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aboutData — Property in class edu.stanford.covertlab.networkanalyzer.NetworkAnalyzer
aboutData — Property in class edu.stanford.covertlab.networkanalyzer.Viewer
AboutData — Class in package edu.stanford.covertlab.networkanalyzer.data
aboutWindow — Property in class edu.stanford.covertlab.networkanalyzer.NetworkAnalyzer
aboutWindow — Property in class edu.stanford.covertlab.networkanalyzer.Viewer
AboutWindow — Class in package edu.stanford.covertlab.networkanalyzer.viewer
	PopUp window displaying meta data about the network and experiment loaded into the viewer.
AboutWindow — Class in package edu.stanford.covertlab.window
	PopUp window displaying metadata about an application (name, version, release date, list of developers, etc.).
AboutWindow(application, aboutData, network, experiment, measurement) — Constructor in class edu.stanford.covertlab.networkanalyzer.viewer.AboutWindow
AboutWindow(application, aboutData) — Constructor in class edu.stanford.covertlab.window.AboutWindow
AcceleratorMenuBar — Class in package com.rphelan.controls
	The AcceleratorMenuBar is a MenuBar which displays windows/mac style accelerators next to the menu labels.
AcceleratorMenuBar() — Constructor in class com.rphelan.controls.AcceleratorMenuBar
	Constructor.
AcceleratorMenuItemRenderer — Class in package com.rphelan.controls.menuClasses
	The AcceleratorMenuItemRenderer class modifies the default MenuItemRenderer to add 'accelerator' labels.
AcceleratorMenuItemRenderer() — Constructor in class com.rphelan.controls.menuClasses.AcceleratorMenuItemRenderer
	Constructor.
action — Property in class edu.stanford.covertlab.diagram.history.HistoryAction
addBiomolecule(biomolecule:edu.stanford.covertlab.diagram.core:Biomolecule) — Method in class edu.stanford.covertlab.diagram.core.Diagram
addBiomoleculeStyle(biomoleculeStyle:edu.stanford.covertlab.diagram.core:BiomoleculeStyle) — Method in class edu.stanford.covertlab.diagram.core.Diagram
addCompartment(compartment:edu.stanford.covertlab.diagram.core:Compartment) — Method in class edu.stanford.covertlab.diagram.core.Diagram
addEdge(fromName, to:edu.stanford.covertlab.diagram.core:Biomolecule, sense) — Method in class edu.stanford.covertlab.diagram.core.Diagram
addFrame(im) — Method in class org.gif.encoder.GIFEncoder
	The addFrame method takes an incoming BitmapData object to create each frames
addHistoryAction(action:edu.stanford.covertlab.diagram.history:HistoryAction) — Method in class edu.stanford.covertlab.diagram.history.HistoryManager
addStyle(style:edu.stanford.covertlab.diagram.core:BiomoleculeStyle) — Method in class edu.stanford.covertlab.diagram.toolbar.NewBiomoleculeToolBar
	add, update, remove styles
AdvancedOptionsPanel — Class in package edu.stanford.covertlab.diagram.panel
	Provides user interface for edit several advanced properties of a diagram.
AdvancedOptionsPanel() — Constructor in class edu.stanford.covertlab.diagram.panel.AdvancedOptionsPanel
allAssociatedExperimentIds — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager
allAssociatedExperiments — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager
allAssociations — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager
allExperimentIds — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager
allExperiments — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager
allPerturbations — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager
angle — Property in class flash.geom.Line
	Angle of incline line at radian.
angleOffset(value, fulcrum) — Method in class flash.geom.Bezier
	Rotate a curve concerning to a point fulcrum on the value angle If point fulcrum is not set, used (0,0)
angleOffset(value, fulcrum) — Method in interface flash.geom.IParametric
angleOffset(rad, fulcrum) — Method in class flash.geom.Line
	Rotate line respection at point fulcrum at current angle.
