| 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 | |
| saveAsNetwork(name, description, publicstatus) — Method in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager | |
| saveAsNetwork(userid, name, description, publicstatus, width, height, showPores, poreFillColor, poreStrokeColor, membraneHeight, membraneCurvature, minCompartmentHeight, ranksep, nodesep, animationFrameRate, maxAnimationLoops, exportShowBiomoleculeSelectedHandles, exportColorBiomoleculesByValue, exportAnimationFrameRate, exportMaxAnimationLoops) — Method in class edu.stanford.covertlab.service.NetworkAnalyzer | |
| SAVE_AS_NETWORK — Constant static property in class edu.stanford.covertlab.service.NetworkAnalyzer | |
| saveAsNetworkQueryHandler(event) — Method in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager | |
| saveAsNetworkWindow — Property in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager | |
| SaveAsNetworkWindow — Class in package edu.stanford.covertlab.networkanalyzer.window | |
| PopUp window allows the user to save the current network to the database. | |
| SaveAsNetworkWindow(application, networkManager:edu.stanford.covertlab.networkanalyzer.manager:NetworkManager) — Constructor in class edu.stanford.covertlab.networkanalyzer.window.SaveAsNetworkWindow | |
| saveNetwork() — Method in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager | |
| save network | |
| saveNetworkProperties(network, permissions) — Method in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager | |
| edit network properties | |
| saveNetworkProperties(networkid, name, description, publicStatus, networkPermissions, permissions) — Method in class edu.stanford.covertlab.service.NetworkAnalyzer | |
| SAVE_NETWORK_PROPERTIES — Constant static property in class edu.stanford.covertlab.service.NetworkAnalyzer | |
| saveUser() — Method in class edu.stanford.covertlab.manager.UserManager | |
| save user profile to database | |
| SBML — Class in package 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. | |
| scale — Property in class edu.stanford.covertlab.chart.ColorScale | |
| scale(colormap, value) — Static method in class edu.stanford.covertlab.colormap.Colormap | |
| SCALE_ARCSINH — Constant static property in class edu.stanford.covertlab.chart.Chart | |
| SCALE_LINEAR — Constant static property in class edu.stanford.covertlab.chart.Chart | |
| scales | |
| SCALE_LOG — Constant static property in class edu.stanford.covertlab.chart.Chart | |
| SELECT — Constant static property in class phi.db.Query | |
| selectAllBiomolecules() — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| selectBiomolecule(biomolecule:edu.stanford.covertlab.diagram.core:Biomolecule, control, shift) — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| selected — Property in class edu.stanford.covertlab.controls.ThumbnailTileListItemRenderer | |
| selected — Property in class edu.stanford.covertlab.diagram.core.Biomolecule | |
| _selected — Property in class edu.stanford.covertlab.diagram.core.CompartmentHotspot | |
| selected — Property in class edu.stanford.covertlab.diagram.core.CompartmentHotspot | |
| select/highlight | |
| selectedIndex — Property in class edu.stanford.covertlab.controls.ThumbnailTileList | |
| selectedItem — Property in class edu.stanford.covertlab.controls.ThumbnailTileList | |
| selectExperiment(experiment) — Method in class edu.stanford.covertlab.networkanalyzer.window.ManageExperimentsWindow | |
| SelectHandles — Class in package edu.stanford.covertlab.graphics | |
| Displays select handles (dashed lines, circles at verticles, squares at midpoints of segments) for a geometry group. | |
| SelectHandles(size, fillColor, strokeColor) — Constructor in class edu.stanford.covertlab.graphics.SelectHandles | |
| selectItem(item, shiftKey, ctrlKey, transition) — Method in class edu.stanford.covertlab.controls.ThumbnailTileList | |
| sense — Property in class edu.stanford.covertlab.diagram.core.Edge | |
| setAxes(channelAxis, conditionAxis, dosageAxis, individualAxis, populationAxis, timepointAxis, biomoleculeAxisControl, animationAxisControl, comparisonXAxisControl, comparisonYAxisControl, statistic, equation, dynamicRange, colormap, clusterBiomoleculeAxis, clusterAnimationAxis, clusterComparisonXAxis, clusterComparisonYAxis, optimalLeafOrder, distanceMetric, linkage) — Method in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager | |
| setBiomoleculeProperties(compartment:edu.stanford.covertlab.diagram.core:CompartmentBase, biomoleculeStyle:edu.stanford.covertlab.diagram.core:BiomoleculeStyle, biomoleculeX, biomoleculeY) — Method in class edu.stanford.covertlab.diagram.window.EditBiomoleculeWindow | |
