| A B C D E F G H I J K L M N O P Q R S T U V W X Y Z |
| CellML — Class in package edu.stanford.covertlab.networkanalyzer.ExchangeFormat |
|
Supports CellML specification v1.1. |
| center(width, height) — Method in class edu.stanford.covertlab.networkanalyzer.preloader.Preloader |
| |
| CentrosomeShape — Class in package edu.stanford.covertlab.graphics.shape |
|
Draws a centrosome. |
| CentrosomeShape(size, strokeColor, fillColor) — Constructor in class edu.stanford.covertlab.graphics.shape.CentrosomeShape |
| |
| channelAxis — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager |
| |
| Chart — Class in package edu.stanford.covertlab.chart |
|
Simple charting class. |
| Chart(chartType, xAxis, yAxis, chartData, colormap, colormapScale, axisFontSize, tickFontSize, createToolTip) — Constructor in class edu.stanford.covertlab.chart.Chart |
| |
| chartData — Property in class edu.stanford.covertlab.chart.Chart |
| |
| ChartTest — Class in package edu.stanford.covertlab.chart |
| |
| ChartToolTip — Class in package edu.stanford.covertlab.chart |
|
ToolTip containing a chart. |
| ChartToolTip(title, chart:edu.stanford.covertlab.chart:Chart) — Constructor in class edu.stanford.covertlab.chart.ChartToolTip |
| |
| chartType — Property in class edu.stanford.covertlab.chart.Chart |
| |
| CHARTTYPE_AREA — Constant static property in class edu.stanford.covertlab.chart.Chart |
| chart types
|
| CHARTTYPE_BAR — Constant static property in class edu.stanford.covertlab.chart.Chart |
| |
| CHARTTYPE_HEATMAP — Constant static property in class edu.stanford.covertlab.chart.Chart |
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| CHARTTYPE_HISTOGRAM — Constant static property in class edu.stanford.covertlab.chart.Chart |
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| CHARTTYPE_LINE — Constant static property in class edu.stanford.covertlab.chart.Chart |
| |
| ChartWindow — Class in package edu.stanford.covertlab.chart |
|
TitleWindow containing a chart. |
| ChartWindow(title, chart:edu.stanford.covertlab.chart:Chart) — Constructor in class edu.stanford.covertlab.chart.ChartWindow |
| |
| children — Property in class edu.stanford.covertlab.window.HelpSection |
| |
| CircleShape — Class in package edu.stanford.covertlab.graphics.shape |
|
Draws a circle. |
| CircleShape(size, strokeColor, fillColor) — Constructor in class edu.stanford.covertlab.graphics.shape.CircleShape |
| |
| clear() — Method in class edu.stanford.covertlab.diagram.history.HistoryManager |
| |
| clearBiomoleculeStyles() — Method in class edu.stanford.covertlab.diagram.toolbar.NewBiomoleculeToolBar |
| remove all buttons
|
| clearDiagram() — Method in class edu.stanford.covertlab.diagram.core.Diagram |
| |
| clearInputs() — Method in class edu.stanford.covertlab.diagram.panel.BiomoleculesPanel |
| |
| clearInputs() — Method in class edu.stanford.covertlab.diagram.panel.CompartmentsPanel |
| |
| clearInputs() — Method in class edu.stanford.covertlab.diagram.panel.StylesPanel |
| |
| clearNetwork() — Method in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager |
| |
| clearNetworkLock(networkid) — Method in class edu.stanford.covertlab.service.NetworkAnalyzer |
| |
| CLEAR_NETWORK_LOCK — Constant static property in class edu.stanford.covertlab.service.NetworkAnalyzer |
| |
| clearSelectedBiomolecules(event) — Method in class edu.stanford.covertlab.diagram.core.Diagram |
| |
| clone() — Method in class flash.geom.Bezier |
|
Creates and returns a copy of current object Bezier. |
| clone() — Method in class flash.geom.Line |
|
|
| clone() — Method in class phi.db.ConnectionData |
| |
| close(event) — Method in class edu.stanford.covertlab.chart.ChartWindow |
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| close() — Method in class edu.stanford.covertlab.diagram.overview.Overview |
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| close(event) — Method in class edu.stanford.covertlab.diagram.window.EditBiomoleculeStyleWindow |
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| close(event) — Method in class edu.stanford.covertlab.diagram.window.EditBiomoleculeWindow |
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| close(event) — Method in class edu.stanford.covertlab.diagram.window.EditCompartmentWindow |
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| close(event) — Method in class edu.stanford.covertlab.networkanalyzer.window.HeatmapWindow |
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| close(event) — Method in class edu.stanford.covertlab.networkanalyzer.window.ImportNetworkWindow |
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| close(event) — Method in class edu.stanford.covertlab.networkanalyzer.window.ManageNetworksWindow |
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| close(event) — Method in class edu.stanford.covertlab.networkanalyzer.window.OpenNetworkWindow |
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| close(event) — Method in class edu.stanford.covertlab.window.UserAccountWindow |
