Name | Description | Type | Package | Framework |
AboutDialog | About page for web service clients or other plugins. | Class | cytoscape.util.swing | CytoScape |
|
Abs | | Class | org.cytoscape.equations.builtins | CytoScape |
|
AbstractCalculator | | Class | cytoscape.visual.calculators | CytoScape |
|
AbstractCellEditor | | Class | cytoscape.util.swing | CytoScape |
|
AbstractCommandHandler | This abstract class provides a convenient (but not necessary) base class for writing CyCommandHandlers. | Class | cytoscape.command | CytoScape |
|
AbstractDCustomGraphics | | Class | cytoscape.visual.customgraphic.impl | CytoScape |
|
AbstractFunction | | Class | org.cytoscape.equations | CytoScape |
|
AbstractGraphReader | | Class | cytoscape.data.readers | CytoScape |
|
AbstractLayout | The AbstractLayout provides nice starting point for Layouts written for Cytoscape. | Class | cytoscape.layout | CytoScape |
|
AbstractMapping | | Class | cytoscape.visual.mappings | CytoScape |
|
AbstractParserControl | Class to inherit from so when in future when new controls are added clients will no have to implement them. | Class | org.apache.commons.cli.avalon | CytoScape |
|
AbstractScaler | Used to scale a list of values to [a,b]Constructor SummaryAbstractScaler() | Class | cytoscape.util | CytoScape |
|
AbstractTreeTableModel | | Class | cytoscape.util.swing | CytoScape |
|
AbstractVisualProperty | | Class | cytoscape.visual.properties | CytoScape |
|
ACos | | Class | org.cytoscape.equations.builtins | CytoScape |
|
AddRemoveTest | | Class | fing.model.test | CytoScape |
|
Aliases | Simpler version of Thesaurus. | Class | cytoscape.data.synonyms | CytoScape |
|
AliasType | enum AliasTypeextends Enum Aliases are always belongs to one of these types. | Class | cytoscape.data.synonyms | CytoScape |
|
AlignHorizontalAction | See Also:Serialized FormFields inherited from class javax. | Class | cytoscape.actions | CytoScape |
|
AlignVerticalAction | See Also:Serialized FormFields inherited from class javax. | Class | cytoscape.actions | CytoScape |
|
AllGraphPerspectiveMethodsTest | | Class | fing.model.test | CytoScape |
|
AllRootGraphMethodsTest | | Class | fing.model.test | CytoScape |
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AlphabeticalSelectionAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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AlreadySelectedException | Thrown when more than one option in an option groupAuthor:John Keyes ( john at integralsource. | Class | org.apache.commons.cli | CytoScape |
|
And | | Class | org.cytoscape.equations.builtins | CytoScape |
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AnimatedLayoutAction | See Also:Serialized FormFields inherited from class javax. | Class | cytoscape.actions | CytoScape |
|
Annotation | Store any number of classifications for named entities, each of which is from a specified species, and where the classifications are all terms from an | Class | cytoscape.data.annotation | CytoScape |
|
AnnotationDescription | Distinguish among different ontologies, by curator and type. | Class | cytoscape.data.annotation | CytoScape |
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AnnotationFlatFileReader | | Class | cytoscape.data.annotation.readers | CytoScape |
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AnnotationXmlReader | | Class | cytoscape.data.annotation.readers | CytoScape |
|
Appearance | A class that holds the appearance information for NodeViews and EdgeViews. | Class | cytoscape.visual | CytoScape |
|
ApplyLayoutAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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ApplyVisualStyleAction | Apply Visual Style for a set of selected networks. | Class | cytoscape.actions | CytoScape |
|
ArbitraryGraphicsCanvas | This class extends cytoscape. | Class | ding.view | CytoScape |
|
ArgDescriptor | A class describing a function argument. | Class | org.cytoscape.equations | CytoScape |
|
ArgType | enum ArgTypeextends EnumAn enum specifying a function argument type. | Class | org.cytoscape.equations | CytoScape |
|
ARowanBugTest | | Class | fing.model.test | CytoScape |
|
ArrangeAction | | Class | cytoscape.actions | CytoScape |
|
ArrayIntEnumerator | A utility class which conveniently converts an array of integers into an IntEnumerator (an enumeration of integers). | Class | cytoscape.util.intr | CytoScape |
|
ArrayIntIterator | A utility class which conveniently converts an array of integers into an IntIterator (an iteration of integers). | Class | cytoscape.util.intr | CytoScape |
|
ArrayTestMethod1 | | Class | cytoscape.geom.rtree.test | CytoScape |
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ArrayTestMethod2 | | Class | cytoscape.geom.rtree.test | CytoScape |
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ArrayTestMethod3 | | Class | cytoscape.geom.rtree.test | CytoScape |
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ArrayTestMethod4 | | Class | cytoscape.geom.rtree.test | CytoScape |
|
Arrow | | Interface | cytoscape.render.immed.arrow | CytoScape |
|
Arrow | This class is a replacement for the yFiles Arrow class. | Class | cytoscape.visual | CytoScape |
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ArrowheadArrow | | Class | cytoscape.render.immed.arrow | CytoScape |
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ArrowIcon | Icon for arrow shape. | Class | cytoscape.visual.ui.icon | CytoScape |
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ArrowParser | Parses a String into a yFiles Arrow object. | Class | cytoscape.visual.parsers | CytoScape |
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ArrowShape | enum ArrowShapeextends EnumDefines arrow shapes. | Class | cytoscape.visual | CytoScape |
|
ArrowShapeParser | | Class | cytoscape.visual.parsers | CytoScape |
|
ASin | | Class | org.cytoscape.equations.builtins | CytoScape |
|
ATan2 | | Class | org.cytoscape.equations.builtins | CytoScape |
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AttribTopoGraphNode | Represents a node in a topological graph. | Class | cytoscape.data | CytoScape |
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Attribute | Java class for anonymous complex type. | Class | cytoscape.bookmarks | CytoScape |
|
AttributeFilter | Interface for defining CyEdge-based filters used for determining which Edges should be used for a particular operation, such as | Interface | cytoscape.data | CytoScape |
|
AttributeImportPanel | General GUI component for importing attributes. | Class | cytoscape.util.swing | CytoScape |
|
AttributeImportQuery | | Class | cytoscape.data.webservice | CytoScape |
|
AttributeSaverDialog | Dialog box to save various attributes. | Class | cytoscape.data | CytoScape |
|
AttributeValueVisitor | Interface for defining attribute value visitors--operations to perform on each attribute value using CyAttributesUtils. | Interface | cytoscape.data | CytoScape |
|
Average | | Class | org.cytoscape.equations.builtins | CytoScape |
|
BackgroundColorAction | Prompts User for New Background Color. | Class | cytoscape.actions | CytoScape |
|
BackwardSlashStroke | Nested Class SummaryNested classes/interfaces inherited from class cytoscape. | Class | cytoscape.visual.strokes | CytoScape |
|
BasicCalculator | | Class | cytoscape.visual.calculators | CytoScape |
|
BasicGraphViewHandler | A basic GraphViewHandler that simply reflects GraphPerspective changes on a given GraphView | Class | cytoscape.view | CytoScape |
|
BasicParser | The class BasicParser provides a very simple implementation of the flatten method. | Class | org.apache.commons.cli | CytoScape |
|
BasicQuietRTreeTest | | Class | cytoscape.geom.rtree.test | CytoScape |
|
BelowAndAbovePanel | Drawing and updating below & above values in Gradient Editor. | Class | cytoscape.visual.ui.editors.continuous | CytoScape |
|
Bend | A class that encapsulates the representation of the bend used for a particular EdgeView. | Interface | giny.view | CytoScape |
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BendSelectedEdgesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
BiModalJSplitPane | The BiModalJSplitPane class extends JSplitPane to provide two modes: MODE_SHOW_SPLIT: The split in the split pane appears as it normally | Class | cytoscape.view.cytopanels | CytoScape |
|
BinOpNode | A node in the parse tree representing a binary operator. | Class | org.cytoscape.equations.parse_tree | CytoScape |
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BioDataServer | | Class | cytoscape.data.servers | CytoScape |
|
BioDataServerInterface | | Interface | cytoscape.data.servers | CytoScape |
|
BioDataServerRmi | This is the actual class which implements BioDataServer Methods. | Class | cytoscape.data.servers | CytoScape |
|
BioDataServerUtil | | Class | cytoscape.util | CytoScape |
|
BiologicalProcessAnnotationReader | The purpose of this class is to convert a 'gene_association. | Class | cytoscape.cruft.obo | CytoScape |
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BiologicalProcessAnnotationTester | | Class | cytoscape.cruft.obo.test | CytoScape |
|
BirdsEyeView | | Class | ding.view | CytoScape |
|
BirdsEyeViewAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
BitmapExporter | Bitmap exporter by the ImageIO class. | Class | cytoscape.util.export | CytoScape |
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BitSetPerformance | | Class | cytoscape.util.intr.test | CytoScape |
|
BList | | Class | org.cytoscape.equations.builtins | CytoScape |
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BookmarkAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
BookmarkDialog | | Class | cytoscape.dialogs.preferences | CytoScape |
|
BookmarkReader | | Class | cytoscape.data.readers | CytoScape |
|
Bookmarks | Java class for anonymous complex type. | Class | cytoscape.bookmarks | CytoScape |
|
BookmarksUtil | Utility methods for getting entries in the bookmark object. | Class | cytoscape.util | CytoScape |
|
BooleanConstantNode | A node in the parse tree representing an integer constant. | Class | org.cytoscape.equations.parse_tree | CytoScape |
|
BooleanList | | Class | org.cytoscape.equations | CytoScape |
|
BooleanParser | Parses a String into a Boolean object. | Class | cytoscape.visual.parsers | CytoScape |
|
BoundaryRangeValues | This class defines a data object representing the range values associated with a particular domain value, called a boundary value. | Class | cytoscape.visual.mappings | CytoScape |
|
Bug646Test | | Class | fing.model.test | CytoScape |
|
C2CMappingEditor | Continuous-Continuous mapping editor. | Class | cytoscape.visual.ui.editors.continuous | CytoScape |
|
C2DMappingEditor | Continuous Mapping editor for discrete values, such as Font, Shape, Label Position, etc. | Class | cytoscape.visual.ui.editors.continuous | CytoScape |
|
Calculator | | Interface | cytoscape.visual.calculators | CytoScape |
|
CalculatorCatalog | Stores various types of Calculators from data attributes to an attribute of a specified type. | Class | cytoscape.visual | CytoScape |
|
CalculatorCatalogFactory | This class provides a static method for reading a CalculatorCatalog object from file, using parameters specified in a supplied CytoscapeConfig. | Class | cytoscape.visual | CytoScape |
|
CalculatorFactory | This class provides static factory methods for constructing instances of Calculators as specified by arguments and static methods for getting names | Class | cytoscape.visual.calculators | CytoScape |
|
CalculatorIO | This class defines static methods for reading calculator definitions from a properties object and installing them into a CalculatorCatalog, and for | Class | cytoscape.visual | CytoScape |
|
Category | Java class for anonymous complex type. | Class | cytoscape.bookmarks | CytoScape |
|
Category | enum Categoryextends EnumEnum Constant SummaryANALYSIS | Class | cytoscape.plugin | CytoScape |
|
CellEditorFactory | | Class | cytoscape.visual.ui | CytoScape |
|
CellHeightManager | | Class | cytoscape.visual.ui | CytoScape |
|
CellRendererFactory | | Class | cytoscape.visual.ui | CytoScape |
|
CellularComponentAnnotationReader | The purpose of this class is to convert a 'gene_association. | Class | cytoscape.cruft.obo | CytoScape |
|
CellularComponentAnnotationTester | | Class | cytoscape.cruft.obo.test | CytoScape |
|
CheckBoxFileChooser | | Class | cytoscape.actions | CytoScape |
|
CheckBoxJList | This class is based on CheckBoxJList: from SWING HACKS ISBN: 0-596-00907-0 | Class | cytoscape.util.swing | CytoScape |
|
Child | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
|
CLArgsParser | Parser for command line arguments. | Class | org.apache.commons.cli.avalon | CytoScape |
|
clear | | Class | cytoscape.data.servers | CytoScape |
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CloneGraphInNewWindowAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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CLOption | Basic class describing an instance of option. | Class | org.apache.commons.cli.avalon | CytoScape |
|
CLOptionDescriptor | Basic class describing an type of option. | Class | org.apache.commons.cli.avalon | CytoScape |
|
CLUtil | CLUtil offers basic utility operations for use both internal and external to package. | Class | org.apache.commons.cli.avalon | CytoScape |
|
CodeAndSourceLocation | A node in the parse tree representing a binary operator. | Class | org.cytoscape.equations | CytoScape |
|
ColorConverter | | Class | cytoscape.visual.converter | CytoScape |
|
ColorPaintFactory | | Class | cytoscape.visual.customgraphic.paint | CytoScape |
|
ColorParser | Parses a String into a Color object. | Class | cytoscape.visual.parsers | CytoScape |
|
ColorRangeValueCalculator | | Class | cytoscape.visual.mappings.rangecalculators | CytoScape |
|
ColorScaleTable | | Class | cytoscape.dialogs | CytoScape |
|
ColorUtil | Color utility class to convert Java color object to string and vice versa. | Class | cytoscape.util | CytoScape |
|
ColumnResizer | Automatically resize column based on the objects in the cell. | Class | cytoscape.util.swing | CytoScape |
|
ColumnTypes | enum ColumnTypesextends EnumEnum Constant SummaryEDGES | Class | cytoscape.view | CytoScape |
|
Combin | | Class | org.cytoscape.equations.builtins | CytoScape |
|
