| 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 | |
| pairwiseDistance(vector1, vector2, metric, p) — Static method in class edu.stanford.covertlab.analysis.HierarchicalClustering | |
| pairwise distance | |
| parabolaFocusPoint — Property in class flash.geom.Bezier | |
| parabolaVertex — Property in class flash.geom.Bezier | |
| Calculates and returns time-iterator of top of the parabola. | |
| ParallelogramShape — Class in package edu.stanford.covertlab.graphics.shape | |
| Draws a parallelogram. | |
| ParallelogramShape(size, strokeColor, fillColor, theta) — Constructor in class edu.stanford.covertlab.graphics.shape.ParallelogramShape | |
| PassTransmembraneReceptorShape — Class in package edu.stanford.covertlab.graphics.shape | |
| Draws a 7-pass transmembrane receptor. | |
| PassTransmembraneReceptorShape(size, strokeColor, fillColor) — Constructor in class edu.stanford.covertlab.graphics.shape.PassTransmembraneReceptorShape | |
| _password — Property in class phi.db.ConnectionData | |
| password — Property in class phi.db.ConnectionData | |
| paste(offset) — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| pasteEnabled — Property in class edu.stanford.covertlab.diagram.core.Diagram | |
| pathData — Property in class edu.stanford.covertlab.diagram.core.Edge | |
| pathway — Property in class edu.stanford.covertlab.service.KEGG | |
| pathway — Property in class edu.stanford.covertlab.service.Reactome | |
| pathways — Property in class edu.stanford.covertlab.service.KEGG | |
| pathways — Property in class edu.stanford.covertlab.service.Reactome | |
| pauseAnimation() — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| PDFRenderer — Class in package edu.stanford.covertlab.graphics.renderer | |
| Generates pdf with vector graphic illustrating of a Degrafa surface. | |
| PDFRenderer() — Constructor in class edu.stanford.covertlab.graphics.renderer.PDFRenderer | |
| permissions — Property in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager | |
| phi.db — Package | |
| phi.interfaces — Package | |
| phospholipidHeadSize — Property in class edu.stanford.covertlab.graphics.renderablerepeater.MembranePhospholipids | |
| phospholipidLayers — Property in class edu.stanford.covertlab.graphics.renderablerepeater.MembranePhospholipids | |
| phospholipidTailGap — Property in class edu.stanford.covertlab.graphics.renderablerepeater.MembranePhospholipids | |
| pi — Property in class edu.stanford.covertlab.manager.UserManager | |
| playAnimation() — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| playPauseAnimation() — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| PNGRenderer — Class in package edu.stanford.covertlab.graphics.renderer | |
| Generates a png image of a UIComponent. | |
| PNGRenderer() — Constructor in class edu.stanford.covertlab.graphics.renderer.PNGRenderer | |
| PolygonShapeBase — Class in package edu.stanford.covertlab.graphics.shape | |
| Base class for convex polygon shapes. | |
| PolygonShapeBase(size, points, strokeColor, fillColor, theta) — Constructor in class edu.stanford.covertlab.graphics.shape.PolygonShapeBase | |
| populationAxis — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager | |
| poreAlpha — Property in class edu.stanford.covertlab.diagram.core.Edge | |
| poreFillColor — Property in class edu.stanford.covertlab.diagram.core.Diagram | |
| poreFillColor — Property in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager | |
| PoreShape — Class in package edu.stanford.covertlab.graphics.shape | |
| Draws a pore. | |
| PoreShape(size, strokeColor, fillColor) — Constructor in class edu.stanford.covertlab.graphics.shape.PoreShape | |
| poreStrokeColor — Property in class edu.stanford.covertlab.diagram.core.Diagram | |
| poreStrokeColor — Property in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager | |
| port(theta, sense) — Method in class edu.stanford.covertlab.graphics.shape.CentrosomeShape | |
| port(theta, sense) — Method in class edu.stanford.covertlab.graphics.shape.CircleShape | |
| port(theta, sense) — Method in class edu.stanford.covertlab.graphics.shape.EllipseShape | |
| port(theta, sense) — Method in class edu.stanford.covertlab.graphics.shape.IgShape | |
| port(theta, sense) — Method in class edu.stanford.covertlab.graphics.shape.MitochondrionShape | |
| port(theta, sense) — Method in class edu.stanford.covertlab.graphics.shape.PolygonShapeBase | |
| port(theta, sense) — Method in class edu.stanford.covertlab.graphics.shape.RectangleShape | |
| port(theta, sense) — Method in class edu.stanford.covertlab.graphics.shape.ShapeBase | |
| port(theta, sense) — Method in class edu.stanford.covertlab.graphics.shape.YReceptorShape | |
| POSITION_BOTTOM — Constant static property in class edu.stanford.covertlab.diagram.core.CompartmentBase | |
| POSITION_MIDDLE — Constant static property in class edu.stanford.covertlab.diagram.core.CompartmentBase | |
| POSITION_ONLY — Constant static property in class edu.stanford.covertlab.diagram.core.CompartmentBase | |
| POSITION_TOP — Constant static property in class edu.stanford.covertlab.diagram.core.CompartmentBase | |
| PRECISION — Constant static property in class flash.geom.Bezier | |
| PRECISION — Constant property in class flash.geom.Line | |
| PRECISION — Constant static property in class flash.math.Equations | |
| preDraw() — Method in class edu.stanford.covertlab.graphics.renderablerepeater.ColorBar | |
| preDraw() — Method in class edu.stanford.covertlab.graphics.renderablerepeater.ColorGrid | |
| preDraw() — Method in class edu.stanford.covertlab.graphics.renderablerepeater.MembranePhospholipids | |
| prefix2Infix(prefix) — Static method in class edu.stanford.covertlab.util.MathML | |
| prefix2MathML(prefix, numberProperties) — Static method in class edu.stanford.covertlab.util.MathML | |
| preloader — Property in class edu.stanford.covertlab.networkanalyzer.preloader.Preloader | |
| Preloader — Class in package edu.stanford.covertlab.networkanalyzer.preloader | |
| Application preloader. | |
| Preloader() — Constructor in class edu.stanford.covertlab.networkanalyzer.preloader.Preloader | |
| preview — Property in class edu.stanford.covertlab.service.NetworkAnalyzer | |
| previewSource(pathway) — Method in class edu.stanford.covertlab.networkanalyzer.window.ImportNetworkWindow | |
| preview source | |
| previewSource(pathway) — Method in class edu.stanford.covertlab.service.KEGG | |
| previewSource(pathway) — Method in class edu.stanford.covertlab.service.Reactome | |
| print() — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| print(image, bounds) — Static method in class edu.stanford.covertlab.graphics.printer.Printer | |
| BUG: node labels print with white background text in vector print mode; this is not a problem in bitmap printing mode; perhaps we want to build a sprite specifically for printing (and png, jpeg rendering) which doesn't contain degrafa raster text and will display at higher quality in vector mode; additionally we can't use degrafa GraphicText because apparently it can't be created programmatically with actionscript, only declaratively in MXML. | |
| print() — Method in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager | |
| printing | |
| Printer — Class in package edu.stanford.covertlab.graphics.printer | |
| Creates flash print job from canvas containing Degrafa surfaces. | |
| printf(raw, ... rest) — Package function in br.com.stimuli.string | |
| Creates a string with variable substitutions. | |
| printTree(tree) — Static method in class edu.stanford.covertlab.analysis.HierarchicalClustering | |
| process() — Method in class org.gif.encoder.NeuQuant | |
| publicstatus — Property in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager | |
| 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 | |