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| cluster(distance, linkage, optimizeLeafOrder, clusters, leafOrder) — Static method in class edu.stanford.covertlab.analysis.HierarchicalClustering |
| hierarchical agglomerative clustering (Eisen et al, 1998). |
| clusterAnimationAxis — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager |
| |
| clusterBiomoleculeAxis — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager |
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| clusterComparisonXAxis — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager |
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| clusterComparisonYAxis — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager |
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| ColorBar — Class in package edu.stanford.covertlab.graphics.renderablerepeater |
|
Draws a rectangle containing a subrectangle of the same width for each element in the color array. |
| ColorBar(x, y, width, height, count, colors) — Constructor in class edu.stanford.covertlab.graphics.renderablerepeater.ColorBar |
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| colorBarHeight — Property in class edu.stanford.covertlab.chart.ColorScale |
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| colorBarWidth — Property in class edu.stanford.covertlab.chart.ColorScale |
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| ColorGrid — Class in package edu.stanford.covertlab.graphics.renderablerepeater |
|
Draws a grid containing a rectangle for each element in the colors array. |
| ColorGrid(x, y, width, height, rows, cols, colors) — Constructor in class edu.stanford.covertlab.graphics.renderablerepeater.ColorGrid |
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| colormap — Property in class edu.stanford.covertlab.chart.Chart |
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| colormap — Property in class edu.stanford.covertlab.chart.ColorScale |
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| colormap — Property in class edu.stanford.covertlab.diagram.core.Diagram |
| |
| colormap — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager |
| |
| colormap — Property in class edu.stanford.covertlab.networkanalyzer.window.HeatmapWindow |
| getters, setter
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| Colormap — Class in package edu.stanford.covertlab.colormap |
|
Converts real numbers on the scale [0,1] to a color using one of several color maps. |
| COLORMAPS — Constant static property in class edu.stanford.covertlab.colormap.Colormap |
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| colormapScale — Property in class edu.stanford.covertlab.chart.Chart |
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| ColormapTest — Class in package edu.stanford.covertlab.colormap |
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| colors — Property in class edu.stanford.covertlab.graphics.renderablerepeater.ColorBar |
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| colors — Property in class edu.stanford.covertlab.graphics.renderablerepeater.ColorGrid |
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| colorScale — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager |
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| ColorScale — Class in package edu.stanford.covertlab.chart |
|
Displays color scale bar with labels. |
| ColorScale(colormap, scale, colorBarWidth, colorBarHeight) — Constructor in class edu.stanford.covertlab.chart.ColorScale |
| |
| ColorUtils — Class in package edu.stanford.covertlab.util |
|
Miscellaneous utility functions for converting between hexadecimal colors and RGB. |
| cols — Property in class edu.stanford.covertlab.graphics.renderablerepeater.ColorGrid |
| |
| com.monkeypatches.blog.kyleq — Package |
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| comparisonHeatmapsVisible — Property in class edu.stanford.covertlab.diagram.core.Diagram |
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| comparisonXAxis — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager |
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| comparisonXAxisControl — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager |
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| comparisonYAxis — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager |
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| comparisonYAxisControl — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager |
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| Compartment — Class in package edu.stanford.covertlab.diagram.core |
|
Main compartment class from which the membrane and hot spot classes derive. |
| Compartment(diagram:edu.stanford.covertlab.diagram.core:Diagram, name, color, membraneColor, phospholipidBodyColor, phospholipidOutlineColor, width, height, myUpperCompartment:edu.stanford.covertlab.diagram.core:Compartment, myLowerCompartment:edu.stanford.covertlab.diagram.core:Compartment) — Constructor in class edu.stanford.covertlab.diagram.core.Compartment |
