Documentation for classes includes syntax, usage information, and code samples for methods, properties, and event handlers and listeners for those APIs that belong to a specific class in ActionScript. The classes are listed alphabetically. If you are not sure to which class a certain method or property belongs, you can look it up in the Index.
| Class | Package | Description | |
|---|---|---|---|
| AboutData
| edu.stanford.covertlab.networkanalyzer.data | ||
| AboutWindow
| edu.stanford.covertlab.window | PopUp window displaying metadata about an application (name, version, release date, list of developers, etc.). | |
| AboutWindow
| edu.stanford.covertlab.networkanalyzer.viewer | PopUp window displaying meta data about the network and experiment loaded into the viewer. | |
| AcceleratorMenuBar
| com.rphelan.controls | The AcceleratorMenuBar is a MenuBar which displays windows/mac style accelerators next to the menu labels. | |
| AcceleratorMenuItemRenderer
| com.rphelan.controls.menuClasses | The AcceleratorMenuItemRenderer class modifies the default MenuItemRenderer to add 'accelerator' labels. | |
| AdvancedOptionsPanel
| edu.stanford.covertlab.diagram.panel | Provides user interface for edit several advanced properties of a diagram. | |
| AnimatedGIFRenderer
| edu.stanford.covertlab.graphics.renderer | Converts an array of bitmap data to an animated gif. | |
| AnimationBar
| edu.stanford.covertlab.diagram.toolbar | Container for animation play, pause, stop, and timeline controls. | |
| AnimationToolBar
| edu.stanford.covertlab.diagram.toolbar | Toolbar which animation play, pause, and stop controls and an animation timeline. | |
| ArrayMathUtils
| edu.stanford.covertlab.util | Defines four mathematical operations for arrays. | |
| AS2MXML
| edu.stanford.covertlab.util | Generates an MXML representation of an actionscript object. | |
| AS2XML
| edu.stanford.covertlab.util | Converts between XML and actionscript representation of an object. | |
| ATPaseShape
| edu.stanford.covertlab.graphics.shape | Draws an ATPase. | |
| Bezier
| flash.geom |
Class |
|
| Biomolecule
| edu.stanford.covertlab.diagram.core | Biomolecule class. | |
| BiomoleculeEvent
| edu.stanford.covertlab.diagram.event | Biomolecule event class. | |
| BiomoleculesPanel
| edu.stanford.covertlab.diagram.panel | Form-based user interface for creating, editing, and deleting biomolecules. | |
| BiomoleculeStyle
| edu.stanford.covertlab.diagram.core | Rendering style object for biomolecules. | |
| BiomoleculeStyleEvent
| edu.stanford.covertlab.diagram.event | Biomolecule style event class. | |
| BioPax
| edu.stanford.covertlab.networkanalyzer.ExchangeFormat | Supports BioPax Level 3, Version 0.92 according to the following mapping: Meta Data -> rdf Membranes/Compartments -> cellular location vocabulary Biomolecule Style -> entity reference group vocabulary Biomolecules -> physical entity Regulation -> control See BioPax specificatons | |
| BooleanSimulation
| edu.stanford.covertlab.networkanalyzer.simulation | Generates MATLAB code for a Boolean simulation of the biological network described by a diagram. | |
| CellML
| edu.stanford.covertlab.networkanalyzer.ExchangeFormat | Supports CellML specification v1.1. | |
| CentrosomeShape
| edu.stanford.covertlab.graphics.shape | Draws a centrosome. | |
| Chart
| edu.stanford.covertlab.chart | Simple charting class. | |
| ChartTest
| edu.stanford.covertlab.chart | ||
| ChartToolTip
| edu.stanford.covertlab.chart | ToolTip containing a chart. | |
| ChartWindow
| edu.stanford.covertlab.chart | TitleWindow containing a chart. | |
| CircleShape
| edu.stanford.covertlab.graphics.shape | Draws a circle. | |
| ColorBar
| edu.stanford.covertlab.graphics.renderablerepeater | Draws a rectangle containing a subrectangle of the same width for each element in the color array. | |
