	Description
class	AbstractNetworkGraph	A graph which explicitly represents a connected network.
class	AbstractNetworkGraphConnection	Represents an edge (i.e., a connection) in a network graph.
class	AbstractNetworkGraphNode	Represents a node in a network graph.

Uses of TreeObject in mgui.interfaces

Subinterfaces of TreeObject in mgui.interfaces

Modifier and Type	Interface	Description
interface	InterfaceObject	Basic interface for all "interface" objects; i.e., objects which provide an interface between the user and the underlying model.

Classes in mgui.interfaces that implement TreeObject

Modifier and Type	Class	Description
class	AbstractInterfaceObject	Abstract class which acts as the base class for all "interface" objects; i.e., objects which provide an interface between user and the underlying model.
class	InterfaceButtonPanel	Interface panel displaying a list of tool-related buttons.
class	InterfaceComboPanel	Interface panel allowing for the display of multiple interface panels, selected by a combo box.
class	InterfaceDisplayPanel	Main interface panel for displaying data graphically.
class	InterfaceHideablePanel
class	InterfaceListPanel
class	InterfaceOptions	Base interface for specifying options or parameters for some process.
class	InterfacePanel	Base class for all Swing panels (i.e., extensions of JPanel) to be show in an instance of InterfaceDisplayPanel.
class	InterfaceSelectionPanel	Provides an interface for creating and managing shape selection sets.
class	InterfaceSplitPanel	Displays two InterfaceGraphicWindows, split either horizontally or vertically.
class	InterfaceStatusBarPanel	Interface panel which acts as a status bar for a given instance of InterfaceFrame.
class	InterfaceTabbedDisplayPanel	This class extends InterfaceDisplayPanel in order to provide a tabbed window pane, similar to a typical web browser.
class	InterfaceWorkspace	A Workspace acts as a container for all data models and graphics windows.
static class	InterfaceWorkspace.CollectionTreeNode

Uses of TreeObject in mgui.interfaces.attributes

Classes in mgui.interfaces.attributes that implement TreeObject

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.
class	InterfaceAttributePanel	Panel to display and modify a given AttributeList.

Uses of TreeObject in mgui.interfaces.attributes.video

Classes in mgui.interfaces.attributes.video that implement TreeObject

Modifier and Type	Class	Description
class	AttributeObjectVideoTaskDialogPanel	Panel for defining an AttributeObjectTask.

Uses of TreeObject in mgui.interfaces.cocomac

Classes in mgui.interfaces.cocomac that implement TreeObject

Modifier and Type	Class	Description
class	InterfaceCoCoMacPanel

Uses of TreeObject in mgui.interfaces.console

Classes in mgui.interfaces.console that implement TreeObject

Modifier and Type	Class	Description
class	InterfaceConsoleDisplay	Window which displays console output.

Uses of TreeObject in mgui.interfaces.datasources

Classes in mgui.interfaces.datasources that implement TreeObject

Modifier and Type	Class	Description
class	DataFieldOptions	Parameters defining a data field.
class	DataQueryOptions	Options for a data query
class	DataSourceDriverOptions	Options which specify a JDBC data source driver.
class	DataSourceOptions
class	DataTableModel	Class extending AbstractTableModel to act as a model for JTable, and in particular for use by InterfaceDataTable.
class	DataTableOptions	Options for a new data table.
class	InterfaceDatasourcePanel	Interface panel for displaying, querying, and managing tables and queries in a connected data source.

Uses of TreeObject in mgui.interfaces.graphics

Classes in mgui.interfaces.graphics that implement TreeObject

Modifier and Type	Class	Description
class	Graphic2DGrid	Defines a 2D grid, for display in an InterfaceGraphic2D window.
class	InterfaceGraphic<T extends Tool>	The base class for all graphical interface windows.
class	InterfaceGraphic2D	Graphical interface window for display 2D shapes (Shape2DInt).
class	InterfaceGraphic3D	Interface class for Java3D display.
class	InterfaceGraphicPanel	Panel to define the display windows in InterfaceDisplayPanel, including: 1.
class	InterfaceGraphicWindow	Provides a title for an InterfaceGraphic window, which is a button.
class	View3D	Represents a specific 3D view, defined by a frozen Camera3D object.