| setDefaultConnection(name) — Method in class phi.db.Database | |
| Set a connection as a default | |
| setDefaultConnection(name) — Method in interface phi.interfaces.IDatabase | |
| Set a connection as a default | |
| setDelay(ms) — Method in class org.gif.encoder.GIFEncoder | |
| Sets the delay time between each frame, or changes it for subsequent frames (applies to last frame added) int delay time in milliseconds | |
| setDispose(code) — Method in class org.gif.encoder.GIFEncoder | |
| Sets the GIF frame disposal code for the last added frame and any subsequent frames. | |
| setFrameRate(fps) — Method in class org.gif.encoder.GIFEncoder | |
| Sets frame rate in frames per second. | |
| setLastUserActivity(event) — Method in class edu.stanford.covertlab.manager.UserManager | |
| time since last user activity | |
| setPoint(time, x, y) — Method in class flash.geom.Bezier | |
Изменяет кривую таким образом, что заданная параметром time точка кривой Pt,
будет находиться в заданных параметрами x и y координатах.Если один из параметров x или y не задан,
то точка Pt не изменит значение соответствующей координаты. |
|
| setPoint(time, x, y) — Method in interface flash.geom.IParametric | |
| Change object, that point with given interator apply coordinates, definite by parameters. | |
| setPoint(time, x, y) — Method in class flash.geom.Line | |
Change position of point end,
that point Ptime take coordinates,
given by parameters x and y. |
|
| setQuality(quality) — Method in class org.gif.encoder.GIFEncoder | |
| Sets quality of color quantization (conversion of images to the maximum 256 colors allowed by the GIF specification). | |
| setRepeat(iter) — Method in class org.gif.encoder.GIFEncoder | |
| Sets the number of times the set of GIF frames should be played. | |
| setTransparent(c) — Method in class org.gif.encoder.GIFEncoder | |
| Sets the transparent color for the last added frame and any subsequent frames. | |
| setupExperimentAssociations(experimentId, channels) — Method in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager | |
| setupExperimentPerturbations(experimentId, conditions) — Method in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager | |
| setupExperimentsMenu() — Method in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager | |
| experiments menu in main menu | |
| setZoomLevel(value) — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| shape — Property in class edu.stanford.covertlab.diagram.core.CompartmentBase | |
| ShapeBase — Class in package edu.stanford.covertlab.graphics.shape | |
| Base class for shapes. | |
| ShapeBase(size, strokeColor, fillColor) — Constructor in class edu.stanford.covertlab.graphics.shape.ShapeBase | |
| shapeGeometryGroup — Property in class edu.stanford.covertlab.diagram.core.CompartmentBase | |
| ShapeTest — Class in package edu.stanford.covertlab.graphics.shape | |
| shortCut — Property in class com.rphelan.controls.menuClasses.AcceleratorMenuItemRenderer | |
| showPores — Property in class edu.stanford.covertlab.diagram.core.Diagram | |
| showPores — Property in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager | |
| SimpleControlBar — Class in package edu.stanford.covertlab.diagram.toolbar | |
| Simplified control toolbar for viewer. | |
| SimpleControlBar(diagram:edu.stanford.covertlab.diagram.core:Diagram) — Constructor in class edu.stanford.covertlab.diagram.toolbar.SimpleControlBar | |
| singleLinkage(distance, cluster1, cluster2) — Static method in class edu.stanford.covertlab.analysis.HierarchicalClustering | |
| size — Property in class edu.stanford.covertlab.graphics.decorators.DashedLineCircleVertexDecorator | |
| size — Property in class edu.stanford.covertlab.graphics.shape.ShapeBase | |
| SIZE — Constant static property in class edu.stanford.covertlab.diagram.core.Biomolecule | |
| snapBiomolecule(x, y) — Method in class edu.stanford.covertlab.diagram.core.Compartment | |
| snap biomolecules | |
| snapBiomolecule(x, y) — Method in class edu.stanford.covertlab.diagram.core.Membrane | |
| snap biomolecules | |
| snapToCompartment(x, y) — Method in class edu.stanford.covertlab.diagram.core.Biomolecule | |
| _solidColor — Property in class edu.stanford.covertlab.graphics.shape.ShapeBase | |
| solidColor — Property in class edu.stanford.covertlab.graphics.shape.ShapeBase | |
| solveCubicEquation(A, B, C, D) — Static method in class flash.math.Equations | |
| Функция для решения кубического уравнения, записанного в форме ax^3 + bx^2 + cx + d = 0 | |
