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d2h(d) — Static method in class edu.stanford.covertlab.util.ColorUtils
DashedLineCircleVertexDecorator — Class in package edu.stanford.covertlab.graphics.decorators
	Extension of SVG dashed line decorator which adds circles at vertices squares at midpoints of line and curve segments
DashedLineCircleVertexDecorator(size, strokeColor, fillColor) — Constructor in class edu.stanford.covertlab.graphics.decorators.DashedLineCircleVertexDecorator
data — Property in class edu.stanford.covertlab.controls.SupSubDataGridItemRenderer
data — Property in class edu.stanford.covertlab.diagram.history.HistoryAction
data — Property in class edu.stanford.covertlab.networkanalyzer.window.ImportNetworkWindow_ThumbnailTileListItemRenderer
data — Property in class edu.stanford.covertlab.networkanalyzer.window.OpenNetworkWindow_ThumbnailTileListItemRenderer
database — Property in class phi.db.Query
database — Property in interface phi.interfaces.IQuery
Database — Class in package phi.db
	A Singleton IDatabase implementation.
Database() — Constructor in class phi.db.Database
	Constructor.
_db — Property in class phi.db.ConnectionData
db — Property in class phi.db.ConnectionData
decorators — Property in class edu.stanford.covertlab.graphics.SelectHandles
DELETE — Constant static property in class phi.db.Query
deleteNetwork(network) — Method in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager
	delete network
deleteNetwork(networkid) — Method in class edu.stanford.covertlab.service.NetworkAnalyzer
DELETE_NETWORK — Constant static property in class edu.stanford.covertlab.service.NetworkAnalyzer
description — Property in class edu.stanford.covertlab.networkanalyzer.manager.NetworkManager
DESTINATION — Constant static property in class edu.stanford.covertlab.service.CytoBank
DESTINATION — Constant static property in class edu.stanford.covertlab.service.KEGG
DESTINATION — Constant static property in class edu.stanford.covertlab.service.NetworkAnalyzer
DESTINATION — Constant static property in class edu.stanford.covertlab.service.Reactome
DESTINATION — Constant static property in class phi.db.ConnectionData
determinePosition() — Method in class edu.stanford.covertlab.diagram.core.CompartmentBase
	display
diagram — Property in class edu.stanford.covertlab.diagram.core.Biomolecule
diagram — Property in class edu.stanford.covertlab.diagram.core.CompartmentBase
diagram — Property in class edu.stanford.covertlab.diagram.panel.AdvancedOptionsPanel
diagram — Property in class edu.stanford.covertlab.diagram.panel.BiomoleculesPanel
diagram — Property in class edu.stanford.covertlab.diagram.panel.CompartmentsPanel
diagram — Property in class edu.stanford.covertlab.diagram.panel.StylesPanel
diagram — Property in class edu.stanford.covertlab.diagram.toolbar.DiagramToolBarDocker
diagram — Property in class edu.stanford.covertlab.diagram.toolbar.ToolBar
diagram — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager
Diagram — Class in package edu.stanford.covertlab.diagram.core
	Main biological network diagram class.
Diagram() — Constructor in class edu.stanford.covertlab.diagram.core.Diagram
DiagramEvent — Class in package edu.stanford.covertlab.diagram.event
	Diagram event class.
DiagramEvent(type) — Constructor in class edu.stanford.covertlab.diagram.event.DiagramEvent
diagramHeight — Property in class edu.stanford.covertlab.diagram.core.Diagram
DiagramToolBarDocker — Class in package edu.stanford.covertlab.diagram.toolbar
	Docker for dockable toolbars -- animation, control, and new biomlecule, biomolecules style, and compartment toolbars.