Uses of TreeObject in mgui.interfaces.graphics.util

Classes in mgui.interfaces.graphics.util that implement TreeObject

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

Uses of TreeObject in mgui.interfaces.graphics.video

Classes in mgui.interfaces.graphics.video that implement TreeObject

Modifier and Type	Class	Description
class	RotateView3DTaskDialogPanel	Dialog panel for a RotateView3DTask.
class	SetView3DTaskDialogPanel	Dialog panel for a SetView3DTask.
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.
class	VideoTaskDialogPanel	A dialog defining a VideoTask object.
class	VideoTaskOptions

Uses of TreeObject in mgui.interfaces.graphs

Classes in mgui.interfaces.graphs that implement TreeObject

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	DefaultGraph	Default implementation of a Graph in ModelGUI.
class	DefaultGraphEdge	Default implementation of a Graph edge.
class	DefaultGraphNode	Default implementation of a Graph in modelGUI.
class	InterfaceAbstractGraph	Abstract representation of a Graph in modelGUI; extends Jung's SparseGraph
class	InterfaceGraphDisplay	Displays graphs and allows user interaction with them.
class	InterfaceGraphDisplayTitle

Uses of TreeObject in mgui.interfaces.graphs.shapes

Classes in mgui.interfaces.graphs.shapes that implement TreeObject

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 TreeObject in mgui.interfaces.io

Classes in mgui.interfaces.io that implement TreeObject

Modifier and Type	Class	Description
class	InterfaceFile
class	InterfaceFilePanel	InterfacePanel providing a standard interface for input & output operations.
class	InterfaceIOType	Specifies an Input/Output interface object; e.g., file loaders or writers.
class	VolumeFileWriteOptions

Uses of TreeObject in mgui.interfaces.layouts

Classes in mgui.interfaces.layouts that implement TreeObject

Modifier and Type	Class	Description
class	InterfaceLayoutPanel	Interface panel allowing interaction with a 2D Layout object.
class	InterfaceLayoutWindow	Provides a window panel which specifies (via InterfaceLayoutObject) and renders a layout containing graphical objects from existing windows or objects.
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 TreeObject in mgui.interfaces.maps

Classes in mgui.interfaces.maps that implement TreeObject

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	ContinuousColourBar	Component displays a continuous colour map as a horizontal bar portraying the colour gradient between anchors.
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	DiscreteColourMapLayout	Layout which displays a discrete colour map as a list of colour boxes, names, and optionally descriptions and indexes.
class	InterfaceMapPanel	Panel to create and modify various maps, including colour maps and value maps.
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 TreeObject in mgui.interfaces.math

Classes in mgui.interfaces.math that implement TreeObject

Modifier and Type	Class	Description
class	MathExpressionOptions	Options for a math expression evaluation.

Uses of TreeObject in mgui.interfaces.models

Classes in mgui.interfaces.models that implement TreeObject

Modifier and Type	Class	Description
class	InterfaceAbstractModel
class	InterfaceDynamicModelPanel

Uses of TreeObject in mgui.interfaces.neuro

Classes in mgui.interfaces.neuro that implement TreeObject

Modifier and Type	Class	Description
class	CorticalThicknessDataTableOptions
class	CorticalThicknessOptions
class	InterfaceCorticalThicknessPanel	Panel providing an interface to cortical thickness databases and subject databases.
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 TreeObject in mgui.interfaces.neuro.imaging.camino

Classes in mgui.interfaces.neuro.imaging.camino that implement TreeObject

Modifier and Type	Class	Description
class	CaminoProcess	Extends JavaProcess specifically for Camino processes.
class	CaminoProcessOptions
class	CaminoProjectOptions
class	CaminoTaskOptions
class	InterfaceCaminoPanel

Uses of TreeObject in mgui.interfaces.pipelines

Classes in mgui.interfaces.pipelines that implement TreeObject

Modifier and Type	Class	Description
class	InterfacePipelinesPanel	Provides a GUI for: creating, viewing, modifying, deleting, and executing pipelines.
class	PipelineProcessInstanceOptions	Options for a pipeline process instance.
class	PipelineProcessOptions	Options for a PipelineProcess.