CommandLine | Represents list of arguments parsed against a Options descriptor. | Class | org.apache.commons.cli | CytoScape |
|
CommandLineParser | A class that implements the CommandLineParser interface can parse a String array according to the Options specified | Interface | org.apache.commons.cli | CytoScape |
|
Concatenate | | Class | org.cytoscape.equations.builtins | CytoScape |
|
ConsoleLogger | The ConsoleLogger is the default log handler for Cytoscape and does nothing much more than issue messages to System. | Class | cytoscape.logger | CytoScape |
|
ContentChangeListener | | Interface | ding.view | CytoScape |
|
ContiguousArrowStroke | Fields inherited from class cytoscape. | Class | cytoscape.visual.strokes | CytoScape |
|
ContinuousLegend | | Class | cytoscape.visual.mappings.continuous | CytoScape |
|
ContinuousMapping | class. | Class | cytoscape.visual.mappings | CytoScape |
|
ContinuousMappingEditorPanel | Abstract class for all Continuous Mapping Editors. | Class | cytoscape.visual.ui.editors.continuous | CytoScape |
|
ContinuousMappingPoint | Encapsulates a ContinuousMapping Point with a single point value and associated BoundaryRangeValues. | Class | cytoscape.visual.mappings.continuous | CytoScape |
|
ContinuousMappingReader | Reads in ContinuousMapping Properties. | Class | cytoscape.visual.mappings.continuous | CytoScape |
|
ContinuousMappingWriter | Writes out ContinuousMapping Properties. | Class | cytoscape.visual.mappings.continuous | CytoScape |
|
ContinuousRangeCalculator | Calculates the Range for Continuous Mappers. | Class | cytoscape.visual.mappings.continuous | CytoScape |
|
ContinuousTrackRenderer | | Class | cytoscape.visual.ui.editors.continuous | CytoScape |
|
Cos | | Class | org.cytoscape.equations.builtins | CytoScape |
|
Cosh | | Class | org.cytoscape.equations.builtins | CytoScape |
|
Count | | Class | org.cytoscape.equations.builtins | CytoScape |
|
CountedIterator | A java. | Interface | cytoscape.data.attr | CytoScape |
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CreateNetworkViewAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
CreditScreen | | Class | cytoscape.util | CytoScape |
|
CustomGraphic | Represents all the information needed to define a custom graphic for a given NodeView. | Class | cytoscape.render.stateful | CytoScape |
|
CustomGraphicsBrowser | Display list of images available as custom graphicsAuthor:konoSee Also:Serialized Form | Class | cytoscape.visual.customgraphic.ui | CytoScape |
|
CustomGraphicsCellRenderer | Cell renderer for Custom Graphics Browser. | Class | cytoscape.visual.customgraphic.ui | CytoScape |
|
CustomGraphicsCellRenderer | | Class | cytoscape.visual.ui.editors.discrete | CytoScape |
|
CustomGraphicsDetailPanel | | Class | cytoscape.visual.customgraphic.ui | CytoScape |
|
CustomGraphicsManager | | Class | cytoscape.visual.customgraphic | CytoScape |
|
CustomGraphicsManagerDialog | Main UI for managing on-memory library of Custom GraphicsAuthor:konoSee Also:Serialized Form | Class | cytoscape.visual.customgraphic.ui | CytoScape |
|
CustomGraphicsPositionCalculator | | Class | ding.view | CytoScape |
|
CustomGraphicsProperty | | Interface | cytoscape.visual.customgraphic.impl.vector | CytoScape |
|
CustomGraphicsPropertyImpl | | Class | cytoscape.visual.customgraphic | CytoScape |
|
CustomGraphicsRangeValueCalculator | | Class | cytoscape.visual.mappings.rangecalculators | CytoScape |
|
CustomGraphicsRangeValueRenderer | | Interface | cytoscape.visual.mappings | CytoScape |
|
CustomGraphicsUtil | | Class | cytoscape.visual.customgraphic | CytoScape |
|
CustomMapping | User-definable visual mapping. | Interface | cytoscape.visual.mappings | CytoScape |
|
CyAbstractEdit | A small convenience class that can be used to create new edits. | Class | cytoscape.util.undo | CytoScape |
|
CyAttributes | CyAttributes provides access to network, node, and edge attributes within Cytoscape. | Interface | cytoscape.data | CytoScape |
|
CyAttributesImpl | | Class | cytoscape.data | CytoScape |
|
CyAttributesReader | | Class | cytoscape.data.readers | CytoScape |
|
CyAttributesUtils | | Class | cytoscape.data | CytoScape |
|
CyAttributesWriter | CyAttributeWriter extracted from AttributeSaverDialog. | Class | cytoscape.data.writers | CytoScape |
|
CyCollapsiblePanel | The user-triggered collapsable panel containing the component (trigger) in the titled borderSee Also:Serialized Form | Class | cytoscape.util.swing | CytoScape |
|
CyColorCellRenderer | CyColorCellRenderer. | Class | cytoscape.visual.ui.editors.discrete | CytoScape |
|
CyColorChooser | This is an annoying re-implementation of JColorChooser. | Class | cytoscape.util | CytoScape |
|
CyColorPropertyEditor | ColorPropertyEditor. | Class | cytoscape.visual.ui.editors.discrete | CytoScape |
|
CyComboBoxPropertyEditor | ComboBoxPropertyEditor. | Class | cytoscape.visual.ui.editors.discrete | CytoScape |
|
CyCommandException | The CyCommandException is thrown when a CyCommandHandler encounters an exception condition. | Class | cytoscape.command | CytoScape |
|
CyCommandHandler | The CyCommandHandler interface allows a Cytoscape plugin to make it's functions available to other plugins in a loosely-coupled manner (by passing command | Interface | cytoscape.command | CytoScape |
|
CyCommandManager | CyCommandManager is a singleton Cytoscape class that provides a global registry of CyCommands and CyCommandNamespaces. | Class | cytoscape.command | CytoScape |
|
CyCommandNamespace | A CyCommandNamespace represents a reservation for a group of CyCommands. | Interface | cytoscape.command | CytoScape |
|
CyCommandResult | CyCommandResult returns the results from the execution of a command. | Class | cytoscape.command | CytoScape |
|
CyCustomGraphics | | Interface | cytoscape.visual.customgraphic | CytoScape |
|
CyCustomGraphicsEditor | Fields inherited from class com. | Class | cytoscape.visual.ui.editors.discrete | CytoScape |
|
CyCustomGraphicsParser | | Interface | cytoscape.visual.customgraphic | CytoScape |
|
CyCustomGraphicsParserFactory | | Interface | cytoscape.visual.customgraphic | CytoScape |
|
CyCustomGraphicsParserFactoryImpl | | Class | cytoscape.visual.customgraphic.impl | CytoScape |
|
CyCustomGraphicsTableCellRenderer | | Class | cytoscape.visual.customgraphic.ui | CytoScape |
|
CyCustomGraphicsTreeCellRenderer | | Class | cytoscape.visual.customgraphic.ui | CytoScape |
|
CyCustomGraphicsTreeNode | Fields inherited from class org. | Class | cytoscape.visual.customgraphic.ui | CytoScape |
|
CyDesktopManager | | Class | cytoscape.view | CytoScape |
|
CyDoublePropertyEditor | Fields inherited from class com. | Class | cytoscape.visual.ui.editors.discrete | CytoScape |
|
CyEdge | | Class | cytoscape | CytoScape |
|
CyEdgeView | Fields inherited from interface giny. | Interface | cytoscape.view | CytoScape |
|
CyFileFilter | A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about. | Class | cytoscape.util | CytoScape |
|
CyFontPropertyEditor | Fields inherited from class com. | Class | cytoscape.visual.ui.editors.discrete | CytoScape |
|
CyGradientTrackRenderer | | Class | cytoscape.visual.ui.editors.continuous | CytoScape |
|
CyGraphAllLOD | CyGraphAllLOD is the level of detail (LOD) class used for the "Show Graphics Details" menu item. | Class | cytoscape.ding | CytoScape |
|
CyGraphLOD | An instance of this class defines the level of detail that goes into a single rendering of a graph. | Class | cytoscape.ding | CytoScape |
|
CyGroup | The CyGroup interface provides the methods for a group model that maintains the list of nodes belonging to a group, the parent of a particular | Interface | cytoscape.groups | CytoScape |
|
CyGroupChangeListener | The CyGroupChangeListener interface provides a mechanism for plugins that track group-related events to get notified of global group changes (new groups, etc. | Interface | cytoscape.groups | CytoScape |
|
CyGroupImpl | The CyGroup class provides the implementation for a group model that maintains the list of nodes belonging to a group, the parent of a particular | Class | cytoscape.groups | CytoScape |
|
CyGroupManager | The CyGroup class provides the implementation for a group model that maintains the list of nodes belonging to a group, the parent of a particular | Class | cytoscape.groups | CytoScape |
|
CyGroupViewer | The CyGroupViewer interface provides a mechanism for group view implementations to register themselves and get notified of group creation and deletion. | Interface | cytoscape.groups | CytoScape |
|
CyHelpBroker | This class creates the Cytoscape Help Broker for managing the JavaHelp system and help set access | Class | cytoscape.view | CytoScape |
|
CyInitParams | An interface that describes the initialization parameters needed by cytoscape. | Interface | cytoscape.init | CytoScape |
|
CyLayoutAlgorithm | | Interface | cytoscape.layout | CytoScape |
|
CyLayouts | | Class | cytoscape.layout | CytoScape |
|
CyLogger | | Class | cytoscape.logger | CytoScape |
|
CyLogHandler | The CyLogHandler interface must be implemented by log handlers for plugins that wish to handle their own logging. | Interface | cytoscape.logger | CytoScape |
|
CyMain | This is the main startup class for Cytoscape. | Class | cytoscape | CytoScape |
|
CyMenus | Creates the menu and tool bars for a Cytoscape window object. | Class | cytoscape.view | CytoScape |
|
CyNetwork | CyNetwork is the primary class for algorithm writing. | Interface | cytoscape | CytoScape |
|
CyNetworkAdapter | Empty implementation of the CyNetworkListener interface, following the adapter pattern useful for defining anonymous inner classes. | Class | cytoscape | CytoScape |
|
CyNetworkData | | Interface | cytoscape | CytoScape |
|
CyNetworkEvent | Events of this class are fired from a CyNetwork object when something happens to the network. | Class | cytoscape | CytoScape |
|
CyNetworkListener | Interface for listeners that respond to CyNetwork events. | Interface | cytoscape | CytoScape |
|
CyNetworkNaming | | Class | cytoscape.util | CytoScape |
|
CyNetworkTitleChange | Class used for passing along information about the network when the network title has changed (firing an event) | Class | cytoscape | CytoScape |
|
CyNetworkUtilities | This class provides static methods that operate on a CyNetwork to perform various useful tasks. | Class | cytoscape.data | CytoScape |
|
CyNetworkView | CyNetworkView is responsible for actually getting a graph to show up on the screen. | Interface | cytoscape.view | CytoScape |
|
CyNode | | Class | cytoscape | CytoScape |
|
CyNodeView | Fields inherited from interface giny. | Interface | cytoscape.view | CytoScape |
|
CyObjectPositionPropertyEditor | Fields inherited from class com. | Class | cytoscape.visual.ui.editors.discrete | CytoScape |
|
Cysession | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
|
CyStartupListener | arguments passed from file assocations set by install4j for Mac OS. | Class | cytoscape | CytoScape |
|
CyStringPropertyEditor | Fields inherited from class com. | Class | cytoscape.visual.ui.editors.discrete | CytoScape |
|
Cytopanel | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
|
CytoPanel | Interface to a CytoPanel. | Interface | cytoscape.view.cytopanels | CytoScape |
|
CytoPanelAction | | Class | cytoscape.actions | CytoScape |
|
CytoPanelContainer | Interface for Container of CytoPanel Objects. | Interface | cytoscape.view.cytopanels | CytoScape |
|
CytoPanelImp | The CytoPanel class extends JPanel to provide the following functionality: Floating/Docking of Panel. | Class | cytoscape.view.cytopanels | CytoScape |
|
CytoPanelListener | This listener interface provides the mechanism to respond to CytoPanel Events. | Interface | cytoscape.view.cytopanels | CytoScape |
|
CytoPanelName | enum CytoPanelNameextends EnumAn enum that maps names to compass directions. | Class | cytoscape.view.cytopanels | CytoScape |
|
Cytopanels | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
|
CytoPanelState | CytoPanelState Class. | Class | cytoscape.view.cytopanels | CytoScape |
|
CytoPanelUtil | Contains methods to assist with various tasks performed by the CytoPanel API. | Class | cytoscape.view.cytopanels | CytoScape |
|
Cytoscape | This class, Cytoscape is the primary class in the API. | Class | cytoscape | CytoScape |
|
CytoscapeAction | | Class | cytoscape.util | CytoScape |
|
CytoscapeDesktop | The CytoscapeDesktop is the central Window for working with CytoscapeSee Also:Serialized Form | Class | cytoscape.view | CytoScape |
|
CytoscapeFingRootGraph | Fields inherited from interface cytoscape. | Class | cytoscape.giny | CytoScape |
|
CytoscapeInit | Cytoscape Init is responsible for starting Cytoscape in a way that makes The comments below are more hopeful than accurate. | Class | cytoscape | CytoScape |
|
CytoscapeMenuBar | | Class | cytoscape.util | CytoScape |
|
CytoscapeModifiedNetworkManager | CytoscapeModifiedNetworkManager manages the modified state settings for the networks and listens for PropertyChangeEvents. | Class | cytoscape | CytoScape |
|
CytoscapePlugin | A CytoscapePlugin is the new "Global" plugin. | Class | cytoscape.plugin | CytoScape |
|
CytoscapeProgressMonitor | CytoscapeProgressMonitor. | Class | cytoscape.util | CytoScape |
|
CytoscapeRootGraph | | Interface | cytoscape.giny | CytoScape |
|
CytoscapeSessionReader | Reader to load CYtoscape Session file (. | Class | cytoscape.data.readers | CytoScape |
|
CytoscapeSessionWriter | Write session states into files. | Class | cytoscape.data.writers | CytoScape |
|
CytoscapeToolBar | | Class | cytoscape.util | CytoScape |
|
CytoscapeVersion | CytoscapeVersion: identify (and describe) successive versions of cytoscape. | Class | cytoscape | CytoScape |
|
CyUndo | A tiny class for supporting undo in the Cytoscape context. | Class | cytoscape.util.undo | CytoScape |
|
CyWebServiceEvent | Event object used by Web Service Clients and the core. | Class | cytoscape.data.webservice | CytoScape |
|
CyWebServiceEventListener | Listener for Web Service Event handling. | Interface | cytoscape.data.webservice | CytoScape |
|
CyWebServiceEventSupport | | Class | cytoscape.data.webservice | CytoScape |
|
CyWebServiceException | | Class | cytoscape.data.webservice | CytoScape |
|
DashDotStroke | Fields inherited from class java. | Class | cytoscape.visual.strokes | CytoScape |
|
DatabaseSearchResult | | Class | cytoscape.data.webservice | CytoScape |