| ColorGrid
| edu.stanford.covertlab.graphics.renderablerepeater | Draws a grid containing a rectangle for each element in the colors array. | |
| Colormap
| edu.stanford.covertlab.colormap | Converts real numbers on the scale [0,1] to a color using one of several color maps. | |
| ColormapTest
| edu.stanford.covertlab.colormap | ||
| ColorScale
| edu.stanford.covertlab.chart | Displays color scale bar with labels. | |
| ColorUtils
| edu.stanford.covertlab.util | Miscellaneous utility functions for converting between hexadecimal colors and RGB. | |
| Compartment
| edu.stanford.covertlab.diagram.core | Main compartment class from which the membrane and hot spot classes derive. | |
| CompartmentBase
| edu.stanford.covertlab.diagram.core | Main compartment class from which the membrane and hot spot classes derive. | |
| CompartmentEvent
| edu.stanford.covertlab.diagram.event | Compartment event class. | |
| CompartmentHotspot
| edu.stanford.covertlab.diagram.core | Displays "hot spots" in a diagram where a compartment can be inserted. | |
| CompartmentsPanel
| edu.stanford.covertlab.diagram.panel | Form-based user interface for creating, editing, and deleting compartments. | |
| ComplexShapeBase
| edu.stanford.covertlab.graphics.shape | Base class for complex shapes. | |
| ConfigureAxesWindow
| edu.stanford.covertlab.networkanalyzer.window | PopUp window for selecting. | |
| ConnectionData
| phi.db |
A class for storing a connection information. |
|
| ControlToolBar
| edu.stanford.covertlab.diagram.toolbar | Toolbar containing controls for copy, cut, pase; undo, redo; zooming, and autolayout. | |
| CytoBank
| edu.stanford.covertlab.service | Provides functions for interacting with CytoBank through a CytoBank AMFPHP object. | |
| DashedLineCircleVertexDecorator
| edu.stanford.covertlab.graphics.decorators |
Extension of SVG dashed line decorator which adds
|
|
| Database
| phi.db |
A Singleton IDatabase implementation. |
|
| Diagram
| edu.stanford.covertlab.diagram.core | Main biological network diagram class. | |
| DiagramEvent
| edu.stanford.covertlab.diagram.event | Diagram event class. | |
| DiagramToolBarDocker
| edu.stanford.covertlab.diagram.toolbar | Docker for dockable toolbars -- animation, control, and new biomlecule, biomolecules style, and compartment toolbars. | |
| DNAShape
| edu.stanford.covertlab.graphics.shape | Draws a double helix. | |
| Edge
| edu.stanford.covertlab.diagram.core | Displays a pictorial representation of a "connection" between two biomolecules. | |
| EditBiomoleculeStyleWindow
| edu.stanford.covertlab.diagram.window | PopUp window user interface for editing a biomolecule style. | |
| EditBiomoleculeWindow
| edu.stanford.covertlab.diagram.window | PopUp window user interface for editing a biomolecule. | |
| EditCompartmentWindow
| edu.stanford.covertlab.diagram.window | PopUp window user interface for editing a compartment. | |
| EllipseShape
| edu.stanford.covertlab.graphics.shape | Draws an ellipse. | |
| EndoplasmicReticulumShape
| edu.stanford.covertlab.graphics.shape | Draws an endoplasmic reticulum. | |
| Equations
| flash.math |
В классе представлены методы для решения уравнений с 1 неизвестным. Если в уравнении n-ой степени ведущие коэффициенты нулевые, то все равно можно использовать метод для n-ой степени, нужный метод перевызовется автоматически. Погрешность решения составляет порядка 10^-5. |
|
| Experiment
| edu.stanford.covertlab.networkanalyzer.viewer.data | ||
| ExperimentManager
| edu.stanford.covertlab.networkanalyzer.manager | Handles several experiment-related operations. | |
| ExperimentManagerEvent
| edu.stanford.covertlab.networkanalyzer.event | Event class for ExperimentManager. | |