| solveEquation(A, B, C, D, E) — Static method in class flash.math.Equations | |
| Универсальная функция для решения уравнений c одним неизвестным. | |
| solveLinearEquation(A, B) — Static method in class flash.math.Equations | |
| Функция для решения линейного уравнения, записанного в форме ax + b = 0 | |
| solveQuadraticEquation(A, B, C) — Static method in class flash.math.Equations | |
| Функция для решения квадратичного уравнения, записанного в форме ax^2 + bx + c = 0 | |
| solveQuarticEquation(A, B, C, D, E) — Static method in class flash.math.Equations | |
| Функция для решения уравнения четвертой степени, записанного в форме ax^4 + bx^3 + cx^2 + dx + e = 0 | |
| sortBiomolecules() — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| sortBiomoleculeStyles() — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| SOURCE — Constant static property in class edu.stanford.covertlab.service.CytoBank | |
| SOURCE — Constant static property in class edu.stanford.covertlab.service.KEGG | |
| SOURCE — Constant static property in class edu.stanford.covertlab.service.NetworkAnalyzer | |
| SOURCE — Constant static property in class edu.stanford.covertlab.service.Reactome | |
| SOURCE — Constant static property in class phi.db.ConnectionData | |
| start — Property in class flash.geom.Bezier | |
| Initial anchor point of Bezier curve. | |
| start — Property in interface flash.geom.IParametric | |
| First control point of figure | |
| __start — Property in class flash.geom.Line | |
| start — Property in class flash.geom.Line | |
| First anchor point of piece of line. | |
| start() — Method in class org.gif.encoder.GIFEncoder | |
| Initiates GIF file creation on the given stream. | |
| START_LOOP — Constant static property in class edu.stanford.covertlab.diagram.event.DiagramEvent | |
| startPoint — Property in class flash.geom.Bezier | |
| startQuery — Event in class phi.db.Query | |
| Dispatched befor starting execute a SQL statement. | |
| statistic — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager | |
| STATISTICS — Constant static property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager | |
| stopAnimation() — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| stopAnimationTween() — Method in class edu.stanford.covertlab.diagram.core.Diagram | |
| stream — Property in class org.gif.encoder.GIFEncoder | |
| retrieves the GIF stream | |
| stretchBiomolecules(deltaX, deltaY, deltaW, deltaH) — Method in class edu.stanford.covertlab.diagram.core.Compartment | |
| biomolecules and edges | |
| stretchBiomolecules(deltaX, deltaY, deltaW, deltaH) — Method in class edu.stanford.covertlab.diagram.core.Membrane | |
| biomolecules and edges | |
| strokeColor — Property in class edu.stanford.covertlab.graphics.decorators.DashedLineCircleVertexDecorator | |
| _strokeColor — Property in class edu.stanford.covertlab.graphics.shape.ShapeBase | |
| strokeColor — Property in class edu.stanford.covertlab.graphics.shape.ShapeBase | |
| strokeStop_color — Property in class edu.stanford.covertlab.diagram.core.CompartmentBase | |
| strokeStop_white — Property in class edu.stanford.covertlab.diagram.core.CompartmentBase | |
| stylebar — Property in class edu.stanford.covertlab.diagram.toolbar.DiagramToolBarDocker | |
| StylesPanel — Class in package edu.stanford.covertlab.diagram.panel | |
| Form-based user interface for creating, editing, and deleting biomolecule styles. | |
| StylesPanel() — Constructor in class edu.stanford.covertlab.diagram.panel.StylesPanel | |
| SupSubDataGridItemRenderer — Class in package edu.stanford.covertlab.controls | |
| DataGridItemRender which supports HTML-like text markup. | |
| SupSubDataGridItemRenderer() — Constructor in class edu.stanford.covertlab.controls.SupSubDataGridItemRenderer | |
| SupSubRasterText — Class in package edu.stanford.covertlab.graphics | |
| Provides support for superscript, subscript, and Greek characters within Degrafa. | |
| SupSubRasterText(text, fontSize) — Constructor in class edu.stanford.covertlab.graphics.SupSubRasterText | |
| SVGRasterizer — Class in package edu.stanford.covertlab.graphics.rasterizer | |
| Uses Inkscape (via webservice) to convert a canvas with Degrafa surfaces to png, ps, eps, or pdf. | |
| SVGRasterizer() — Constructor in class edu.stanford.covertlab.graphics.rasterizer.SVGRasterizer | |
| SVGRenderer — Class in package edu.stanford.covertlab.graphics.renderer | |
| Translates canvas with Degrafa surfaces to SVG. | |
| SVGRenderer() — Constructor in class edu.stanford.covertlab.graphics.renderer.SVGRenderer | |
| 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 | |