| |
| CompartmentBase — Class in package edu.stanford.covertlab.diagram.core |
|
Main compartment class from which the membrane and hot spot classes derive. |
| CompartmentBase(diagram:edu.stanford.covertlab.diagram.core:Diagram, color, width, height, myUpperCompartment:edu.stanford.covertlab.diagram.core:Compartment, myLowerCompartment:edu.stanford.covertlab.diagram.core:Compartment) — Constructor in class edu.stanford.covertlab.diagram.core.CompartmentBase |
| |
| CompartmentEvent — Class in package edu.stanford.covertlab.diagram.event |
|
Compartment event class. |
| CompartmentEvent(type) — Constructor in class edu.stanford.covertlab.diagram.event.CompartmentEvent |
| |
| CompartmentHotspot — Class in package edu.stanford.covertlab.diagram.core |
|
Displays "hot spots" in a diagram where a compartment can be inserted. |
| CompartmentHotspot(diagram:edu.stanford.covertlab.diagram.core:Diagram, myUpperCompartment:edu.stanford.covertlab.diagram.core:Compartment, width, height, myPosition) — Constructor in class edu.stanford.covertlab.diagram.core.CompartmentHotspot |
| |
| COMPARTMENT_REMOVE — Constant static property in class edu.stanford.covertlab.diagram.event.CompartmentEvent |
| |
| compartmentResizeEnable — Property in class edu.stanford.covertlab.diagram.core.Diagram |
| |
| compartments — Property in class edu.stanford.covertlab.diagram.core.Diagram |
| Compartments
|
| compartments — Property in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager |
| |
| compartmentsAndMembranes — Property in class edu.stanford.covertlab.diagram.core.Diagram |
| |
| CompartmentsPanel — Class in package edu.stanford.covertlab.diagram.panel |
|
Form-based user interface for creating, editing, and deleting compartments. |
| CompartmentsPanel() — Constructor in class edu.stanford.covertlab.diagram.panel.CompartmentsPanel |
| |
| COMPARTMENT_UPDATE — Constant static property in class edu.stanford.covertlab.diagram.event.CompartmentEvent |
| |
| completeInitialization() — Method in class edu.stanford.covertlab.diagram.core.Diagram |
| initialization
|
| completeLinkage(distance, cluster1, cluster2) — Static method in class edu.stanford.covertlab.analysis.HierarchicalClustering |
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| completeNetworkImport(network) — Method in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager |
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| ComplexShapeBase — Class in package edu.stanford.covertlab.graphics.shape |
|
Base class for complex shapes. |
| ComplexShapeBase(size, strokeColor, fillColor) — Constructor in class edu.stanford.covertlab.graphics.shape.ComplexShapeBase |
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| componentbar — Property in class edu.stanford.covertlab.diagram.toolbar.DiagramToolBarDocker |
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| compress(init_bits, outs) — Method in class org.gif.encoder.LZWEncoder |
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| computeConvexPolygonPort(points, theta, sense) — Method in class edu.stanford.covertlab.graphics.shape.ShapeBase |
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| computePort(theta, sense) — Method in class edu.stanford.covertlab.diagram.core.Biomolecule |
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| com.rphelan.controls — Package |
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| com.rphelan.controls.menuClasses — Package |
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| conditionAxis — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager |
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| configureAxesWindow — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager |
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| ConfigureAxesWindow — Class in package edu.stanford.covertlab.networkanalyzer.window |
|
PopUp window for selecting. |
| ConfigureAxesWindow(experimentManager:edu.stanford.covertlab.networkanalyzer.manager:ExperimentManager) — Constructor in class edu.stanford.covertlab.networkanalyzer.window.ConfigureAxesWindow |
| |
| connect(name, user, pass, host, db, bDefault) — Method in class phi.db.Database |
|
Create a new connection with a remote application server. |
| connect(connection, db:phi.interfaces:IDatabase) — Method in class phi.db.Query |
|
This function allow to select the connection you want to
use for executing a SQL statements. |
| connect(name, user, pass, host, db, bDefault) — Method in interface phi.interfaces.IDatabase |
|
Create a new connection with a remote application server. |
| connect(connection, db:phi.interfaces:IDatabase) — Method in interface phi.interfaces.IQuery |
|
This function allow to select the connection you want to
use for executing a SQL statements. |
| connection — Property in class phi.db.Database |
| |
| connection — Property in interface phi.interfaces.IDatabase |
| |
| ConnectionData — Class in package phi.db |
|
A class for storing a connection information.
