| 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 | |
| range — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager | |
| rankdir — Property in class edu.stanford.covertlab.diagram.core.Diagram | |
| ranksep — Property in class edu.stanford.covertlab.diagram.core.Diagram | |
| ranksep — Property in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager | |
| rasterize(format, metaData, fileName) — Method in class edu.stanford.covertlab.chart.ColorScale | |
| rasterize(format, metaData) — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| rasterize(format, fileName, image, bounds, metaData) — Method in class edu.stanford.covertlab.graphics.rasterizer.SVGRasterizer | |
| Rasterizer — Class in package edu.stanford.covertlab.networkanalyzer | |
| Reactome — Class in package edu.stanford.covertlab.service | |
| Provides three functions for importing pathways from the Reactome database via a Reactome AMFPHP object. | |
| Reactome() — Constructor in class edu.stanford.covertlab.service.Reactome | |
| reactomeFault — Event in class edu.stanford.covertlab.service.Reactome | |
| REACTOME_FAULT — Constant static property in class edu.stanford.covertlab.service.Reactome | |
| reactomeGetPathway — Event in class edu.stanford.covertlab.service.Reactome | |
| REACTOME_GETPATHWAY — Constant static property in class edu.stanford.covertlab.service.Reactome | |
| reactomeListPathways — Event in class edu.stanford.covertlab.service.Reactome | |
| REACTOME_LISTPATHWAYS — Constant static property in class edu.stanford.covertlab.service.Reactome | |
| Records — Property in class phi.db.Query | |
| Records — Property in interface phi.interfaces.IQuery | |
| RectangleShape — Class in package edu.stanford.covertlab.graphics.shape | |
| Draws a rectangle or rounded rectangle. | |
| RectangleShape(size, strokeColor, fillColor, rounded) — Constructor in class edu.stanford.covertlab.graphics.shape.RectangleShape | |
| rectangleToPoints(rectangle) — Method in class edu.stanford.covertlab.graphics.shape.ShapeBase | |
| redo() — Method in class edu.stanford.covertlab.diagram.history.HistoryManager | |
| redoEnabled — Property in class edu.stanford.covertlab.diagram.history.HistoryManager | |
| reflectX(graphicPoints) — Static method in class edu.stanford.covertlab.util.GraphicPointUtils | |
| reflectY(graphicPoints) — Static method in class edu.stanford.covertlab.util.GraphicPointUtils | |
| refresh(shapeBounds) — Method in class edu.stanford.covertlab.graphics.SelectHandles | |
| refreshColorScale() — Method in class edu.stanford.covertlab.chart.Chart | |
| refreshData() — Method in class edu.stanford.covertlab.chart.Chart | |
| regularPolygonPoints(size, nsides, rotation) — Method in class edu.stanford.covertlab.graphics.shape.RegularPolygonShape | |
| RegularPolygonShape — Class in package edu.stanford.covertlab.graphics.shape | |
| Draws a regular polygon. | |
| RegularPolygonShape(size, strokeColor, fillColor, nsides, theta) — Constructor in class edu.stanford.covertlab.graphics.shape.RegularPolygonShape | |
| remoteObj — Property in class phi.db.ConnectionData | |
| remove(addHistoryAction) — Method in class edu.stanford.covertlab.diagram.core.Biomolecule | |
| remove(addHistoryAction) — Method in class edu.stanford.covertlab.diagram.core.BiomoleculeStyle | |
| remove(addHistoryAction) — Method in class edu.stanford.covertlab.diagram.core.Compartment | |
| remove() — Method in class edu.stanford.covertlab.diagram.core.Edge | |
| removeBiomolecule(biomolecule:edu.stanford.covertlab.diagram.core:Biomolecule) — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| removeBiomoleculeStyle(biomoleculeStyle:edu.stanford.covertlab.diagram.core:BiomoleculeStyle) — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| removeCompartment(compartment:edu.stanford.covertlab.diagram.core:Compartment) — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| removeEdge(edge:edu.stanford.covertlab.diagram.core:Edge) — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| render(format, metaData) — Method in class edu.stanford.covertlab.chart.ColorScale | |
| render, rasterize | |
| render(format, metaData, overrideShowBiomoleculeSelectedHandles, overrideColorBiomoleculesByValue) — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| render(frames, maxAnimationLoops, animationFrameRate, metaData) — Method in class edu.stanford.covertlab.graphics.renderer.AnimatedGIFRenderer | |
| render(image, bounds, metaData) — Method in class edu.stanford.covertlab.graphics.renderer.GIFRenderer | |
| render(image, bounds, metaData) — Method in class edu.stanford.covertlab.graphics.renderer.JPEGRenderer | |
| render(frames, metaData) — Method in class edu.stanford.covertlab.graphics.renderer.MultipagePDFRenderer | |
| render(surface, bounds, metaData) — Method in class edu.stanford.covertlab.graphics.renderer.PDFRenderer | |
| render(image, bounds, metaData) — Method in class edu.stanford.covertlab.graphics.renderer.PNGRenderer | |
| render(image, bounds, metaData) — Method in class edu.stanford.covertlab.graphics.renderer.SVGRenderer | |
| RenderableRepeater — Class in package edu.stanford.covertlab.graphics.renderablerepeater | |
| Exposes object stack of a degrafa repeater so that it can be accessed by the renderers. | |
| RenderableRepeater() — Constructor in class edu.stanford.covertlab.graphics.renderablerepeater.RenderableRepeater | |
| renderAnimation(format, metaData) — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| renewNetworkLock(userid, networkid) — Method in class edu.stanford.covertlab.service.NetworkAnalyzer | |
| RENEW_NETWORK_LOCK — Constant static property in class edu.stanford.covertlab.service.NetworkAnalyzer | |
| resizeToFit(rescale) — Method in class edu.stanford.covertlab.diagram.core.Compartment | |
| auto-layout | |
| resizeToFit(rescale) — Method in class edu.stanford.covertlab.diagram.core.Membrane | |
| auto-layout | |
| retrieveConnection(connectionName) — Method in class phi.db.Database | |
| Retrieve an connection information. | |
| retrieveConnection(connectionName) — Method in interface phi.interfaces.IDatabase | |
| Retrieve an connection information. | |
| reverseTree(tree) — Static method in class edu.stanford.covertlab.analysis.HierarchicalClustering | |
| rgbToHex(r, g, b) — Static method in class edu.stanford.covertlab.util.ColorUtils | |
| rollOutHandler(evt) — Method in class edu.stanford.covertlab.controls.ToolBarButton | |
| rollOutHandler(evt) — Method in class edu.stanford.covertlab.controls.ToolBarCanvasButton | |
| rollOverHandler(evt) — Method in class edu.stanford.covertlab.controls.ToolBarButton | |
| rollOverHandler(evt) — Method in class edu.stanford.covertlab.controls.ToolBarCanvasButton | |
| rotateScalePoints(graphicPoints, scale, rotation) — Static method in class edu.stanford.covertlab.util.GraphicPointUtils | |
| rows — Property in class edu.stanford.covertlab.graphics.renderablerepeater.ColorGrid | |
| 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 | |