AnimatedGIFRenderer — Class in package edu.stanford.covertlab.graphics.renderer
	Converts an array of bitmap data to an animated gif.
AnimatedGIFRenderer() — Constructor in class edu.stanford.covertlab.graphics.renderer.AnimatedGIFRenderer
animationAlpha — Property in class edu.stanford.covertlab.diagram.core.Diagram
animationAxis — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager
animationAxisControl — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager
animationbar — Property in class edu.stanford.covertlab.diagram.toolbar.DiagramToolBarDocker
AnimationBar — Class in package edu.stanford.covertlab.diagram.toolbar
	Container for animation play, pause, stop, and timeline controls.
AnimationBar(diagram:edu.stanford.covertlab.diagram.core:Diagram, standalone) — Constructor in class edu.stanford.covertlab.diagram.toolbar.AnimationBar
animationFrameRate — Property in class edu.stanford.covertlab.diagram.core.Diagram
animationFrameRate — Property in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager
animationIdx — Property in class edu.stanford.covertlab.diagram.core.Diagram
animationIdxMax — Property in class edu.stanford.covertlab.diagram.core.Diagram
animationNotStopped — Property in class edu.stanford.covertlab.diagram.core.Diagram
animationPlaying — Property in class edu.stanford.covertlab.diagram.core.Diagram
animationPos — Property in class edu.stanford.covertlab.diagram.core.Diagram
animationPosMax — Property in class edu.stanford.covertlab.diagram.core.Diagram
animationTime — Property in class edu.stanford.covertlab.diagram.core.Diagram
animationTimeMax — Property in class edu.stanford.covertlab.diagram.core.Diagram
AnimationToolBar — Class in package edu.stanford.covertlab.diagram.toolbar
	Toolbar which animation play, pause, and stop controls and an animation timeline.
AnimationToolBar(diagram:edu.stanford.covertlab.diagram.core:Diagram) — Constructor in class edu.stanford.covertlab.diagram.toolbar.AnimationToolBar
application — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager
area — Property in class flash.geom.Bezier
	Calculates and returns the area of the figure limited by Bezier curve and line SE.
array2mxml(arr, depth) — Static method in class edu.stanford.covertlab.util.AS2MXML
arrayInsert(table, arr) — Method in class phi.db.Query
	Execute a INSERT query on a table.
arrayInsert(table, arr) — Method in interface phi.interfaces.IQuery
	Execute a INSERT query on a table.
ArrayMathUtils — Class in package edu.stanford.covertlab.util
	Defines four mathematical operations for arrays.
arrayUpdate(table, arr, cond) — Method in class phi.db.Query
	Execute a UPDATE query on a table.
arrayUpdate(table, arr, cond) — Method in interface phi.interfaces.IQuery
	Execute a UPDATE query on a table.
arrowPoints(sense, theta) — Static method in class edu.stanford.covertlab.diagram.core.Edge
	arrow shapes
as2mxml(object) — Static method in class edu.stanford.covertlab.util.AS2MXML
AS2MXML — Class in package edu.stanford.covertlab.util
	Generates an MXML representation of an actionscript object.
as2xml(object, objectName) — Static method in class edu.stanford.covertlab.util.AS2XML
AS2XML — Class in package edu.stanford.covertlab.util
	Converts between XML and actionscript representation of an object.
ATPaseShape — Class in package edu.stanford.covertlab.graphics.shape
	Draws an ATPase.
ATPaseShape(size, strokeColor, fillColor) — Constructor in class edu.stanford.covertlab.graphics.shape.ATPaseShape
autoLayoutDiagram() — Method in class edu.stanford.covertlab.diagram.core.Diagram
autosaveid — Property in class edu.stanford.covertlab.manager.UserManager
averageLinkage(distance, cluster1, cluster2) — Static method in class edu.stanford.covertlab.analysis.HierarchicalClustering
averages — Property in class edu.stanford.covertlab.service.CytoBank
axisFontSize — Property in class edu.stanford.covertlab.chart.Chart
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