|
| ConnectionData(user, pass, host, db, name) — Constructor in class phi.db.ConnectionData |
|
Constructor. |
| content — Property in class edu.stanford.covertlab.window.HelpSection |
| |
| control — Property in class flash.geom.Bezier |
|
Direction point of Bezier curve. |
| controlbar — Property in class edu.stanford.covertlab.diagram.toolbar.DiagramToolBarDocker |
| |
| controlPoint — Property in class flash.geom.Bezier |
| |
| CONTROLS — Constant static property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager |
| |
| ControlToolBar — Class in package edu.stanford.covertlab.diagram.toolbar |
|
Toolbar containing controls for copy, cut, pase; undo, redo; zooming, and autolayout. |
| ControlToolBar(diagram:edu.stanford.covertlab.diagram.core:Diagram) — Constructor in class edu.stanford.covertlab.diagram.toolbar.ControlToolBar |
| |
| copy() — Method in class edu.stanford.covertlab.diagram.core.Biomolecule |
| |
| copy() — Method in class edu.stanford.covertlab.diagram.core.Diagram |
| |
| copyEnabled — Property in class edu.stanford.covertlab.diagram.core.Diagram |
| |
| cornerRadius — Style in class edu.stanford.covertlab.controls.ImageBorder |
| |
| countMyEdges() — Method in class edu.stanford.covertlab.diagram.core.Biomolecule |
| |
| createToolTip — Property in class edu.stanford.covertlab.chart.Chart |
| |
| createToolTip(event) — Method in class edu.stanford.covertlab.controls.ThumbnailTileListItemRenderer |
| |
| createToolTip(event) — Method in class edu.stanford.covertlab.networkanalyzer.window.ImportNetworkWindow_ThumbnailTileListItemRenderer |
| |
| createToolTip(event) — Method in class edu.stanford.covertlab.networkanalyzer.window.OpenNetworkWindow_ThumbnailTileListItemRenderer |
| |
| creation — Property in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager |
| |
| currentTimes — Constant property in class flash.geom.Intersection |
|
Array, having time-interators of points of crossing. |
| curveTo(cx, cy, x, y, graphics) — Method in class edu.stanford.covertlab.graphics.decorators.DashedLineCircleVertexDecorator |
| |
| cut(addHistoryAction, addToPasteArray) — Method in class edu.stanford.covertlab.diagram.core.Diagram |
| |
| cutEnabled — Property in class edu.stanford.covertlab.diagram.core.Diagram |
| cut, copy, paste, trash
|
| CytoBank — Class in package edu.stanford.covertlab.service |
|
Provides functions for interacting with CytoBank through a CytoBank AMFPHP object. |
| CytoBank() — Constructor in class edu.stanford.covertlab.service.CytoBank |
| |
| cytobank1DDistribution — Event in class edu.stanford.covertlab.service.CytoBank |
| |
| CYTOBANK_1DDISTRIBUTION — Constant static property in class edu.stanford.covertlab.service.CytoBank |
| |
| cytobank5DAverages — Event in class edu.stanford.covertlab.service.CytoBank |
| |
| CYTOBANK_BLUE_YELLOW — Constant static property in class edu.stanford.covertlab.colormap.Colormap |
| |
| cytobankExperiment — Event in class edu.stanford.covertlab.service.CytoBank |
| |
| CYTOBANK_EXPERIMENT — Constant static property in class edu.stanford.covertlab.service.CytoBank |
| |
| cytobankExperiments — Event in class edu.stanford.covertlab.service.CytoBank |
| |
| CYTOBANK_EXPERIMENTS — Constant static property in class edu.stanford.covertlab.service.CytoBank |
| |
| CYTOBANK_EXPERIMENTSTATISTICS — Constant static property in class edu.stanford.covertlab.service.CytoBank |
| |
| cytobankFault — Event in class edu.stanford.covertlab.service.CytoBank |
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| CYTOBANK_FAULT — Constant static property in class edu.stanford.covertlab.service.CytoBank |
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| A B C D E F G H I J K L M N O P Q R S T U V W X Y Z |