|
DataSource | Java class for anonymous complex type. | Class | cytoscape.bookmarks | CytoScape |
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DBCrossReferenceReader | Reader for database cross reference file. | Class | cytoscape.data.ontology.readers | CytoScape |
|
DBCrossReferences | Database cress reference. | Class | cytoscape.data.ontology | CytoScape |
|
DBReference | Represents an entry in the database cross reference. | Class | cytoscape.data.ontology | CytoScape |
|
DBXrefKeywords | enum DBXrefKeywordsextends EnumEnum Constant SummaryABBREVIATION | Class | cytoscape.data.ontology.readers | CytoScape |
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DefaultAppearenceBuilder | Dialog for editing default visual property values. | Class | cytoscape.visual.ui | CytoScape |
|
DefaultCyCustomGraphicsParser | | Class | cytoscape.visual.customgraphic | CytoScape |
|
DefaultViewPanel | Panel to show the default properties visually (as graphics). | Class | cytoscape.visual.ui | CytoScape |
|
Degrees | | Class | org.cytoscape.equations.builtins | CytoScape |
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DeleteAction | action for deleting selected Cytoscape nodes and edgesVersion:1. | Class | cytoscape.actions | CytoScape |
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DeltaArrow | | Class | cytoscape.render.immed.arrow | CytoScape |
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DeselectAllAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
DeSelectAllEdgesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
DeSelectAllNodesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
Desktop | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
|
DesktopSize | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
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DestroyNetworkAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
DestroyNetworkViewAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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DGraphView | DING implementation of the GINY view. | Class | ding.view | CytoScape |
|
DiamondArrow | | Class | cytoscape.render.immed.arrow | CytoScape |
|
DiamondNodeShape | | Class | cytoscape.render.immed.nodeshape | CytoScape |
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DingCanvas | This class is meant to be extended by a class which is meant to exist within the InternalFrameComponent class. | Class | ding.view | CytoScape |
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DingNetworkView | Nested Class SummaryNested classes/interfaces inherited from class ding. | Class | cytoscape.ding | CytoScape |
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DiscArrow | | Class | cytoscape.render.immed.arrow | CytoScape |
|
DiscreteLegend | | Class | cytoscape.visual.mappings.discrete | CytoScape |
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DiscreteMapping | data value is extracted from a bundle of attributes by using a specified dataFields inherited from class cytoscape. | Class | cytoscape.visual.mappings | CytoScape |
|
DiscreteMappingReader | Reads in DiscreteMapping Properties. | Class | cytoscape.visual.mappings.discrete | CytoScape |
|
DiscreteMappingWriter | Writes DiscreteMapping Properties. | Class | cytoscape.visual.mappings.discrete | CytoScape |
|
DiscretePropertySetter | | Class | cytoscape.visual.ui | CytoScape |
|
DiscreteRangeCalculator | Range Calculator for the Discrete Mapper. | Class | cytoscape.visual.mappings.discrete | CytoScape |
|
DiscreteTrackRenderer | | Class | cytoscape.visual.ui.editors.continuous | CytoScape |
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DLayer | | Class | cytoscape.visual.customgraphic.impl | CytoScape |
|
DotStroke | Fields inherited from class cytoscape. | Class | cytoscape.visual.strokes | CytoScape |
|
DoubleList | | Class | org.cytoscape.equations | CytoScape |
|
DoubleParser | Parses a String into a Double object. | Class | cytoscape.visual.parsers | CytoScape |
|
DoubleRangeValueCalculator | | Class | cytoscape.visual.mappings.rangecalculators | CytoScape |
|
DownloadableInfo | | Class | cytoscape.plugin | CytoScape |
|
DownloadableType | enum DownloadableTypeextends EnumEnum Constant SummaryFILE | Class | cytoscape.plugin | CytoScape |
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DropDownMenuButton | Button with drop down menu. | Class | cytoscape.util.swing | CytoScape |
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DuplicateCalculatorNameException | This Exception is thrown when one attempts to add a Calculator to a CalculatorCatalog that already has a Calculator of the same name and | Class | cytoscape.visual | CytoScape |
|
DuplicatePluginClassException | See Also:Serialized FormConstructor SummaryDuplicatePluginClassException() | Class | cytoscape.plugin | CytoScape |
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DynamicGraph | A graph whose topology can be modified. | Interface | cytoscape.graph.dynamic | CytoScape |
|
DynamicGraphFactory | A factory for getting cytoscape. | Class | cytoscape.graph.dynamic.util | CytoScape |
|
DynamicLayoutMenu | A DynamicLayoutMenu is a more complicated layout menu that constructs layout menu items on-the-fly based on the capabilities of the layout algorithm and environment | Class | cytoscape.layout.ui | CytoScape |
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Edge | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
|
Edge | | Interface | giny.model | CytoScape |
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EdgeAnchors | | Interface | cytoscape.render.immed | CytoScape |
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EdgeAppearance | Objects of this class hold data describing the appearance of an Edge. | Class | cytoscape.visual | CytoScape |
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EdgeAppearanceCalculator | This class calculates the appearance of an Edge. | Class | cytoscape.visual | CytoScape |
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EdgeAttributesPopupDetails | This class provides a detailed list of attribute information for a givenSee Also:Serialized Form | Class | cytoscape.dialogs | CytoScape |
|
EdgeColorProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
|
EdgeContextMenuListener | an interface for responding to PhoebeCanvasDropEvents. | Interface | ding.view | CytoScape |
|
EdgeDetails | Defines the visual properties of an edge. | Class | cytoscape.render.stateful | CytoScape |
|
EdgeFontFaceProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
|
EdgeFontSizeProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
|
EdgeLabelColorProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
|
EdgeLabelOpacityProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
|
EdgeLabelPositionProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
|
EdgeLabelProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
|
EdgeLabelWidthProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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EdgeLineStyleProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
|
EdgeLineWidthProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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EdgeManipulationAction | See Also:Serialized FormFields inherited from class javax. | Class | cytoscape.actions | CytoScape |
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EdgeOpacityProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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EdgeSourceArrowColorProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
|
EdgeSourceArrowOpacityProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
|
EdgeSourceArrowShapeProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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EdgeTargetArrowColorProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
|
EdgeTargetArrowOpacityProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
|
EdgeTargetArrowShapeProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
|
EdgeToolTipProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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EdgeView | | Interface | giny.view | CytoScape |
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EditBookmarkDialog | | Class | cytoscape.dialogs.preferences | CytoScape |
|
EditNetworkTitleDialog | | Class | cytoscape.dialogs | CytoScape |
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EditorDisplayer | enum EditorDisplayerextends EnumManaging value editors in for each data types. | Class | cytoscape.visual.ui | CytoScape |
|
EditorManager | | Interface | cytoscape.visual.ui | CytoScape |
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EditorValueRangeTracer | | Class | cytoscape.visual.ui.editors.continuous | CytoScape |
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EllipseNodeShape | | Class | cytoscape.render.immed.nodeshape | CytoScape |
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EqnAttrTracker | Constructor SummaryEqnAttrTracker()Methods inherited from class java. | Class | cytoscape.data.readers | CytoScape |
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EqnCompiler | | Class | org.cytoscape.equations | CytoScape |
|
EqnParser | | Interface | org.cytoscape.equations | CytoScape |
|
EqualDashStroke | Fields inherited from class java. | Class | cytoscape.visual.strokes | CytoScape |
|
Equation | | Class | org.cytoscape.equations | CytoScape |
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EquationUtil | | Class | org.cytoscape.equations | CytoScape |
|
Error | | Class | org.cytoscape.equations.builtins | CytoScape |
|
Exec | | Class | cytoscape.util | CytoScape |
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ExitAction | | Class | cytoscape.actions | CytoScape |
|
Exp | | Class | org.cytoscape.equations.builtins | CytoScape |
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ExpFileChooser | adds a JCheckBox at the bottom of the chooser, asking whether to copy expression data to attributes. | Class | cytoscape.actions | CytoScape |
|
ExportAction | | Class | cytoscape.actions | CytoScape |
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ExportAsGMLAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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ExportAsGraphicsAction | Action for exporting a network view to bitmap or vector graphics. | Class | cytoscape.actions | CytoScape |
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ExportAsGraphicsFileChooser | Dialog that chooses file to export to. | Class | cytoscape.dialogs | CytoScape |
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ExportAsInteractionsAction | write out the current graph to the specified file, using the standard interactions format: nodeA edgeType nodeB. | Class | cytoscape.actions | CytoScape |
|
ExportAsXGMMLAction | This action is for exporting network and attributes in XGMML file. | Class | cytoscape.actions | CytoScape |
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ExportBitmapOptionsDialog | Options dialog for exporting to bitmap images. | Class | cytoscape.dialogs | CytoScape |
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ExportEdgeAttributesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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Exporter | Interface for exporting a network view to a graphics file. | Interface | cytoscape.util.export | CytoScape |
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ExportNetworksAsNNFAction | This action is for exporting network and attributes in XGMML file. | Class | cytoscape.actions | CytoScape |
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ExportNodeAttributesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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ExportVizmapAction | Export visual styles as a vizmap. | Class | cytoscape.actions | CytoScape |
|
ExpressionData | This class provides a reader for the common file format for expression data and an interface to access the data. | Class | cytoscape.data | CytoScape |
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ExpressionDataPopupTable | | Class | cytoscape.dialogs | CytoScape |
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ExtensibleMultiHashMapModel | Please try to restrain from using this class. | Class | cytoscape.data.attr.util | CytoScape |
|
FConvNode | | Class | org.cytoscape.equations.parse_tree | CytoScape |
|
FileUtil | Provides a platform-dependent way to open files. | Class | cytoscape.util | CytoScape |
|
Filter | | Interface | giny.filter | CytoScape |
|
FilterHistoryJList | JList with incremntal search & search history. | Class | cytoscape.util.swing | CytoScape |
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FingCyNetwork | FinhCyNetwork provides an implementation of the CyNetwork interface, as well as the GraphPerspective inteface, and also provides the | Class | cytoscape.giny | CytoScape |
|
FingEdgeDepot | Please try to restrain from using this class, or even looking at it. | Interface | fing.model | CytoScape |
|
FingExtensibleGraphPerspective | Please try to restrain from using this class. | Class | fing.model | CytoScape |
|
FingExtensibleRootGraph | Please try to restrain from using this class. | Class | fing.model | CytoScape |
|
FingNodeDepot | Please try to restrain from using this class, or even looking at it. | Interface | fing.model | CytoScape |
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FingRootGraphFactory | This class defines static methods that provide new instances of giny. | Class | fing.model | CytoScape |
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First | | Class | org.cytoscape.equations.builtins | CytoScape |
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FitContentAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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FixedGraph | Edges and nodes are non-negative integers; a given node and a given edge in a single graph can be the same integer. | Interface | cytoscape.graph.fixed | CytoScape |
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FlagAndSelectionHandler | This class synchronizes the flagged status of nodes and edges as held by a SelectFilter object of a network with the selection status of the corresponding | Class | cytoscape.view | CytoScape |
|