| FindBiomoleculeWindow
| edu.stanford.covertlab.diagram.window | PopUp window user interface for searching through the list of biomolecules for a biomolecule with a matching name or label. | |
| FlagellumShape
| edu.stanford.covertlab.graphics.shape | Draws a flagellum. | |
| GIFEncoder
| org.gif.encoder | ||
| GIFRenderer
| edu.stanford.covertlab.graphics.renderer | Generates a gif image of a UIComponent. | |
| GolgiShape
| edu.stanford.covertlab.graphics.shape | Draws a golgi apparatus. | |
| GraphicPointUtils
| edu.stanford.covertlab.util | Miscellaneous utility functions for rotating, scaling, and reflecting arrays of graphic points | |
| GreekKeyboard
| edu.stanford.covertlab.controls | Visual keyboard for entering Greek characters into a text box. | |
| HeatmapWindow
| edu.stanford.covertlab.networkanalyzer.window | PopUp window displaying an experiment in the form of a heatmap. | |
| HelpData
| edu.stanford.covertlab.networkanalyzer.data | ||
| HelpSection
| edu.stanford.covertlab.window | Object for an application help or tutorial section. | |
| HelpWindow
| edu.stanford.covertlab.window | PopUp window displaying help for an application. | |
| HierarchicalClustering
| edu.stanford.covertlab.analysis | Implements hierarchical agglomerative clustering using the O(n^3) algorithm described in Eisen et al.(1998) and the recursive O(n^4) optimal leaf ordering described in Bar-Joseph et al (2001). | |
| HierarchicalClusteringTest
| edu.stanford.covertlab.analysis | Tester for HierarchicalClustering class. | |
| HistoryAction
| edu.stanford.covertlab.diagram.history | Stores information about an undo/redo command. | |
| HistoryManager
| edu.stanford.covertlab.diagram.history | Controls undo, redo stacks for diagram. | |
| HouseShape
| edu.stanford.covertlab.graphics.shape | Draws an ATPase. | |
| HTML
| edu.stanford.covertlab.util | Utility class for operations on HTML-like text markup. | |
| IDatabase
| phi.interfaces |
The interface definition for a Database object. |
|
| IgShape
| edu.stanford.covertlab.graphics.shape | Draws a Ig receptor. | |
| IHistory
| edu.stanford.covertlab.diagram.history | ... | |
| ImageBorder
| edu.stanford.covertlab.controls | Image with border. | |
| ImportNetworkWindow
| edu.stanford.covertlab.networkanalyzer.window | Provides a window for a user to select a pathway to import from a database. | |
| ImportNetworkWindow_ThumbnailTileListItemRenderer
| edu.stanford.covertlab.networkanalyzer.window | Thumbnails in ImportNetworkWindow. | |
| ImportNetworkWindow_ThumbnailTileListToolTip
| edu.stanford.covertlab.networkanalyzer.window | Tooltip for thumbnails in ImportNetworkWindow. | |
| Intersection
| flash.geom |
If crossing exist, then result can be of array of points,
or full or brownout coincidence of shapes. If variable isCoincidence=false, it means that shapes are crossing and not equally. |
|
| IonChannelShape
| edu.stanford.covertlab.graphics.shape | Draws an ion channel. | |
| IParametric
| flash.geom | ||
| IQuery
| phi.interfaces |
The interface definition for a Query object. |
|
| JPEGRenderer
| edu.stanford.covertlab.graphics.renderer | Generates a jpeg image of a UIComponent. | |
| KEGG
| edu.stanford.covertlab.service | Provides three functions for importing pathways from the KEGG database via a KEGG AMFPHP object. | |
| Line
| flash.geom |
Class Line introdaction line at parametrical introduction,
given by points on plane start and end
and realized to support internal method lineTo().At class realized properties and methods, they help you take access to basic geometry properties of line. Points, belongs to line defines by time-iterator. |
|
| LogoffWindow
| edu.stanford.covertlab.window | PopUp window which prompts user whether or not they wish to logoff. | |
| LZWEncoder