Uses of TreeObject in mgui.interfaces.pipelines.libraries

Classes in mgui.interfaces.pipelines.libraries that implement TreeObject

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

Uses of TreeObject in mgui.interfaces.plots

Classes in mgui.interfaces.plots that implement TreeObject

Modifier and Type	Class	Description
class	InterfacePlot<T extends MguiNumber>	Represents an abstract plot object.
class	InterfacePlotDisplay	General graphic interface for all plots.
class	InterfacePlotMulti	Allows the display of multiple plots in a single InterfacePlot panel.
class	InterfacePlotObject	Abstract representation of a plottable object; allows objects to be represented generically as interface objects.
class	InterfacePlotOptions<T extends InterfacePlot<?>>	Options for a plot object.
class	InterfacePlotPanel

Uses of TreeObject in mgui.interfaces.plots.mgui

Classes in mgui.interfaces.plots.mgui that implement TreeObject

Modifier and Type	Class	Description
class	InterfacePlotMgui	General class for displaying ModelGUI plots.
class	MatrixImagePlot	Plots a matrix as an image, with a specified colour map.
class	PlotMap2D	Specifies a mapping from data units to plot units and to graphic units.

Uses of TreeObject in mgui.interfaces.plots.osp

Classes in mgui.interfaces.plots.osp that implement TreeObject

Modifier and Type	Class	Description
class	InterfacePlotOsp	General class for displaying Open Source Physics (OSP) plots.
class	InterfaceStripChart	Displays an OSP StripChart; i.e., time vs.

Uses of TreeObject in mgui.interfaces.plots.sgt

Classes in mgui.interfaces.plots.sgt that implement TreeObject

Modifier and Type	Class	Description
class	InterfacePlotSgt<T extends SgtPlotObject<?>>	Abstract class for displaying Scientific Graphics Toolkit (SGT) plots.
class	SgtAxis<A extends gov.noaa.pmel.sgt.Axis>	Interface for displaying an axis on a plot.
class	SgtCartesianLayout<T extends SgtPlotObject<?>>	Abstract extension of SgtPlotObject for CartesianGraph objects.
class	SgtLine	A plotted line in a Scientific Graphics Toolkit (SGT) plot.
class	SgtLineLayout	Layout for SGT line plots.
class	SgtMultilinePlot	Displays a line plot using the Scientific Graphics Toolkit (SGT) library.
class	SgtPlotLayout<T extends SgtPlotObject<?>,G extends gov.noaa.pmel.sgt.Graph,A extends gov.noaa.pmel.sgt.Axis>	The base layout panel for an SGT plot.
class	SgtPlotLayoutOptions	Options defining an SGT plot layout
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.
class	SgtPointSetLayout	Layout for point sets.
class	SgtScatterplot	Displays an XY scatter plot using the Scientific Graphics Toolkit (SGT) library.

Uses of TreeObject in mgui.interfaces.projects

Classes in mgui.interfaces.projects that implement TreeObject

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	InterfaceProjectOptions
class	InterfaceProjectPanel	Panel which provides a user interface for InterfaceProjects.
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	ProjectDirectoryOptions	Options for a ProjectDirectory.
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 TreeObject in mgui.interfaces.projects.util

Classes in mgui.interfaces.projects.util that implement TreeObject

Modifier and Type	Class	Description
class	ProjectOptions	Options for a project.

Uses of TreeObject in mgui.interfaces.queries

Classes in mgui.interfaces.queries that implement TreeObject

Modifier and Type	Class	Description
class	InterfaceQuery	Interface for a class which allows it to query a given InterfaceQueryObject.
class	InterfaceQueryPanel	Provides an interface for queries; selecting and launching query tools, displaying query results, etc.