FlatInterpolator | This simple Interpolator returns the value at either the lower or upper boundary of the domain. | Class | cytoscape.visual.mappings | CytoScape |
|
FlattenIntVectors | given a vector which nests other vectors, each resolving eventually to a list of Integers, flatten it out into a simple 1-level-deep | Class | cytoscape.data.annotation | CytoScape |
|
FList | | Class | org.cytoscape.equations.builtins | CytoScape |
|
FloatConstantNode | A node in the parse tree representing an integer constant. | Class | org.cytoscape.equations.parse_tree | CytoScape |
|
FloatParser | | Class | cytoscape.visual.parsers | CytoScape |
|
FloatRangeValueCalculator | | Class | cytoscape.visual.mappings.rangecalculators | CytoScape |
|
FontCellRenderer | | Class | cytoscape.visual.ui.editors.discrete | CytoScape |
|
FontChooser | Defines a generalized font chooser class. | Class | cytoscape.visual.ui | CytoScape |
|
FontConverter | | Class | cytoscape.visual.converter | CytoScape |
|
FontParser | Parses a String into a Font object. | Class | cytoscape.visual.parsers | CytoScape |
|
FontRenderer | FontRenderer describes a class that renders each font name in a JList or JComboBox in the face specified. | Class | cytoscape.visual.ui | CytoScape |
|
ForwardSlashStroke | Nested Class SummaryNested classes/interfaces inherited from class cytoscape. | Class | cytoscape.visual.strokes | CytoScape |
|
FuncCallNode | A node in the parse tree representing a function call. | Class | org.cytoscape.equations.parse_tree | CytoScape |
|
Function | | Interface | org.cytoscape.equations | CytoScape |
|
FunctionError | | Class | org.cytoscape.equations | CytoScape |
|
FunctionUtil | A collection of static methods that may be useful for the implementation of built-in functions. | Class | org.cytoscape.equations | CytoScape |
|
GCTest | | Class | fing.model.test | CytoScape |
|
GeneOntology | Gene Ontology object based on general Ontology. | Class | cytoscape.data.ontology | CytoScape |
|
GenericNodeCustomGraphicCalculator | Nested Class SummaryNested classes/interfaces inherited from class cytoscape. | Class | cytoscape.visual.calculators | CytoScape |
|
GeoMean | | Class | org.cytoscape.equations.builtins | CytoScape |
|
getCanonicalName | | Class | cytoscape.data.servers | CytoScape |
|
getCommonName | | Class | cytoscape.data.servers | CytoScape |
|
GinyEdgeControlDialog | present a JTree with edge attributes names as top level nodes, and attribute values as child nodes; any node/s, once selected, are operated on by buttons in the bottom | Class | cytoscape.dialogs | CytoScape |
|
GinyUtils | Utility operations for selection and hiding/unhiding nodes and edges in a Giny GraphView. | Class | cytoscape.actions | CytoScape |
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GlobalAppearance | Objects of this class hold data describing global appearance attributes ofConstructor SummaryGlobalAppearance() | Class | cytoscape.visual | CytoScape |
|
GlobalAppearanceCalculator | This class calculates global visual attributes such as the background color of the graph window. | Class | cytoscape.visual | CytoScape |
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GMLException | Exception for GML Reader. | Class | cytoscape.data.readers | CytoScape |
|
GMLFileFilter | FileFilter for Reading in GML Files. | Class | cytoscape.util | CytoScape |
|
GMLNode | This class represents a GMLNode. | Class | cytoscape.data.readers | CytoScape |
|
GMLParser | The purpose of this class is to translate GML into an object tree, and print out an object tree into GML | Class | cytoscape.data.readers | CytoScape |
|
GMLReader | This class is responsible for converting a gml object tree into cytoscape objects New features to the current version: 1. | Class | cytoscape.data.readers | CytoScape |
|
GMLTag | enum GMLTagextends EnumEnum Constant SummaryARROW | Class | cytoscape.data.readers | CytoScape |
|
GMLTree | This class wraps around GMLNode and provides various methods for constructing a tree structure given other data. | Class | cytoscape.data.readers | CytoScape |
|
GMLWriter | The purpse of this class is to translate cytoscape data structures into a gml object tree, we can then use the gml parser to write this tree out into a | Class | cytoscape.data.readers | CytoScape |
|
GnuParser | The class GnuParser provides an implementation of theVersion:$Revision: 155404 $Author:John Keyes (john at integralsource. | Class | org.apache.commons.cli | CytoScape |
|
GOTerm | A Gene Ontology term. | Class | cytoscape.data.ontology | CytoScape |
|
GradientEditorPanel | | Class | cytoscape.visual.ui.editors.continuous | CytoScape |
|
GradientLayerCustomGraphics | Proof of concept code to generate Custom Graphics dynamically as vector graphics. | Class | cytoscape.visual.customgraphic.impl.vector | CytoScape |
|
GradientOvalLayer | Fields inherited from class cytoscape. | Class | cytoscape.visual.customgraphic.impl.vector | CytoScape |
|
GradientPaintFactory | | Class | cytoscape.visual.customgraphic.paint | CytoScape |
|
GradientRoundRectangleLayer | Fields inherited from class cytoscape. | Class | cytoscape.visual.customgraphic.impl.vector | CytoScape |
|
GraphGraphics | The purpose of this class is to make the proper calls on a Graphics2D object to efficiently render nodes, labels, and edges. | Class | cytoscape.render.immed | CytoScape |
|
GraphicsParser | | Class | cytoscape.visual.parsers | CytoScape |
|
GraphLOD | An instance of this class defines the level of detail that goes into a single rendering of a graph. | Class | cytoscape.render.stateful | CytoScape |
|
GraphObject | | Interface | giny.model | CytoScape |
|
GraphObjectSelection | | Class | cytoscape.dialogs | CytoScape |
|
GraphObjectSelectionAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
GraphPerspective | TODO: Remove deprecated methods and add generics parameters. | Interface | giny.model | CytoScape |
|
GraphPerspectiveChangeEvent | The event source must be the GraphPerspective that changed. | Class | giny.model | CytoScape |
|
GraphPerspectiveChangeListener | | Interface | giny.model | CytoScape |
|
GraphReader | Interface for Reading in Cytoscape Graphs. | Interface | cytoscape.data.readers | CytoScape |
|
GraphRenderer | This class contains a chunk of procedural code that stitches together several external modules in an effort to efficiently render graphs. | Class | cytoscape.render.stateful | CytoScape |
|
GraphSetUtils | | Class | cytoscape.util | CytoScape |
|
GraphView | | Interface | giny.view | CytoScape |
|
GraphViewChangeEvent | The event source must be the GraphPerspective that changed. | Class | giny.view | CytoScape |
|
GraphViewChangeListener | | Interface | giny.view | CytoScape |
|
GraphViewController | | Class | cytoscape.view | CytoScape |
|
GraphViewHandler | This interface represents an object that handles a change in a giny. | Interface | cytoscape.view | CytoScape |
|
GridBagGroup | | Class | cytoscape.dialogs | CytoScape |
|
GridNodeLayout | The GridNodeLayout provides a very simple layout, suitable as the default layout for Cytoscape data readers. | Class | cytoscape.layout.algorithms | CytoScape |
|
HalfBottomArrow | | Class | cytoscape.render.immed.arrow | CytoScape |
|
HalfTopArrow | | Class | cytoscape.render.immed.arrow | CytoScape |
|
Haltable | A hook for requesting that a running process be halted. | Interface | cytoscape.task | CytoScape |
|
HarMean | | Class | org.cytoscape.equations.builtins | CytoScape |
|
HelpAboutAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
HelpContactHelpDeskAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
HelpContentsAction | Really just a wrapper for the CSH. | Class | cytoscape.actions | CytoScape |
|
HelpFormatter | A formatter of help messages for the current command line optionsAuthor:Slawek Zachcial, John Keyes (john at integralsource. | Class | org.apache.commons.cli | CytoScape |
|
HexagonNodeShape | | Class | cytoscape.render.immed.nodeshape | CytoScape |
|
HiddenEdges | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
|
HiddenNodes | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
|
HideEdgeListener | Adds EdgeView and EdgeView vizmap bypass listeners to network views as the views are created. | Class | cytoscape.visual.ui | CytoScape |
|
HideNodeListener | Adds NodeView and EdgeView vizmap bypass listeners to network views as the views are created. | Class | cytoscape.visual.ui | CytoScape |
|
HideSelectedAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
HideSelectedEdgesAction | | Class | cytoscape.actions | CytoScape |
|
HideSelectedNodesAction | | Class | cytoscape.actions | CytoScape |
|
IconPopupButton | | Class | cytoscape.dialogs | CytoScape |
|
IconTableCellRenderer | | Class | cytoscape.view | CytoScape |
|
IdentDescriptor | | Class | org.cytoscape.equations.interpreter | CytoScape |
|
IdentNode | A node in the parse tree representing an attribute reference. | Class | org.cytoscape.equations.parse_tree | CytoScape |
|
IDGenerator | | Class | cytoscape.visual.customgraphic | CytoScape |
|
If | | Class | org.cytoscape.equations.builtins | CytoScape |
|
IList | | Class | org.cytoscape.equations.builtins | CytoScape |
|
ImageImposter | The primary purpose of this class is to enable an arbitrary Graphics object to receive rendering calls from a | Class | cytoscape.render.export | CytoScape |
|
ImageUtil | | Class | cytoscape.visual.customgraphic | CytoScape |
|
ImplementsGraphTest | | Class | fing.model.test | CytoScape |
|
ImportAttributeMatrixDialog | This class prompts the user for data for entry of the attribute matrix, which includes expression data as a use case. | Class | cytoscape.dialogs | CytoScape |
|
ImportEdgeAttributesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
ImportExpressionMatrixAction | User has requested loading of an Expression Matrix File. | Class | cytoscape.actions | CytoScape |
|
ImportGraphFileAction | Imports a graph of arbitrary type. | Class | cytoscape.actions | CytoScape |
|
ImportHandler | Central registry for all Cytoscape import classes. | Class | cytoscape.data | CytoScape |
|
ImportNetworkDialog | | Class | cytoscape.dialogs | CytoScape |
|
ImportNodeAttributesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
ImportVizmapAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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IndeterminateProgressBar | This class creates a dialog with a JProgressBar in indeterminate state. | Class | cytoscape.util | CytoScape |
|
InnerCanvas | The GUI component for drawing networks. | Class | ding.view | CytoScape |
|
InnerCanvasEvent | See Also:Serialized FormFields inherited from class java. | Class | ding.view | CytoScape |
|
InnerCanvasListener | | Interface | ding.view | CytoScape |
|
Installable | | Interface | cytoscape.plugin | CytoScape |
|
InstallablePlugin | | Class | cytoscape.plugin | CytoScape |
|
InstallableTheme | | Class | cytoscape.plugin | CytoScape |
|
Instruction | enum Instructionextends EnumEnum Constant SummaryAREF | Class | org.cytoscape.equations.interpreter | CytoScape |
|
IntArray | A dynamically growing array of integers. | Class | cytoscape.util.intr | CytoScape |
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IntBTree | An in-memory B+-tree that stores integers. | Class | cytoscape.util.intr | CytoScape |
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IntBTreeConstructionTuner | | Class | cytoscape.util.intr.test | CytoScape |
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IntBTreePerformance | | Class | cytoscape.util.intr.test | CytoScape |
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IntBTreeQueryTuner | | Class | cytoscape.util.intr.test | CytoScape |
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IntegerEntryField | | Class | cytoscape.dialogs | CytoScape |
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IntEnumerator | An enumeration over a list of 32 bit integers. | Interface | cytoscape.util.intr | CytoScape |
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Interaction | Interaction. | Class | cytoscape.data | CytoScape |
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InteractionsReader | Reader for graphs in the interactions file format. | Class | cytoscape.data.readers | CytoScape |
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InteractionWriter | A few utility methods to assist in writing SIF files. | Class | cytoscape.data.writers | CytoScape |
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InternalFrameComponent | This class manages the JLayeredPane that resides in each internal frame of cytoscape. | Class | cytoscape.view | CytoScape |
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Interpolator | This interface defines an interpolation function that takes two pairs of (domain,range) values plus a target domain value, and calculates an | Interface | cytoscape.visual.mappings | CytoScape |
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InterpolatorFactory | Provides static factory methods for constructing known interpolators from a recognized name, for example from a properties object. | Class | cytoscape.visual.mappings | CytoScape |
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Interpreter | | Class | org.cytoscape.equations.interpreter | CytoScape |
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IntHash | An insert-only hashtable that has non-negative 32 bit integer keys; no satellite data is stored in this hashtable. | Class | cytoscape.util.intr | CytoScape |
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IntHashPerformance | | Class | cytoscape.util.intr.test | CytoScape |
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IntIntHash | An insert-only hashtable that has non-negative 32 bit integer keys and non-negative 32 bit integer values. | Class | cytoscape.util.intr | CytoScape |
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IntIterator | An iteration over a list of 32 bit integers. | Interface | cytoscape.util.intr | CytoScape |
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IntObjHash | An insert-only hashtable that has non-negative 32 bit integer keys and non-null object values. | Class | cytoscape.util.intr | CytoScape |
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IntQueue | A first-in, first-out container of 32 bit integers. | Class | cytoscape.util.intr | CytoScape |