| org.gif.encoder | ||
| ManageExperimentsWindow
| edu.stanford.covertlab.networkanalyzer.window | PopUp window which allows the user to specify experimentally observed channels a biomolecule in the current network correspond to, as well as what the experimentally applied conditions corresponded to in terms of biomolecules. | |
| ManageNetworksWindow
| edu.stanford.covertlab.networkanalyzer.window | PopUp window which allows management of networks a user has access to. | |
| MathML
| edu.stanford.covertlab.util | Contains functions for (very limited) conversion between actionscript infix mathematical formulae and MathML. | |
| MathMLTest
| edu.stanford.covertlab.util | Test class for MathML class. | |
| Measurement
| edu.stanford.covertlab.networkanalyzer.viewer.data | ||
| Membrane
| edu.stanford.covertlab.diagram.core | Displays a pictorial representation of a membrane. | |
| MembranePhospholipids
| edu.stanford.covertlab.graphics.renderablerepeater | Draws a curved phospholipid membrane with phospholipid heads and tails. | |
| MitochondrionShape
| edu.stanford.covertlab.graphics.shape | Draws a mitochondrion. | |
| MultipagePDFRenderer
| edu.stanford.covertlab.graphics.renderer | Generates a multi-page pdf with a page for each element in an array of bitmap data of frames. | |
| MyPanelSkin
| com.monkeypatches.blog.kyleq | The PanelSkin class defines the skin for the Panel, TitleWindow, and Alert components. | |
| Network
| edu.stanford.covertlab.networkanalyzer.viewer.data | ||
| NetworkAnalyzer
| edu.stanford.covertlab.networkanalyzer | ||
| NetworkAnalyzer
| edu.stanford.covertlab.service | Provides functions for interacting with the NetworkAnalyzer database via an AMFPHP class. | |
| NetworkManager
| edu.stanford.covertlab.networkanalyzer.manager | Handles several network operations. | |
| NetworkManagerEvent
| edu.stanford.covertlab.networkanalyzer.event | Event class for NetworkManager. | |
| NetworkPropertiesWindow
| edu.stanford.covertlab.networkanalyzer.window | PopUp window diplaying the name and description of the current network. | |
| NeuQuant
| org.gif.encoder | ||
| NewBiomoleculeToolBar
| edu.stanford.covertlab.diagram.toolbar | Toolbar for add a new biomolecue to a diagram by dragging a button from a toolbar. | |
| NewComponentToolBar
| edu.stanford.covertlab.diagram.toolbar | Toolbar containing buttons for adding new compartments and biomolecule styles to a diagram. | |
| OpenNetworkWindow
| edu.stanford.covertlab.networkanalyzer.window | PopUp window displaying the list of networks, and the properties of those networks, that a user has access to. | |
| OpenNetworkWindow_ThumbnailTileListItemRenderer
| edu.stanford.covertlab.networkanalyzer.window | Thumbnails in OpenNetworkWindow. | |
| OpenNetworkWindow_ThumbnailTileListToolTip
| edu.stanford.covertlab.networkanalyzer.window | Tooltip for thumbnails in OpenNetworkWindow. | |
| Overview
| edu.stanford.covertlab.diagram.overview | Displays a small window which shows the entirety of the current biological network. | |
| ParallelogramShape
| edu.stanford.covertlab.graphics.shape | Draws a parallelogram. | |
| PassTransmembraneReceptorShape
| edu.stanford.covertlab.graphics.shape | Draws a 7-pass transmembrane receptor. | |
| PDFRenderer
| edu.stanford.covertlab.graphics.renderer | Generates pdf with vector graphic illustrating of a Degrafa surface. | |
| PNGRenderer
| edu.stanford.covertlab.graphics.renderer | Generates a png image of a UIComponent. | |
| PolygonShapeBase
| edu.stanford.covertlab.graphics.shape | Base class for convex polygon shapes. | |
| PoreShape
| edu.stanford.covertlab.graphics.shape | Draws a pore. | |
| Preloader
| edu.stanford.covertlab.networkanalyzer.preloader | Application preloader. | |
| Printer