Uses of TreeObject in mgui.interfaces.shapes

Classes in mgui.interfaces.shapes that implement TreeObject

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	InterfacePolygonPanel
class	InterfaceSectionSetPanel	Updated version of InterfaceSectionSet that sets a current section set for a given Graphic2D window, and sets current sections for that window.
class	InterfaceShape	Abstract base class for all shape interfaces (ShapeInts).
class	InterfaceShape.VertexDataSet
class	InterfaceShapesPanel	Interface panel providing a GUI for general shape-related functions.
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	ShapeStatsPanel	Interface panel for performing statistical procedures on shapes.
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 TreeObject in mgui.interfaces.shapes.attributes

Classes in mgui.interfaces.shapes.attributes that implement TreeObject

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 TreeObject in mgui.interfaces.shapes.datasources

Classes in mgui.interfaces.shapes.datasources that implement TreeObject

Modifier and Type	Class	Description
class	DataSourceLinkOptions	Options for specifying a vertex data column link to a data source.

Uses of TreeObject in mgui.interfaces.shapes.dynamic

Classes in mgui.interfaces.shapes.dynamic that implement TreeObject

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

Uses of TreeObject in mgui.interfaces.shapes.graphs

Classes in mgui.interfaces.shapes.graphs that implement TreeObject

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

Uses of TreeObject in mgui.interfaces.shapes.mesh

Classes in mgui.interfaces.shapes.mesh that implement TreeObject

Modifier and Type	Class	Description
class	InterfaceMeshPanel	Provides an interface to Mesh3DInt objects.
class	MeshDataMaskOptions
class	MeshDataOptions
class	MeshDataThresholdOptions
class	MeshPlaneMaskOptions
class	MeshSubmeshOptions
class	VertexSelection	Defines a selection of nodes for a shape object.

Uses of TreeObject in mgui.interfaces.shapes.neuro

Classes in mgui.interfaces.shapes.neuro that implement TreeObject

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).
class	InterfaceNeuroMeshPanel
class	InterfaceNeuroMeshPanel2

Uses of TreeObject in mgui.interfaces.shapes.paths

Classes in mgui.interfaces.shapes.paths that implement TreeObject

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

Uses of TreeObject in mgui.interfaces.shapes.queries

Classes in mgui.interfaces.shapes.queries that implement TreeObject

Modifier and Type	Class	Description
class	InterfaceShapeQuery	Base class for all shape queries.
class	ShapeSummaryQuery	Extension of InterfaceShapeQuery to provide summary values for a shape, or a vertex selection within that shape.

Uses of TreeObject in mgui.interfaces.shapes.selection

Classes in mgui.interfaces.shapes.selection that implement TreeObject

Modifier and Type	Class	Description
class	InterfaceSelectionSet	Interface panel providing user interaction with selection sets.
class	ShapeSelectionSet

Uses of TreeObject in mgui.interfaces.shapes.util

Classes in mgui.interfaces.shapes.util that implement TreeObject

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

Uses of TreeObject in mgui.interfaces.shapes.video

Classes in mgui.interfaces.shapes.video that implement TreeObject

Modifier and Type	Class	Description
class	ChangeSectionVideoTaskDialogPanel	Dialog panel for a ChangeSectionVideoTask.

Uses of TreeObject in mgui.interfaces.shapes.volume

Classes in mgui.interfaces.shapes.volume that implement TreeObject

Modifier and Type	Class	Description
class	GridVertexDataColumn	Vertex data column defined for a Volume3DInt.
class	InterfaceVolumePanel	Interface panel which allows the user to interact with Volume3DInt objects.
class	InterfaceVolumeSetPanel	Panel to provide an interface with a volume overlay set.
class	VolumeMaskOptions
class	VolumeMaskOptions_old	Class to specify parameters for volume masking.

Uses of TreeObject in mgui.interfaces.tables

Classes in mgui.interfaces.tables that implement TreeObject

Modifier and Type	Class	Description
class	InterfaceDataTable	Interface panel for displaying a data table or query.
class	InterfaceDataTableTitle
class	InterfaceTableModel	Abstract Table Model interface class.

Uses of TreeObject in mgui.interfaces.tools

Classes in mgui.interfaces.tools that implement TreeObject

Modifier and Type	Class	Description
class	InterfaceTool2DPanel	Deprecated.
class	InterfaceToolPanel	Panel displaying buttons for various tools, categorized.