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IntStack | A first-in, last-out container of 32 bit integers. | Class | cytoscape.util.intr | CytoScape |
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IntTHash | An insert-only hashtable that has non-negative 32 bit integer keys and non-null object values. | Class | cytoscape.util.intr | CytoScape |
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InvalidDownloadable | | Class | cytoscape.plugin | CytoScape |
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InvertSelectedEdgesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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InvertSelectedNodesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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JErrorPanel | Common UI element for displaying errors and stack traces. | Class | cytoscape.task.ui | CytoScape |
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JnlpWriterUtil | | Class | cytoscape.util | CytoScape |
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JointIntegerEntry | | Class | cytoscape.dialogs | CytoScape |
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JStatusBar | Simple status bar with 3 fields. | Class | cytoscape.util.swing | CytoScape |
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JTask | Common UI element for visually monitoring task progress. | Class | cytoscape.task.ui | CytoScape |
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JTaskConfig | Used to configure the JTask UI component. | Class | cytoscape.task.ui | CytoScape |
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JTreeTable | This example shows how to create a simple JTreeTable component, by using a JTree as a renderer (and editor) for the cells in a particular column in the | Class | cytoscape.util.swing | CytoScape |
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Justification | enum Justificationextends EnumEnum Constant SummaryJUSTIFY_CENTER | Class | giny.view | CytoScape |
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KeyValue | Key and Value pair in GML file. | Class | cytoscape.data.readers | CytoScape |
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Label | | Interface | giny.view | CytoScape |
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LabelPlacerGraphic | A drag and drop graphic that allows users to set the placement Deprecated. | Class | cytoscape.visual.ui | CytoScape |
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LabelPosition | Deprecated. | Class | cytoscape.visual | CytoScape |
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LabelPositionParser | Parses a String into a LabelPosition object. | Class | cytoscape.visual.parsers | CytoScape |
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LabelTextPanel | | Class | cytoscape.dialogs | CytoScape |
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Largest | | Class | org.cytoscape.equations.builtins | CytoScape |
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Last | | Class | org.cytoscape.equations.builtins | CytoScape |
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Layer | Wrapper for actual implementations of layers. | Interface | cytoscape.visual.customgraphic | CytoScape |
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LayoutAdapter | LayoutAdapter provides a *very* minimal interface to implement a layout algorithm. | Class | cytoscape.layout | CytoScape |
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LayoutAlgorithm | | Interface | cytoscape.layout | CytoScape |
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LayoutMenu | A DynamicLayoutMenu is a more complicated layout menu that constructs layout menu items on-the-fly based on the capabilities of the layout algorithm and environment | Class | cytoscape.layout.ui | CytoScape |
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LayoutMenuManager | | Class | cytoscape.layout.ui | CytoScape |
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LayoutProperties | The LayoutProperties class is a helper class to support the management of settings and properties for layout algorithms that implement | Class | cytoscape.layout | CytoScape |
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LayoutSettingsDialog | The LayoutSettingsDialog is a dialog that provides an interface into all of the various settings for layout algorithms. | Class | cytoscape.layout.ui | CytoScape |
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LayoutTask | A wrapper for applying a layout in a task. | Class | cytoscape.layout | CytoScape |
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Left | | Class | org.cytoscape.equations.builtins | CytoScape |
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LegacyCustomNodeShape | | Class | cytoscape.render.immed.nodeshape | CytoScape |
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LegendDialog | | Class | cytoscape.visual.ui | CytoScape |
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LegendTable | | Class | cytoscape.visual.mappings | CytoScape |
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Len | | Class | org.cytoscape.equations.builtins | CytoScape |
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LicenseDialog | | Class | cytoscape.dialogs.plugins | CytoScape |
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LinearNumberInterpolator | This subclass of NumberInterpolator further assumes a linear interpolation, and calculates the fractional distance of the target domain value from | Class | cytoscape.visual.mappings | CytoScape |
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LinearNumberToColorInterpolator | The class provides a linear interpolation between color values. | Class | cytoscape.visual.mappings | CytoScape |
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LinearNumberToNumberInterpolator | The class assumes that the supplied range objects are Numbers, and returns a linearly interplated value according to the value of frac. | Class | cytoscape.visual.mappings | CytoScape |
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LineStyle | enum LineStyleextends EnumEnum Constant SummaryBACKWARD_SLASH | Class | cytoscape.visual | CytoScape |
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LineStyleParser | Parses a String into a yFiles shape, which is represented by a byte identifier. | Class | cytoscape.visual.parsers | CytoScape |
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LineTypeIcon | | Class | cytoscape.visual.ui.icon | CytoScape |
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ListFromFileSelectionAction | Select nodes from a text list of node IDs. | Class | cytoscape.actions | CytoScape |
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ListToString | | Class | org.cytoscape.equations.builtins | CytoScape |
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Ln | | Class | org.cytoscape.equations.builtins | CytoScape |
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loadAnnotation | load an annotation into an rmi biodata server. | Class | cytoscape.data.servers | CytoScape |
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loadAnnotationFromFlatFiles | load an annotation into an rmi biodata server. | Class | cytoscape.data.servers | CytoScape |
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LoadImageTask | | Class | cytoscape.visual.customgraphic | CytoScape |
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LoadNetworkTask | Task to load a new network. | Class | cytoscape.actions | CytoScape |
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loadThesaurus | load an thesaurus into an rmi biodata server. | Class | cytoscape.data.servers | CytoScape |
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Log | | Class | org.cytoscape.equations.builtins | CytoScape |
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LoggerAction | Created by IntelliJ IDEA. | Class | cytoscape.actions | CytoScape |
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LoggerDialog | | Class | cytoscape.dialogs.logger | CytoScape |
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LogLevel | enum LogLevelextends EnumThe levels of logged messages | Class | cytoscape.logger | CytoScape |
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LongDashStroke | Fields inherited from class java. | Class | cytoscape.visual.strokes | CytoScape |
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LongEnumerator | An enumeration over a list of 64 bit integers. | Interface | cytoscape.util.intr | CytoScape |
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LongList | | Class | org.cytoscape.equations | CytoScape |
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LongLongHash | An insert-only hashtable that has non-negative 64 bit integer keys and non-negative 64 bit integer values. | Class | cytoscape.util.intr | CytoScape |
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Lower | | Class | org.cytoscape.equations.builtins | CytoScape |
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MacAppConfig | Configures the Mac OS X Info. | Class | cytoscape.util | CytoScape |
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ManagerException | Thrown to indicate PluginManager errorsAuthor:skillcoyneSee Also:Serialized Form | Class | cytoscape.plugin | CytoScape |
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ManagerModel | Fairly similar to DefaultTreeModel but I wanted to add some extra functionality to removing/adding nodes and use my own node objects | Class | cytoscape.dialogs.plugins | CytoScape |
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ManagerUtil | | Class | cytoscape.plugin | CytoScape |
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MapperAndAttribute | | Class | cytoscape.visual.ui | CytoScape |
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MappingFactory | This class provides a static factory method for constructing an instance of ObjectMapping as specified by a Properties object and other arguments. | Class | cytoscape.visual.mappings | CytoScape |
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MappingKeyFactory | | Class | cytoscape.visual.ui | CytoScape |
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MappingManager | | Interface | cytoscape.visual.mappings | CytoScape |
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MappingManagerImpl | | Class | cytoscape.visual.mappings | CytoScape |
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MappingType | enum MappingTypeextends EnumDefines visual mapping types. | Class | cytoscape.visual.mappings | CytoScape |
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MappingUtil | Provides simple utility methods for the Mapping classes. | Class | cytoscape.visual.mappings | CytoScape |
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MathUtil | | Class | cytoscape.util | CytoScape |
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Max | | Class | org.cytoscape.equations.builtins | CytoScape |
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Median | | Class | org.cytoscape.equations.builtins | CytoScape |
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MemoryReporter | A class used to track JVM memory usage. | Class | cytoscape.util | CytoScape |
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MemoryUsageAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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MetadataEntries | enum MetadataEntriesextends EnumEntries in the network metadata. | Class | cytoscape.data.readers | CytoScape |
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MetadataParser | Manipulates network metadata for loading and saving. | Class | cytoscape.data.readers | CytoScape |
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Mid | | Class | org.cytoscape.equations.builtins | CytoScape |
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Min | | Class | org.cytoscape.equations.builtins | CytoScape |
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MinIntHeap | A heap is an implementation of a priority queue. | Class | cytoscape.util.intr | CytoScape |
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MinIntHeapPerformance | | Class | cytoscape.util.intr.test | CytoScape |
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MinMaxDialog | | Class | cytoscape.visual.ui.editors.continuous | CytoScape |
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MinMaxDouble | find the min and max of a 1- or 2-d aarray of doubles. | Class | cytoscape.util | CytoScape |
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MinMaxInt | find the min and max of a 1- or 2-d array of ints. | Class | cytoscape.util | CytoScape |
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Misc | | Class | cytoscape.util | CytoScape |
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MiscGB | We DO need to replace this with swing-layout! Miscellaneous static GridBagLayout utilities | Class | cytoscape.dialogs | CytoScape |
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MissingArgumentException | Thrown when an option requiring an argument is not provided with an argument. | Class | org.apache.commons.cli | CytoScape |
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MissingOptionException | Thrown when a required option has not been provided. | Class | org.apache.commons.cli | CytoScape |
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Mod | | Class | org.cytoscape.equations.builtins | CytoScape |
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Mode | | Class | org.cytoscape.equations.builtins | CytoScape |
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ModuleProperties | | Interface | cytoscape.util | CytoScape |
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ModulePropertiesImpl | | Class | cytoscape.util | CytoScape |
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MolecularFunctionAnnotationReader | The purpose of this class is to convert a 'gene_association. | Class | cytoscape.cruft.obo | CytoScape |
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MolecularFunctionAnnotationTester | | Class | cytoscape.cruft.obo.test | CytoScape |
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MonitoredTask | | Interface | cytoscape.util | CytoScape |
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mRNAMeasurement | | Class | cytoscape.data | CytoScape |