| edu.stanford.covertlab.graphics.printer | Creates flash print job from canvas containing Degrafa surfaces. | |
| Query
| phi.db |
A IQuery implementation. |
|
| Rasterizer
| edu.stanford.covertlab.networkanalyzer | ||
| Reactome
| edu.stanford.covertlab.service | Provides three functions for importing pathways from the Reactome database via a Reactome AMFPHP object. | |
| RectangleShape
| edu.stanford.covertlab.graphics.shape | Draws a rectangle or rounded rectangle. | |
| RegularPolygonShape
| edu.stanford.covertlab.graphics.shape | Draws a regular polygon. | |
| RenderableRepeater
| edu.stanford.covertlab.graphics.renderablerepeater | Exposes object stack of a degrafa repeater so that it can be accessed by the renderers. | |
| SaveAsNetworkWindow
| edu.stanford.covertlab.networkanalyzer.window | PopUp window allows the user to save the current network to the database. | |
| SBML
| edu.stanford.covertlab.networkanalyzer.ExchangeFormat | Supports SBML Level 2 Version 1-4 according to the following mapping: Meta Data -> notes Membranes/Compartments -> sbml:compartment, sbml:compartmenttype Biomolecule Style -> sbml:speciesType, networkanalyzer:biomoleculeStyle Biomolecules -> sbml:species Regulation -> sbml:assignmentRule Support for compartmentType and speciesType were introduced with SBML Level 2 Version 2. | |
| SelectHandles
| edu.stanford.covertlab.graphics | Displays select handles (dashed lines, circles at verticles, squares at midpoints of segments) for a geometry group. | |
| ShapeBase
| edu.stanford.covertlab.graphics.shape | Base class for shapes. | |
| ShapeTest
| edu.stanford.covertlab.graphics.shape | ||
| SimpleControlBar
| edu.stanford.covertlab.diagram.toolbar | Simplified control toolbar for viewer. | |
| StylesPanel
| edu.stanford.covertlab.diagram.panel | Form-based user interface for creating, editing, and deleting biomolecule styles. | |
| SupSubDataGridItemRenderer
| edu.stanford.covertlab.controls | DataGridItemRender which supports HTML-like text markup. | |
| SupSubRasterText
| edu.stanford.covertlab.graphics | Provides support for superscript, subscript, and Greek characters within Degrafa. | |
| SVGRasterizer
| edu.stanford.covertlab.graphics.rasterizer | Uses Inkscape (via webservice) to convert a canvas with Degrafa surfaces to png, ps, eps, or pdf. | |
| SVGRenderer
| edu.stanford.covertlab.graphics.renderer | Translates canvas with Degrafa surfaces to SVG. | |
| ThumbnailTileList
| edu.stanford.covertlab.controls | Thumbnails tile list. | |
| ThumbnailTileListItemRenderer
| edu.stanford.covertlab.controls | Thumbnails tile list item renderer. | |
| ThumbnailTileListToolTip
| edu.stanford.covertlab.controls | Tooltip for thumbnails in thumbnail tile list. | |
| ToolBar
| edu.stanford.covertlab.diagram.toolbar | Base dockable toolbar class. | |
| ToolBarButton
| edu.stanford.covertlab.controls | Base class for toolbar buttons. | |
| ToolBarCanvasButton
| edu.stanford.covertlab.controls | Base class for NewBiomoleculeToolBar buttons. | |
| TrapeziumShape
| edu.stanford.covertlab.graphics.shape | Draws a trapezium. | |
| TutorialData
| edu.stanford.covertlab.networkanalyzer.data | ||
| TutorialWindow
| edu.stanford.covertlab.window | PopUp window which displays the tutorial for an application. | |
| UserAccountWindow
| edu.stanford.covertlab.window | PopUp window which allows to review and edit their user profile (name, email, affiliation, PI, etc.). | |
| UserManager
| edu.stanford.covertlab.manager | Implements user security and manages user id and profile. | |
| UserManagerEvent
| edu.stanford.covertlab.event | Event class for UserManager. | |
| Viewer
| edu.stanford.covertlab.networkanalyzer | ||
| YReceptorShape
| edu.stanford.covertlab.graphics.shape | Draws a y-shaped receptor. |