Uses of TreeObject in mgui.interfaces.tools.shapes

Classes in mgui.interfaces.tools.shapes that implement TreeObject

Modifier and Type	Class	Description
class	ToolCreateMeshFromPolylinesOptions
class	ToolCutMeshWithPlaneOptions
class	ToolGetConvexHull2DOptions
class	ToolGetMeshIntersectionPolylinesOptions

Uses of TreeObject in mgui.interfaces.trees

Classes in mgui.interfaces.trees that implement TreeObject

Modifier and Type	Class	Description
class	InterfaceTreePanel	Provides a tree interface for model objects

Uses of TreeObject in mgui.interfaces.variables

Classes in mgui.interfaces.variables that implement TreeObject

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 TreeObject in mgui.interfaces.variables.tables

Classes in mgui.interfaces.variables.tables that implement TreeObject

Modifier and Type	Class	Description
class	VariableTableModel

Uses of TreeObject in mgui.io

Classes in mgui.io that implement TreeObject

Modifier and Type	Class	Description
class	DefaultIOOptions	Implements a default IO options object, specifying files and a generic file chooser.
class	InterfaceIOOptions	Extends InterfaceOptions specifically for I/O methods.

Uses of TreeObject in mgui.io.domestic

Classes in mgui.io.domestic that implement TreeObject

Modifier and Type	Class	Description
class	WorkspaceOutputOptions	Specifies options for writing a workspace (i.e., an instance of InterfaceWorkspace) to XML.

Uses of TreeObject in mgui.io.domestic.datasources

Classes in mgui.io.domestic.datasources that implement TreeObject

Modifier and Type	Class	Description
class	DataSourceOutOptions	Specifies options for writing a Data Source to file.
class	ExportDataTableExcelOptions	Options for exporting data from a DataSourceItem to a Microsoft Excel format file.
class	ExportDataTableOptions	Options for exporting data from a data source to an external file format.
class	ExportDataTableTextOptions	Options for exporting data from a data source to a delimited text file.
class	ImportDataTableOptions	Specifies options for importing data to a data source table.
class	ImportDataTableTextOptions	Specifies options for importing data from a text file to a data source table.

Uses of TreeObject in mgui.io.domestic.graphs

Classes in mgui.io.domestic.graphs that implement TreeObject

Modifier and Type	Class	Description
class	GraphInputOptions	General options for loading a graph
class	GraphOutputOptions	General options for writing a graph to file.

Uses of TreeObject in mgui.io.domestic.maps

Classes in mgui.io.domestic.maps that implement TreeObject

Modifier and Type	Class	Description
class	DiscreteColourMapInOptions	Options for inputting a DiscreteColourMap.
class	DiscreteColourMapOutOptions	Options for outputting a DiscreteColourMap.
class	NameMapInOptions
class	NameMapOutOptions	Specifies options for writing a name map (or multiple name maps) to file.
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 TreeObject in mgui.io.domestic.network

Classes in mgui.io.domestic.network that implement TreeObject

Modifier and Type	Class	Description
class	CorticalNetworkMatrixInOptions	Inputs a matrix as a weighted cortical network.

Uses of TreeObject in mgui.io.domestic.pipelines

Classes in mgui.io.domestic.pipelines that implement TreeObject

Modifier and Type	Class	Description
class	PipelineInputOptions	Options for loading a pipeline or multiple pipelines.
class	PipelineOutputOptions

Uses of TreeObject in mgui.io.domestic.printing

Classes in mgui.io.domestic.printing that implement TreeObject

Modifier and Type	Class	Description
class	StlOutputOptions	Options defining an output operation to STL format.

Uses of TreeObject in mgui.io.domestic.shapes

Classes in mgui.io.domestic.shapes that implement TreeObject

Modifier and Type	Class	Description
class	Graph3DOutputOptions	Output options for a Graph3DWriter
class	PointSet2DInputOptions	Options for loading a PointSet2DInt object.
class	PointSet3DDataInputOptions
class	PointSet3DInputOptions	Options for loading a PointSet3DInt object.
class	PolygonSet3DInputOptions	Options for loading a PolygonSet3DInt object.
class	ShapeDataInputOptions	Options for loading vertex-wise data into a shape.
class	ShapeInputOptions	Options for loading an InterfaceShape object.
class	ShapeModel3DInputOptions	Options for loading a ShapeModel3D object.
class	ShapeModel3DOutputOptions	Specifies options for writing a ShapeModel3D object to XML.
class	ShapeOutputOptions	Output options for an InterfaceShapeWriter.
class	SurfaceDataInputOptions
class	SurfaceDataOutputOptions	Options for outputting surface data to a text file (single column)
class	SurfaceInputOptions	Options for inputting a Mesh3DInt object.
class	SurfaceOutputOptions	Standard options for writing a surface to file.
class	VectorSet3DInputOptions	Options for loading a VectorSet3DInt object.
class	VolumeInputOptions	Options specifying a Volume3DInt object.
class	VolumeOutputOptions	Specifies options for outputting a Volume3DInt to persistent storage.