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MultiHashMap | This interface consists of the API specification to bind attribute values to objects. | Interface | cytoscape.data.attr | CytoScape |
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MultiHashMapDefinition | This interface contains the API specification for creating attribute definitions. | Interface | cytoscape.data.attr | CytoScape |
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MultiHashMapDefinitionListener | | Interface | cytoscape.data.attr | CytoScape |
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MultiHashMapFactory | This class provides access to implementations of MultiHashMap and MultiHashMapDefinition. | Class | cytoscape.data.attr.util | CytoScape |
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MultiHashMapHelpers | This class contains static utilitarian methods that return information pertaining to attributes. | Class | cytoscape.data.attr.util | CytoScape |
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MultiHashMapListener | | Interface | cytoscape.data.attr | CytoScape |
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MutableBool | | Class | cytoscape.util | CytoScape |
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MutableInt | | Class | cytoscape.util | CytoScape |
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MutableSpacialIndex2D | A spacial index for objects in two dimensions, with support for insertions and deletions. | Interface | cytoscape.geom.spacial | CytoScape |
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MutableString | | Class | cytoscape.util | CytoScape |
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NestedNetworkChangeEvent | This event will be fired when nested network is created/removed. | Class | giny.model | CytoScape |
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NestedNetworkChangeEventListener | Listener for nested network change events. | Interface | giny.model | CytoScape |
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NestedNetworkListener | Adds NodeView and EdgeView vizmap bypass listeners to network views as the views are created. | Class | cytoscape.visual.ui | CytoScape |
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NestedNetworkReader | Special interface for Graph readers which read nested networks from a file. | Interface | cytoscape.data.readers | CytoScape |
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NestedNetworkViewUpdater | This class manages images that represent nested networks. | Class | cytoscape.util | CytoScape |
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Network | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
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NetworkData | There is an event fired anytime that a value is modified, you need to be listener to the attribute name though. | Class | cytoscape.data | CytoScape |
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NetworkExpansionMenu | | Class | cytoscape.data.webservice.util | CytoScape |
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NetworkFrame | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
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NetworkFrames | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
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NetworkImportWebServiceClient | | Interface | cytoscape.data.webservice | CytoScape |
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NetworkMetaDataDialog | Dialog for editing network metadata in RDF. | Class | cytoscape.dialogs | CytoScape |
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NetworkMetaDataTableModel | Table model for the Network Metadata Dialog. | Class | cytoscape.dialogs | CytoScape |
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NetworkPanel | GUI component for managing network list in current session. | Class | cytoscape.view | CytoScape |
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NetworkSelectorPanel | | Class | cytoscape.util.swing | CytoScape |
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NetworkTree | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
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NetworkTreeNode | See Also:Serialized FormFields inherited from class javax. | Class | cytoscape.view | CytoScape |
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NetworkTreeTableModel | Inner class that extends the AbstractTreeTableModelFields inherited from class cytoscape. | Class | cytoscape.view | CytoScape |
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NetworkViewManager | | Class | cytoscape.view | CytoScape |
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NewMappingBuilder | Constructor SummaryNewMappingBuilder()Methods inherited from class java. | Class | cytoscape.visual.ui | CytoScape |
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NewNetworkAction | creates a new network and associates an editor with itVersion:1. | Class | cytoscape.actions | CytoScape |
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NewSessionAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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NewSlider | | Class | cytoscape.dialogs | CytoScape |
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NewStringPopupDialog | NewStringPopupDialog: a dialog that is used for creating a new string. | Class | cytoscape.dialogs | CytoScape |
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NewWindowSelectedNodesEdgesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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NewWindowSelectedNodesOnlyAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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NNFFileFilter | File filter for Nested Network Format (NNF). | Class | cytoscape.util | CytoScape |
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NNFParser | Parser for NNF files. | Class | cytoscape.data.readers | CytoScape |
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NNFReader | Graph file reader for NNF files. | Class | cytoscape.data.readers | CytoScape |
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NoArrow | | Class | cytoscape.render.immed.arrow | CytoScape |
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Node | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
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Node | | Interface | giny.model | CytoScape |
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Node | A node in the parse tree. | Class | org.cytoscape.equations.parse_tree | CytoScape |
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NodeAppearance | Objects of this class hold data describing the appearance of a Node. | Class | cytoscape.visual | CytoScape |
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NodeAppearanceCalculator | This class calculates the appearance of a Node. | Class | cytoscape.visual | CytoScape |
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NodeBorderColorProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeBorderOpacityProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeContextMenuListener | an interface for responding to PhoebeCanvasDropEvents. | Interface | ding.view | CytoScape |
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NodeCustomGraphicsPositionProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeCustomGraphicsProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeDetails | Defines visual properties of a node modulo the node size and location Even though this class is not declared abstract, in most situations it | Class | cytoscape.render.stateful | CytoScape |
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NodeFillColorProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeFontFaceProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeFontSizeProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeHeightProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeIcon | Icon for node shapes. | Class | cytoscape.visual.ui.icon | CytoScape |
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NodeLabelColorProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeLabelOpacityProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeLabelPositionProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeLabelProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeLabelWidthProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeLineStyleProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeLineWidthProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeOpacityProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeShape | An interface defining the methods necessary to render a node shape in GraphGraphics. | Interface | cytoscape.render.immed.nodeshape | CytoScape |
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NodeShape | enum NodeShapeextends EnumSince:Cytoscape 2. | Class | cytoscape.visual | CytoScape |
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NodeShapeConverter | | Class | cytoscape.visual.converter | CytoScape |
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NodeShapeParser | Parses a String into a yFiles shape, which is represented by a byte identifier. | Class | cytoscape.visual.parsers | CytoScape |
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NodeShapeProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeShapeRangeValueCalculator | | Class | cytoscape.visual.mappings.rangecalculators | CytoScape |
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NodeShowNestedNetworkProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeSizeProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeToolTipProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NodeView | Any and all questions should be directed to me. | Interface | giny.view | CytoScape |
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NodeWidthProp | Fields inherited from class cytoscape. | Class | cytoscape.visual.properties | CytoScape |
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NormDist | | Class | org.cytoscape.equations.builtins | CytoScape |
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NoRTreeQueryPerformance | | Class | cytoscape.geom.rtree.test | CytoScape |
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Not | | Class | org.cytoscape.equations.builtins | CytoScape |
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NotAPluginException | Thrown to indicate that a class cannot be used as a plugin becuase it does not extend CytoscapePlugin. | Class | cytoscape.plugin | CytoScape |
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Now | | Class | org.cytoscape.equations.builtins | CytoScape |
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Nth | | Class | org.cytoscape.equations.builtins | CytoScape |
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NullCustomGraphics | Null object for Custom Graphics. | Class | cytoscape.visual.customgraphic | CytoScape |
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NumberInterpolator | This partial implementation of Interpolator assumes that the domain values are some kind of number, and extracts the values into ordinary | Class | cytoscape.visual.mappings | CytoScape |
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ObjectFactory | This object contains factory methods for each Java content interface and Java element interface | Class | cytoscape.bookmarks | CytoScape |
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ObjectFactory | This object contains factory methods for each Java content interface and Java element interface | Class | cytoscape.generated | CytoScape |
|
ObjectMapping | Mappings should implement this interface. | Interface | cytoscape.visual.mappings | CytoScape |
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ObjectPlacerControl | | Class | cytoscape.visual.ui | CytoScape |
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ObjectPlacerGraphic | | Class | cytoscape.visual.ui | CytoScape |
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ObjectPosition | Interface representing relative location of graphics objects, such as labels or custom graphics. | Interface | giny.view | CytoScape |
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ObjectPositionCellRenderer | | Class | cytoscape.visual.ui.editors.discrete | CytoScape |
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ObjectPositionConverter | | Class | cytoscape.visual.converter | CytoScape |
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ObjectPositionImpl | | Class | ding.view | CytoScape |
|
ObjectPositionParser | | Class | cytoscape.visual.parsers | CytoScape |
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ObjectToString | This class contains a method that does the reverse of the various parsing classes in this package, i. | Class | cytoscape.visual.parsers | CytoScape |
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OBOFlatFileReader | This is a general OBO (Open Biomedical Ontologies: http://obo. | Class | cytoscape.data.ontology.readers | CytoScape |
|
OBOHeaderTags | enum OBOHeaderTagsextends EnumEnum Constant SummaryAUTO_GENERATED_BY | Class | cytoscape.data.ontology.readers | CytoScape |
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OboOntologyReader | The purpose of this class is to convert a 'gene_ontology. | Class | cytoscape.cruft.obo | CytoScape |
|
OboOntologyReader2 | The purpose of this class is to convert a 'gene_ontology. | Class | cytoscape.cruft.obo | CytoScape |
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OboOntologyTester | | Class | cytoscape.cruft.obo.test | CytoScape |
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OBOTags | enum OBOTagsextends EnumTags used in OBO file: | Class | cytoscape.data.ontology.readers | CytoScape |
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OctagonNodeShape | | Class | cytoscape.render.immed.nodeshape | CytoScape |
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Ontology | Contains a collection of OntologyTerms, each of which may have pointers to other terms, creating a hierarchical controlled vocabulary. | Class | cytoscape.data.annotation | CytoScape |
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Ontology | General Ontology class which implements interface from BioJava project. | Class | cytoscape.data.ontology | CytoScape |
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Ontology | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