DiagramToolBarDocker(diagram:edu.stanford.covertlab.diagram.core:Diagram) — Constructor in class edu.stanford.covertlab.diagram.toolbar.DiagramToolBarDocker
diagramWidth — Property in class edu.stanford.covertlab.diagram.core.Diagram
dim — Property in class edu.stanford.covertlab.diagram.core.Biomolecule
dim — Property in class edu.stanford.covertlab.diagram.core.Compartment
_dim — Property in class edu.stanford.covertlab.diagram.core.CompartmentBase
dim — Property in class edu.stanford.covertlab.diagram.core.CompartmentBase
dim — Property in class edu.stanford.covertlab.diagram.core.Edge
dim — Property in class edu.stanford.covertlab.diagram.core.Membrane
	setters/getters
dimComponents(dim) — Method in class edu.stanford.covertlab.diagram.core.Diagram
DIMENSIONS — Constant static property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager
dimGrey — Constant static property in class edu.stanford.covertlab.diagram.core.Diagram
disconnect(name) — Method in class phi.db.Database
	Disconnect from a previous connection
disconnect(name) — Method in interface phi.interfaces.IDatabase
	Disconnect from a previous connection
distanceMetric — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager
DISTANCE_METRIC_CHEBYCHEV — Constant static property in class edu.stanford.covertlab.analysis.HierarchicalClustering
DISTANCE_METRIC_CITYBLOCK — Constant static property in class edu.stanford.covertlab.analysis.HierarchicalClustering
DISTANCE_METRIC_CORRELATION — Constant static property in class edu.stanford.covertlab.analysis.HierarchicalClustering
DISTANCE_METRIC_COSINE — Constant static property in class edu.stanford.covertlab.analysis.HierarchicalClustering
DISTANCE_METRIC_EUCLIDEAN — Constant static property in class edu.stanford.covertlab.analysis.HierarchicalClustering
DISTANCE_METRIC_HAMMING — Constant static property in class edu.stanford.covertlab.analysis.HierarchicalClustering
DISTANCE_METRIC_JACCARD — Constant static property in class edu.stanford.covertlab.analysis.HierarchicalClustering
DISTANCE_METRIC_MINKOWSKI — Constant static property in class edu.stanford.covertlab.analysis.HierarchicalClustering
DISTANCE_METRICS — Constant static property in class edu.stanford.covertlab.analysis.HierarchicalClustering
distribution — Property in class edu.stanford.covertlab.service.CytoBank
DNAShape — Class in package edu.stanford.covertlab.graphics.shape
	Draws a double helix.
DNAShape(size, strokeColor, fillColor) — Constructor in class edu.stanford.covertlab.graphics.shape.DNAShape
dosageAxis — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager
dotCode(scale) — Method in class edu.stanford.covertlab.diagram.core.Biomolecule
	dot code
dotCode(scale) — Method in class edu.stanford.covertlab.diagram.core.Compartment
	export
dotCode(scale, metaData) — Method in class edu.stanford.covertlab.diagram.core.Diagram
dotCode(scale) — Method in class edu.stanford.covertlab.diagram.core.Edge
	dot code
dotCode(scale) — Method in class edu.stanford.covertlab.diagram.core.Membrane
	export
dragDropHandler(event) — Method in class edu.stanford.covertlab.diagram.core.CompartmentHotspot
dragEnterHandler(event) — Method in class edu.stanford.covertlab.diagram.core.CompartmentHotspot
	dragging
dragExitHandler(event) — Method in class edu.stanford.covertlab.diagram.core.CompartmentHotspot
draw(graphics, rc) — Method in class edu.stanford.covertlab.graphics.renderablerepeater.ColorBar
	Begins the draw phase for geometry objects.
draw(graphics, rc) — Method in class edu.stanford.covertlab.graphics.renderablerepeater.ColorGrid
	Begins the draw phase for geometry objects.
draw(graphics, rc) — Method in class edu.stanford.covertlab.graphics.renderablerepeater.MembranePhospholipids
	Begins the draw phase for geometry objects.
drawCompartment() — Method in class edu.stanford.covertlab.diagram.core.CompartmentBase
dynamicRange — Property in class edu.stanford.covertlab.networkanalyzer.manager.ExperimentManager
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