Uses of TreeObject in mgui.io.domestic.variables

Classes in mgui.io.domestic.variables that implement TreeObject

Modifier and Type	Class	Description
class	MatrixInOptions	Options for loading a matrix from file.
class	MatrixOutOptions
class	StringVectorInOptions	Options for reading an array of String objects into a StringVectorInt instance.

Uses of TreeObject in mgui.io.domestic.videos

Classes in mgui.io.domestic.videos that implement TreeObject

Modifier and Type	Class	Description
class	ImageStackVideoOptions	Options for a video stack output operation; i.e., vis ImageStackVideoWriter.
class	VideoInputOptions
class	VideoOutputOptions

Uses of TreeObject in mgui.io.domestic.views

Classes in mgui.io.domestic.views that implement TreeObject

Modifier and Type	Class	Description
class	View3DInputOptions	Options for loading View3D objects.
class	View3DOutputOptions	Options for writing a set of View3D objects to file.

Uses of TreeObject in mgui.io.foreign.caret

Classes in mgui.io.foreign.caret that implement TreeObject

Modifier and Type	Class	Description
class	CaretAreaColourInOptions
class	CaretAreaColourOutputOptions	Options for outputting a DiscreteColourMap as a Caret areacolor file.
class	CaretMetricInOptions
class	CaretMetricOptions	Options for a Caret metric file.
class	CaretPaintInOptions
class	CaretPaintOptions	Deprecated. use CaretPaintInOptions or CaretPaintOutOptions
class	CaretPaintOutOptions
class	CaretSurfaceInOptions	Options specifying how to read a Caret surface
class	CaretSurfaceOutOptions

Uses of TreeObject in mgui.io.foreign.freesurfer

Classes in mgui.io.foreign.freesurfer that implement TreeObject

Modifier and Type	Class	Description
class	FreesurferSurfaceOutputOptions	Options for a FreesurferSurfaceWriter.
class	FreesurferVertexDataInOptions	Options for FreesurferVertexDataLoader.

Uses of TreeObject in mgui.io.foreign.minc

Classes in mgui.io.foreign.minc that implement TreeObject

Modifier and Type	Class	Description
class	MincSurfaceDataInOptions
class	MincSurfaceDataOutOptions

Uses of TreeObject in mgui.io.foreign.pajek

Classes in mgui.io.foreign.pajek that implement TreeObject

Modifier and Type	Class	Description
class	PajekGraphInputOptions	Options for Pajek graph input.

Uses of TreeObject in mgui.io.foreign.vol

Classes in mgui.io.foreign.vol that implement TreeObject

Modifier and Type	Class	Description
class	Volume4DInputOptions
class	VolumeInputOptions

Uses of TreeObject in mgui.io.standard.gifti

Classes in mgui.io.standard.gifti that implement TreeObject

Modifier and Type	Class	Description
class	GiftiInputOptions	Options specific for Gifti surfaces.
class	GiftiOutputOptions	Options for writing a surface to a Gifti format file.

Uses of TreeObject in mgui.io.standard.xml

Classes in mgui.io.standard.xml that implement TreeObject

Modifier and Type	Class	Description
class	XMLOutputOptions	Specifies options for writing an XML object (i.e., an instance of XMLObject).