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OntologyDescription | Distinguish among different ontologies, by curator and type. | Class | cytoscape.data.annotation | CytoScape |
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OntologyFactory | | Class | cytoscape.data.ontology | CytoScape |
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OntologyFlatFileReader | | Class | cytoscape.data.annotation.readers | CytoScape |
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OntologyReader | Interface for all ontology file readers. | Interface | cytoscape.data.ontology.readers | CytoScape |
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OntologyServer | Ontology Server which manages ontologies, aliases, and bookmarks. | Class | cytoscape.data.servers | CytoScape |
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OntologyServer | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
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OntologyTerm | Represents one node in an ontology, which is a hierarchical classification of entities using a controlled vocabulary. | Class | cytoscape.data.annotation | CytoScape |
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OntologyTerm | Simple in-memory implementation of an ontology term based on BioJava's This implementation uses CyNetwork and CyAttributes as its actual data | Class | cytoscape.data.ontology | CytoScape |
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OntologyXmlReader | | Class | cytoscape.data.annotation.readers | CytoScape |
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OpenBrowser | | Class | cytoscape.util | CytoScape |
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OpenSessionAction | Call the session reader and read everything in the zip archive. | Class | cytoscape.actions | CytoScape |
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Option | Describes a single command-line option. | Class | org.apache.commons.cli | CytoScape |
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OptionBuilder | OptionBuilder allows the user to create Options using descriptive Details on the Builder pattern can be found at | Class | org.apache.commons.cli | CytoScape |
|
OptionGroup | A group of mutually exclusive options. | Class | org.apache.commons.cli | CytoScape |
|
Options | Main entry-point into the library. | Class | org.apache.commons.cli | CytoScape |
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OptionValidator | Validates an Option string. | Class | org.apache.commons.cli | CytoScape |
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Or | | Class | org.cytoscape.equations.builtins | CytoScape |
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PaintFactory | Factory for creating paint object for a rectangulaer bounds. | Interface | cytoscape.render.stateful | CytoScape |
|
Panel | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
|
Panels | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
|
ParallelogramNodeShape | | Class | cytoscape.render.immed.nodeshape | CytoScape |
|
ParallelStroke | Fields inherited from class cytoscape. | Class | cytoscape.visual.strokes | CytoScape |
|
Parent | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
|
ParseException | Base for Exceptions thrown during parsing of a command-line. | Class | org.apache.commons.cli | CytoScape |
|
Parser | Parser creates CommandLines. | Class | org.apache.commons.cli | CytoScape |
|
Parser | A singleton EqnParserConstructor SummaryParser() | Class | org.cytoscape.equations | CytoScape |
|
ParserControl | ParserControl is used to control particular behaviour of the parser. | Interface | org.apache.commons.cli.avalon | CytoScape |
|
PassThroughMapping | Defines a mapping from a bundle of data attributes to a visual attribute. | Class | cytoscape.visual.mappings | CytoScape |
|
PatternOptionBuilder | Allows Options to be created from a single String. | Class | org.apache.commons.cli | CytoScape |
|
PDFExporter | PDF exporter by the iText library. | Class | cytoscape.util.export | CytoScape |
|
PercentUtil | Helper Class for Calculating Percentage of Multi-Step Processes. | Class | cytoscape.util | CytoScape |
|
Permut | | Class | org.cytoscape.equations.builtins | CytoScape |
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PersistImageTask | | Class | cytoscape.visual.customgraphic | CytoScape |
|
PhoebeCanvasDropEvent | forwards the drop event and its locationSee Also:Serialized Form | Class | phoebe | CytoScape |
|
PhoebeCanvasDropListener | an interface for responding to PhoebeCanvasDropEvents. | Interface | phoebe | CytoScape |
|
PhoebeCanvasDroppable | interface for maintaining listeners for PhoebeCanvasDropEvents. | Interface | phoebe | CytoScape |
|
PhoebeNodeControl | An Adobe style node organizer. | Class | cytoscape.dialogs | CytoScape |
|
Pi | | Class | org.cytoscape.equations.builtins | CytoScape |
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PipeStroke | | Class | cytoscape.visual.strokes | CytoScape |
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Plugin | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
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PluginException | | Class | cytoscape.plugin | CytoScape |
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PluginFileReader | | Class | cytoscape.plugin | CytoScape |
|
PluginIndex | | Class | cytoscape.dialogs.plugins | CytoScape |
|
PluginInfo | | Class | cytoscape.plugin | CytoScape |
|
PluginInquireAction | Object should be implmeneted by anyone using the PluginManager#inquireThread(String, PluginInquireAction) method to get plugins from a given site. | Class | cytoscape.plugin | CytoScape |
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PluginManageDialog | | Class | cytoscape.dialogs.plugins | CytoScape |
|
PluginManager | | Class | cytoscape.plugin | CytoScape |
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PluginManagerAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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PluginManagerInquireTask | | Class | cytoscape.plugin | CytoScape |
|
PluginProperties | This class reads the plugin. | Class | cytoscape.plugin | CytoScape |
|
Plugins | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
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PluginsTableModel | See Also:Serialized FormFields inherited from class javax. | Class | cytoscape.dialogs.preferences | CytoScape |
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PluginStatus | enum PluginStatusextends EnumEnum Constant SummaryCURRENT | Class | cytoscape.plugin | CytoScape |
|
PluginTracker | | Class | cytoscape.plugin | CytoScape |
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PluginUpdateAction | | Class | cytoscape.actions | CytoScape |
|
PluginUpdateDialog | | Class | cytoscape.dialogs.plugins | CytoScape |
|
PluginUrlDialog | | Class | cytoscape.dialogs.plugins | CytoScape |
|
PluginVersionUtils | | Class | cytoscape.plugin | CytoScape |
|
PluginXml | enum PluginXmlextends EnumEnum Constant SummaryAUTHOR | Class | cytoscape.plugin | CytoScape |
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PointTextListener | Listens for a User Initiated Change in any of the JTextFields in the Continuous Mapper UI. | Class | cytoscape.visual.mappings.continuous | CytoScape |
|
PopupFontChooser | | Class | cytoscape.visual.ui | CytoScape |
|
PopupIconChooser | PopupIconChooser borrows all of its functionality from IconPopupButton. | Class | cytoscape.visual.ui | CytoScape |
|
PopupObjectPositionChooser | | Class | cytoscape.visual.ui | CytoScape |
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PopupStringChooser | An input dialog for strings, ints, and doubles. | Class | cytoscape.visual.ui | CytoScape |
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PopupTextArea | | Class | cytoscape.dialogs | CytoScape |
|
Position | enum Positionextends EnumConstants represent position of graphics objects. | Class | giny.view | CytoScape |
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PosixParser | The class PosixParser provides an implementation of theVersion:$Revision: 155404 $Author:John Keyes (john at integralsource. | Class | org.apache.commons.cli | CytoScape |
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PreferenceAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
PreferencesDialog | | Class | cytoscape.dialogs.preferences | CytoScape |
|
PreferenceTableModel | | Class | cytoscape.dialogs.preferences | CytoScape |
|
PreferenceValueDialog | | Class | cytoscape.dialogs.preferences | CytoScape |
|
PrimesGenerator | | Class | cytoscape.util.intr.test | CytoScape |
|
PrintAction | | Class | cytoscape.actions | CytoScape |
|
PrintLOD | | Class | ding.view | CytoScape |
|
Product | | Class | org.cytoscape.equations.builtins | CytoScape |
|
PropUtil | A stateless utility class that makes it easy to parse int and boolean values from a Properties object. | Class | cytoscape.util | CytoScape |
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ProxyHandler | | Class | cytoscape.util | CytoScape |
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ProxyServerAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
ProxyServerDialog | | Class | cytoscape.dialogs.preferences | CytoScape |
|
PSExporter | | Class | cytoscape.util.export | CytoScape |
|
Radians | | Class | org.cytoscape.equations.builtins | CytoScape |
|
RandomColorListener | User wants to Seed the Discrete Mapper with Random Color Values. | Class | cytoscape.visual.mappings.discrete | CytoScape |
|
RangeValueCalculator | | Interface | cytoscape.visual.mappings | CytoScape |
|
RangeValueCalculatorFactory | | Interface | cytoscape.visual.mappings | CytoScape |
|
RangeValueCalculatorFactoryImpl | Constructor SummaryRangeValueCalculatorFactoryImpl()> | Class | cytoscape.visual.mappings | CytoScape |
|
RecentlyOpenedTracker | A class to keep track of a short list of recently opened URLs. | Class | cytoscape.util | CytoScape |
|
RectangleNodeShape | | Class | cytoscape.render.immed.nodeshape | CytoScape |
|
RedoAction | An action that calls redo for the most recent edit in the undoable edit stack. | Class | cytoscape.util.undo | CytoScape |
|
RedrawTask | | Class | cytoscape.visual.ui | CytoScape |
|
RenderingContext | | Interface | cytoscape.visual.customgraphic | CytoScape |
|
RepeatedAllRootGraphMethodsTest | | Class | fing.model.test | CytoScape |
|
RestoreImageTask | | Class | cytoscape.visual.customgraphic | CytoScape |
|
Right | | Class | org.cytoscape.equations.builtins | CytoScape |
|
RootGraph | A graph model consisting of nodes and the edges between them. | Interface | giny.model | CytoScape |
|
RootGraphAddRemoveTest | | Class | fing.model.test | CytoScape |
|
RootGraphChangeEvent | The event source must be the RootGraph that changed. | Class | giny.model | CytoScape |
|
RootGraphChangeListener | | Interface | giny.model | CytoScape |
|
RootGraphPerformanceTest | | Class | fing.model.test | CytoScape |
|
RotateSelectedNodesAction | Rotates the given selection by the specified amount. | Class | cytoscape.actions | CytoScape |
|
Round | | Class | org.cytoscape.equations.builtins | CytoScape |
|
RoundedRectangleNodeShape | | Class | cytoscape.render.immed.nodeshape | CytoScape |
|
RTree | An in-memory R-tree over real numbers in two dimensions. | Class | cytoscape.geom.rtree | CytoScape |
|
RTreeQueryPerformance | | Class | cytoscape.geom.rtree.test | CytoScape |
|
RTreeSerializationPerformance | | Class | cytoscape.geom.rtree.test | CytoScape |
|
RTreeUpdatePerformance | | Class | cytoscape.geom.rtree.test | CytoScape |
|
RunBareBones | Illustrates how to execute a sample task via the TaskManager. | Class | cytoscape.task.sample | CytoScape |
|
RunSampleTask | Runs the Sample Task and demonstrate various UI options. | Class | cytoscape.task.sample | CytoScape |
|
SampleTask | Sample Task, used to illustrate the Task Framework. | Class | cytoscape.task.sample | CytoScape |
|
SanityTest | | Class | ding.view.test | CytoScape |
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SaveImageTask | | Class | cytoscape.visual.customgraphic | CytoScape |
|
SaveSessionAction | Save Session action. | Class | cytoscape.actions | CytoScape |
|
SaveSessionAsAction | Same as SaveSessionAction, but always opens file chooser. | Class | cytoscape.actions | CytoScape |
|
Scaler | | Interface | cytoscape.util | CytoScape |
|
ScalerFactory | | Class | cytoscape.util | CytoScape |
|
ScalingMethod | enum ScalingMethodextends EnumEnum Constant SummaryLINEAR_LOWER | Class | cytoscape.util | CytoScape |
|
SConvNode | | Class | org.cytoscape.equations.parse_tree | CytoScape |
|
SelectAdjacentEdgesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
SelectAllAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
SelectAllEdgesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
SelectAllNodesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
SelectConnectedNodesAction | select every node connected to the current selected edges. | Class | cytoscape.actions | CytoScape |
|
SelectedEdges | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
|
SelectedNodes | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
|
SelectEvent | Events that are fired when the selected state of a Node or Edge, or a group of Nodes or Edges, is changed. | Class | cytoscape.data | CytoScape |
|
SelectEventListener | Listener for SelectEvents fired by a SelectFilter object. | Interface | cytoscape.data | CytoScape |
|
SelectFilter | This class implements the ability to set the selected state of every node or edge in a GraphPerspective. | Class | cytoscape.data | CytoScape |
|
SelectFirstNeighborsAction | select every first neighbor (directly connected nodes) of the currentlySee Also:Serialized Form | Class | cytoscape.actions | CytoScape |
|
SelectionModeAction | | Class | cytoscape.actions | CytoScape |
|
Semantics | This class defines names for certain data attributes that are commonly used within Cytoscape. | Class | cytoscape.data | CytoScape |
|
SeparateArrowStroke | Fields inherited from class cytoscape. | Class | cytoscape.visual.strokes | CytoScape |
|
Server | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
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SessionState | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