Uses of TreeObject in mgui.io.standard.xml.x3d

Classes in mgui.io.standard.xml.x3d that implement TreeObject

Modifier and Type	Class	Description
class	Vector3DInputOptions

Uses of TreeObject in mgui.models.dynamic

Subinterfaces of TreeObject in mgui.models.dynamic

Modifier and Type	Interface	Description
interface	DynamicModelComponent	Interface which must be implemented by all components of a dynamic model.
interface	DynamicModelEnvironment<T extends MguiNumber>	Interface for a dynamic model's environment.
interface	DynamicModelEnvironmentSensor	Acts as a sensor for a model environment, which responds to state change events via the stimulate method.

Uses of TreeObject in mgui.models.dynamic.functions

Classes in mgui.models.dynamic.functions that implement TreeObject

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 TreeObject in mgui.models.dynamic.ode

Subinterfaces of TreeObject in mgui.models.dynamic.ode

Modifier and Type	Interface	Description
interface	DynamicModelODEComponent	Interface for components which solve ordinary differential equations (ODEs).

Uses of TreeObject in mgui.models.environments

Classes in mgui.models.environments that implement TreeObject

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 TreeObject in mgui.models.networks

Classes in mgui.models.networks that implement TreeObject

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

Uses of TreeObject in mgui.models.networks.components

Classes in mgui.models.networks.components that implement TreeObject

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

Uses of TreeObject in mgui.models.updaters

Classes in mgui.models.updaters that implement TreeObject

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

Uses of TreeObject in mgui.morph.sections

Classes in mgui.morph.sections that implement TreeObject

Modifier and Type	Class	Description
class	InterfaceMorphPanel
class	InterfaceMorphPanel2
class	InterfaceRadialRep
class	InterfaceRadialRep2
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 TreeObject in mgui.neuro.components

Subinterfaces of TreeObject in mgui.neuro.components

Modifier and Type	Interface	Description
interface	Axon
interface	Dendrite
interface	Dendrites
interface	MotorNeuron
interface	Neuron
interface	NeuronalComponent
interface	SensoryNeuron
interface	Soma
interface	Synapse

Classes in mgui.neuro.components that implement TreeObject

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 TreeObject in mgui.neuro.components.compartments

Classes in mgui.neuro.components.compartments that implement TreeObject

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 TreeObject in mgui.neuro.components.cortical

Classes in mgui.neuro.components.cortical that implement TreeObject

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 TreeObject in mgui.neuro.components.cortical.functions

Classes in mgui.neuro.components.cortical.functions that implement TreeObject

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 TreeObject in mgui.neuro.components.cortical.simple

Classes in mgui.neuro.components.cortical.simple that implement TreeObject

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

Uses of TreeObject in mgui.neuro.components.simple

Classes in mgui.neuro.components.simple that implement TreeObject

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 TreeObject in mgui.neuro.components.types

Classes in mgui.neuro.components.types that implement TreeObject

Modifier and Type	Class	Description
class	ConnectableNeuron

Uses of TreeObject in mgui.neuro.graphs

Classes in mgui.neuro.graphs that implement TreeObject

Modifier and Type	Class	Description
class	CorticalNetworkGraph
class	CorticalNetworkGraphConnection
class	CorticalNetworkGraphNode
class	NeuralNetConnection
class	NeuralNetGraph	Extension of JUNG's DirectedSparseGraph designed to specifically represent instances of NeuralNet.
class	NeuralNetNode	Extension of DirectedSparseVertex to specifically represent nodes in neural networks, i.e., containing references to instances of Neuron.

Uses of TreeObject in mgui.neuro.networks

Classes in mgui.neuro.networks that implement TreeObject

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

Uses of TreeObject in mgui.neuro.updaters

Classes in mgui.neuro.updaters that implement TreeObject

Modifier and Type	Class	Description
class	PulseTrainUpdater
class	PulseTrainUpdater.CurrentPulse

Uses of TreeObject in mgui.pipelines

Classes in mgui.pipelines that implement TreeObject

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	JavaProcess	Represents a Java process; i.e., a class containing a main method which allows it to be run as a process.
class	NativeProcess	Represents a native process; i.e., one which runs from the OS command console.
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	PipelineProcess	Represents a Java process specification, specified by an executable process (native or Java) and a set of parameters.
class	PipelineProcessInstance	Represents a specific instance of a Java process.
class	PipelineTask	A task is a launchable component of a pipeline.
class	TaskParameterInstance	An instance of a task parameter.