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SetNestedNetworkDialog | | Class | cytoscape.dialogs | CytoScape |
|
SettingsAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.layout.ui | CytoScape |
|
SetVisualPropertiesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
ShapeCellRenderer | | Class | cytoscape.visual.ui.editors.discrete | CytoScape |
|
ShapeStroke | | Class | cytoscape.visual.strokes | CytoScape |
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ShowAllAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
ShowCustomGraphicsManagerAction | Display Custom Graphics Manager GUI. | Class | cytoscape.actions | CytoScape |
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ShowGraphicsDetailsAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
ShrinkExpandGraph | This class shifts the nodes to shrink or expand the graph: it averages the coordinates of all the nodes to find the center | Class | cytoscape.dialogs | CytoScape |
|
ShrinkExpandGraphUI | | Class | cytoscape.dialogs | CytoScape |
|
SIFFileFilter | FileFilter for Reading in Cytoscape SIF Files. | Class | cytoscape.util | CytoScape |
|
Sign | | Class | org.cytoscape.equations.builtins | CytoScape |
|
Sin | | Class | org.cytoscape.equations.builtins | CytoScape |
|
SineWaveStroke | Fields inherited from class cytoscape. | Class | cytoscape.visual.strokes | CytoScape |
|
Sinh | | Class | org.cytoscape.equations.builtins | CytoScape |
|
SList | | Class | org.cytoscape.equations.builtins | CytoScape |
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SolidStroke | Fields inherited from class java. | Class | cytoscape.visual.strokes | CytoScape |
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SpacialEntry2DEnumerator | An enumeration over a set of entries in a SpacialIndex2D structure. | Interface | cytoscape.geom.spacial | CytoScape |
|
SpacialIndex2D | A spacial index for objects in two dimensions. | Interface | cytoscape.geom.spacial | CytoScape |
|
Sqrt | | Class | org.cytoscape.equations.builtins | CytoScape |
|
StaticLayoutMenu | StaticLayoutMenu provides a simple menu item to be added to a layoutSee Also:Serialized Form | Class | cytoscape.layout.ui | CytoScape |
|
status | | Class | cytoscape.data.servers | CytoScape |
|
StDev | | Class | org.cytoscape.equations.builtins | CytoScape |
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StraightenSelectedEdgesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
StringConstantNode | A node in the parse tree representing an integer constant. | Class | org.cytoscape.equations.parse_tree | CytoScape |
|
StringList | | Class | org.cytoscape.equations | CytoScape |
|
StringParser | simply returning the supplied argument. | Class | cytoscape.visual.parsers | CytoScape |
|
StringRangeValueCalculator | | Class | cytoscape.visual.mappings.rangecalculators | CytoScape |
|
StringUtils | Misc Utilities for Formatting Times and Strings. | Class | cytoscape.task.ui | CytoScape |
|
StringWrap | | Class | cytoscape.task.util | CytoScape |
|
SubjectBase | Abstract Base Class for Subject in the Subject / Observer Pattern. | Class | cytoscape.visual | CytoScape |
|
Substitute | | Class | org.cytoscape.equations.builtins | CytoScape |
|
Sum | | Class | org.cytoscape.equations.builtins | CytoScape |
|
SVGExporter | SVG exporter by the batik library. | Class | cytoscape.util.export | CytoScape |
|
SwingWorker | This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to | Class | cytoscape.util | CytoScape |
|
SynonymReader | The purpose of this class is to convert a 'gene_association. | Class | cytoscape.cruft.obo | CytoScape |
|
SynonymTester | | Class | cytoscape.cruft.obo.test | CytoScape |
|
Taggable | | Interface | cytoscape.visual.customgraphic | CytoScape |
|
Tan | | Class | org.cytoscape.equations.builtins | CytoScape |
|
Tanh | | Class | org.cytoscape.equations.builtins | CytoScape |
|
Task | Represents a task that can be terminated prematurely by the same entity that started the task - tasks are started with | Interface | cytoscape.task | CytoScape |
|
TaskManager | Utility class used to execute tasks and visually monitor their progress. | Class | cytoscape.task.util | CytoScape |
|
TaskMonitor | Interface for monitoring the progress of a task. | Interface | cytoscape.task | CytoScape |
|
TeeArrow | | Class | cytoscape.render.immed.arrow | CytoScape |
|
Text | | Class | org.cytoscape.equations.builtins | CytoScape |
|
TextFileReader | | Class | cytoscape.data.readers | CytoScape |
|
TextHttpReader | | Class | cytoscape.data.readers | CytoScape |
|
TextJarReader | | Class | cytoscape.data.readers | CytoScape |
|
TexturePaintFactory | | Class | cytoscape.visual.customgraphic.paint | CytoScape |
|
ThemeInfo | Nested Class SummaryNested classes/interfaces inherited from class cytoscape. | Class | cytoscape.plugin | CytoScape |
|
Thesaurus | todo (pshannon, 25 oct 2002): there may be multiple canonicalNames for the same common name. | Class | cytoscape.data.synonyms | CytoScape |
|
ThesaurusFlatFileReader | Read synonyms from flat file. | Class | cytoscape.data.synonyms.readers | CytoScape |
|
Today | | Class | org.cytoscape.equations.builtins | CytoScape |
|
ToggleVisualMapperAction | This class implements two menu items that allow enabling and disabling theSee Also:Serialized Form | Class | cytoscape.actions | CytoScape |
|
Token | enum Tokenextends EnumEnum Constant SummaryAMPERSAND | Class | org.cytoscape.equations | CytoScape |
|
Tokeniser | | Class | org.cytoscape.equations | CytoScape |
|
TopoGraphNode | Represents a node in a topological graph. | Interface | cytoscape.util | CytoScape |
|
TopologicalSort | See for example http://en. | Class | cytoscape.util | CytoScape |
|
TrackerException | See Also:Serialized FormConstructor SummaryTrackerException() | Class | cytoscape.plugin | CytoScape |
|
Transform | | Class | cytoscape.util | CytoScape |
|
TreeCellRenderer | | Class | cytoscape.dialogs.plugins | CytoScape |
|
TreeCellRenderer | | Class | cytoscape.view | CytoScape |
|
TreeNode | See Also:Serialized FormFields inherited from class javax. | Class | cytoscape.dialogs.plugins | CytoScape |
|
TreeTableModel | TreeTableModel is the model used by a JTreeTable. | Interface | cytoscape.util.swing | CytoScape |
|
TreeTableModelAdapter | This is a wrapper class takes a TreeTableModel and implements the table model interface. | Class | cytoscape.util.swing | CytoScape |
|
TriangleNodeShape | | Class | cytoscape.render.immed.nodeshape | CytoScape |
|
TriangleThumbRenderer | | Class | cytoscape.visual.ui.editors.continuous | CytoScape |
|
Triple | Extract partial graph structure. | Class | cytoscape.data.ontology | CytoScape |
|
Trunc | | Class | org.cytoscape.equations.builtins | CytoScape |
|
Tunable | Tunables are typed objects that maintain properties and an easy way to generate a settings panel to allow user manipulation | Class | cytoscape.layout | CytoScape |
|
TunableListener | The TunableListener interface provides a way to encapsulate CyLayoutAlgorithm property and settings values. | Interface | cytoscape.layout | CytoScape |
|
TypeHandler | This is a temporary implementation. | Class | org.apache.commons.cli | CytoScape |
|
UnaryOpNode | A node in the parse tree representing a unary operator application. | Class | org.cytoscape.equations.parse_tree | CytoScape |
|
Undo | Rudimentary support for undo. | Class | undo | CytoScape |
|
UndoAction | An action that calls undo for the most recent edit in the undoable edit stack. | Class | cytoscape.util.undo | CytoScape |
|
UnHideSelectedAction | See Also:Serialized FormFields inherited from class javax. | Class | cytoscape.actions | CytoScape |
|
UnHideSelectedEdgesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
UnHideSelectedNodesAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
UnifiedNetworkImportDialog | Default GUI component for network import web service clients. | Class | cytoscape.data.webservice.ui | CytoScape |
|
UnrecognizedOptionException | Exception thrown during parsing signalling an unrecognizedVersion:$Revision: 155404 $Author:bob mcwhiter (bob @ werken. | Class | org.apache.commons.cli | CytoScape |
|
Upper | | Class | org.cytoscape.equations.builtins | CytoScape |
|
URLImageCustomGraphics | Fields inherited from class cytoscape. | Class | cytoscape.visual.customgraphic.impl.bitmap | CytoScape |
|
URLImageCustomGraphicsParser | Create instance of URLImageCustomGraphics object from String. | Class | cytoscape.visual.customgraphic | CytoScape |
|
URLUtil | | Class | cytoscape.util | CytoScape |
|
Value | | Class | org.cytoscape.equations.builtins | CytoScape |
|
ValueParser | | Interface | cytoscape.visual.parsers | CytoScape |
|
ValueSelectDialog | Visual Property selector for discrete valuesAuthor:konoSee Also:Serialized Form | Class | cytoscape.visual.ui | CytoScape |
|
ValueToStringConverter | Provide special type of toString for the given class. | Interface | cytoscape.visual.converter | CytoScape |
|
ValueToStringConverterManager | Replacement for ObjectToString. | Class | cytoscape.visual.converter | CytoScape |
|
Var | | Class | org.cytoscape.equations.builtins | CytoScape |
|
VectorCustomGraphics | | Interface | cytoscape.visual.customgraphic.impl.vector | CytoScape |
|
VeeNodeShape | | Class | cytoscape.render.immed.nodeshape | CytoScape |
|
VerticalSlashStroke | Nested Class SummaryNested classes/interfaces inherited from class cytoscape. | Class | cytoscape.visual.strokes | CytoScape |
|
ViewableNodes | Java class for anonymous complex type. | Class | cytoscape.generated | CytoScape |
|
ViewChangeEdit | A Ding specific undoable edit. | Class | ding.view | CytoScape |
|
ViewportChangeListener | | Interface | ding.view | CytoScape |
|
VisualMappingManager | Top-level class for controlling the visual appearance of nodes and edges according to data attributes, as well as some global visual attributes. | Class | cytoscape.visual | CytoScape |
|
VisualProperty | Represents a visual property. | Interface | cytoscape.visual | CytoScape |
|
VisualPropertyDependency | Define dependency of visual properties. | Interface | cytoscape.visual | CytoScape |
|
VisualPropertyIcon | Icon created from Shape object passed from rendering engine. | Class | cytoscape.visual.ui.icon | CytoScape |
|
VisualPropertyType | enum VisualPropertyTypeextends EnumEnum for calculator types. | Class | cytoscape.visual | CytoScape |
|
VisualStyle | This class encapsulates a full set of visual mapping specifications for Cytoscape. | Class | cytoscape.visual | CytoScape |
|
VisualStyleBuilder | Based on the graph/node/edge view information, build new Visual Style. | Class | cytoscape.data.readers | CytoScape |
|
VizMapBypassNetworkListener | Adds NodeView and EdgeView vizmap bypass listeners to network views as the views are created. | Class | cytoscape.visual.ui | CytoScape |
|
VizMapperMainPanel | New VizMapper UI main panel. | Class | cytoscape.visual.ui | CytoScape |
|
VizMapperProperty | | Class | cytoscape.visual.ui | CytoScape |
|
VizMapperTrackRenderer | | Interface | cytoscape.visual.ui.editors.continuous | CytoScape |
|
WebServiceClient | Web service client wrapper for Cytoscape. | Interface | cytoscape.data.webservice | CytoScape |
|
WebServiceClientGUI | Web service client which has custom component should implements this interface. | Interface | cytoscape.data.webservice.ui | CytoScape |
|
WebServiceClientImpl | Abstract class for all web service clients. | Class | cytoscape.data.webservice | CytoScape |
|
WebServiceClientImplWithGUI | | Class | cytoscape.data.webservice | CytoScape |
|
WebServiceClientManager | Web Service Client Manager manages available web service clients in Cytoscape. | Class | cytoscape.data.webservice | CytoScape |
|
WebServiceContextMenu | Context menu for web service clients. | Class | cytoscape.data.webservice.ui | CytoScape |
|
WebServiceContextMenuListener | | Class | cytoscape.data.webservice.ui | CytoScape |
|
WebServiceNetworkImportAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
|
WebServiceThemeInstall | | Class | cytoscape.data.webservice.util | CytoScape |
|
WebstartException | This exception is used when methods that can't be used from the PluginManager if webstart is running are called. | Class | cytoscape.plugin | CytoScape |
|
WidestStringComboBoxModel | This ComboBoxModel tracks the widest string getLabel(Object anObject) should be overridden to derive the String from | Class | cytoscape.util.swing | CytoScape |
|
WidestStringComboBoxPopupMenuListener | Listener that can be attached to a JComboBox. | Class | cytoscape.util.swing | CytoScape |
|
WidestStringProvider | Marker interface to decouple WidestStringComboBoxPopupMenuListener from WidestStringComboBoxModel. | Interface | cytoscape.util.swing | CytoScape |
|
WidthStroke | A simple extension of Stroke that allows Stroke objects to be coupled with LineStyle enum values and allows the width of the | Interface | cytoscape.visual.strokes | CytoScape |
|
WindowUtilities | WindowUtilities keeps track of open windows and may close down the JVM when all primary windows are closed (see #setExitJVMWhenAllWindowsClose | Class | cytoscape.util.shadegrown | CytoScape |
|
WSImportResultDialog | | Class | cytoscape.data.webservice.ui | CytoScape |
|
XGMMLException | Exception for XGMML Reader. | Class | cytoscape.data.readers | CytoScape |
|
XGMMLFileFilter | FileFilter for Reading in XGMML Files. | Class | cytoscape.util | CytoScape |
|
XGMMLReader | This version is Metanode-compatible. | Class | cytoscape.data.readers | CytoScape |
|
XGMMLWriter | Write network and attributes in XGMML format and marshall it in a streme. | Class | cytoscape.data.writers | CytoScape |
|
YValueLegendPanel | | Class | cytoscape.visual.ui.editors.continuous | CytoScape |
|
ZeroStroke | Rather than handle strokes of width 0 for all implementations of WidthStroke, use this wrapper class that, when the width is less than or equal to 0 a | Class | cytoscape.visual.strokes | CytoScape |
|
ZigzagStroke | | Class | cytoscape.visual.strokes | CytoScape |
|
ZipUtil | Compression-related methods mainly for Session Writer. | Class | cytoscape.util | CytoScape |
|
ZoomAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |
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ZoomSelectedAction | See Also:Serialized FormFields inherited from class cytoscape. | Class | cytoscape.actions | CytoScape |