| Name | Description | Type | Package | Framework |
| AboutDialog | About page for web service clients or other plugins. | Class | cytoscape.util.swing | CytoScape |
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| AbstractCellEditor | | Class | cytoscape.util.swing | CytoScape |
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| AbstractScaler | Used to scale a list of values to [a,b]Constructor SummaryAbstractScaler() | Class | cytoscape.util | CytoScape |
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| AbstractTreeTableModel | | Class | cytoscape.util.swing | CytoScape |
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| ArrayIntEnumerator | A utility class which conveniently converts an array of integers into an IntEnumerator (an enumeration of integers). | Class | cytoscape.util.intr | CytoScape |
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| ArrayIntIterator | A utility class which conveniently converts an array of integers into an IntIterator (an iteration of integers). | Class | cytoscape.util.intr | CytoScape |
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| AttributeImportPanel | General GUI component for importing attributes. | Class | cytoscape.util.swing | CytoScape |
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| BioDataServerUtil | | Class | cytoscape.util | CytoScape |
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| BitmapExporter | Bitmap exporter by the ImageIO class. | Class | cytoscape.util.export | CytoScape |
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| BitSetPerformance | | Class | cytoscape.util.intr.test | CytoScape |
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| BookmarksUtil | Utility methods for getting entries in the bookmark object. | Class | cytoscape.util | CytoScape |
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| CheckBoxJList | This class is based on CheckBoxJList: from SWING HACKS ISBN: 0-596-00907-0 | Class | cytoscape.util.swing | CytoScape |
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| ColorUtil | Color utility class to convert Java color object to string and vice versa. | Class | cytoscape.util | CytoScape |
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| ColumnResizer | Automatically resize column based on the objects in the cell. | Class | cytoscape.util.swing | CytoScape |
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| CreditScreen | | Class | cytoscape.util | CytoScape |
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| CyAbstractEdit | A small convenience class that can be used to create new edits. | Class | cytoscape.util.undo | CytoScape |
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| CyCollapsiblePanel | The user-triggered collapsable panel containing the component (trigger) in the titled borderSee Also:Serialized Form | Class | cytoscape.util.swing | CytoScape |
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| CyColorChooser | This is an annoying re-implementation of JColorChooser. | Class | cytoscape.util | CytoScape |
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| CyFileFilter | A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about. | Class | cytoscape.util | CytoScape |
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| CyNetworkNaming | | Class | cytoscape.util | CytoScape |
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| CytoscapeAction | | Class | cytoscape.util | CytoScape |
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| CytoscapeMenuBar | | Class | cytoscape.util | CytoScape |
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| CytoscapeProgressMonitor | CytoscapeProgressMonitor. | Class | cytoscape.util | CytoScape |
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| CytoscapeToolBar | | Class | cytoscape.util | CytoScape |
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| CyUndo | A tiny class for supporting undo in the Cytoscape context. | Class | cytoscape.util.undo | CytoScape |
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| DropDownMenuButton | Button with drop down menu. | Class | cytoscape.util.swing | CytoScape |
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| Exec | | Class | cytoscape.util | 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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| FileUtil | Provides a platform-dependent way to open files. | Class | cytoscape.util | CytoScape |
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| FilterHistoryJList | JList with incremntal search & search history. | Class | cytoscape.util.swing | CytoScape |
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| GMLFileFilter | FileFilter for Reading in GML Files. | Class | cytoscape.util | CytoScape |
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| GraphSetUtils | | Class | cytoscape.util | CytoScape |
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| IndeterminateProgressBar | This class creates a dialog with a JProgressBar in indeterminate state. | Class | cytoscape.util | CytoScape |
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| 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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| IntEnumerator | An enumeration over a list of 32 bit integers. | Interface | cytoscape.util.intr | 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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| JnlpWriterUtil | | Class | cytoscape.util | CytoScape |
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| JStatusBar | Simple status bar with 3 fields. | Class | cytoscape.util.swing | 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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| LongEnumerator | An enumeration over a list of 64 bit integers. | Interface | cytoscape.util.intr | 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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| MacAppConfig | Configures the Mac OS X Info. | Class | cytoscape.util | CytoScape |
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| MathUtil | | Class | cytoscape.util | CytoScape |
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| MemoryReporter | A class used to track JVM memory usage. | Class | cytoscape.util | 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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| 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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| ModuleProperties | | Interface | cytoscape.util | CytoScape |
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| ModulePropertiesImpl | | Class | cytoscape.util | CytoScape |
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| MonitoredTask | | Interface | cytoscape.util | CytoScape |
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| MutableBool | | Class | cytoscape.util | CytoScape |
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| MutableInt | | Class | cytoscape.util | CytoScape |
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| MutableString | | Class | cytoscape.util | CytoScape |
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| NestedNetworkViewUpdater | This class manages images that represent nested networks. | Class | cytoscape.util | CytoScape |
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| NetworkSelectorPanel | | Class | cytoscape.util.swing | CytoScape |
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| NNFFileFilter | File filter for Nested Network Format (NNF). | Class | cytoscape.util | CytoScape |
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| OpenBrowser | | Class | cytoscape.util | CytoScape |
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| PDFExporter | PDF exporter by the iText library. | Class | cytoscape.util.export | CytoScape |
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| PercentUtil | Helper Class for Calculating Percentage of Multi-Step Processes. | Class | cytoscape.util | CytoScape |
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| PrimesGenerator | | Class | cytoscape.util.intr.test | CytoScape |
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| 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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| PSExporter | | Class | cytoscape.util.export | CytoScape |
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| RecentlyOpenedTracker | A class to keep track of a short list of recently opened URLs. | Class | cytoscape.util | CytoScape |
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| RedoAction | An action that calls redo for the most recent edit in the undoable edit stack. | Class | cytoscape.util.undo | CytoScape |
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| Scaler | | Interface | cytoscape.util | CytoScape |
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| ScalerFactory | | Class | cytoscape.util | CytoScape |
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| ScalingMethod | enum ScalingMethodextends EnumEnum Constant SummaryLINEAR_LOWER | Class | cytoscape.util | CytoScape |
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| SIFFileFilter | FileFilter for Reading in Cytoscape SIF Files. | Class | cytoscape.util | CytoScape |
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| SVGExporter | SVG exporter by the batik library. | Class | cytoscape.util.export | CytoScape |
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| SwingWorker | This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to | Class | cytoscape.util | CytoScape |
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| TopoGraphNode | Represents a node in a topological graph. | Interface | cytoscape.util | CytoScape |
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| TopologicalSort | See for example http://en. | Class | cytoscape.util | CytoScape |
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| Transform | | Class | cytoscape.util | CytoScape |
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| TreeTableModel | TreeTableModel is the model used by a JTreeTable. | Interface | cytoscape.util.swing | CytoScape |
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| TreeTableModelAdapter | This is a wrapper class takes a TreeTableModel and implements the table model interface. | Class | cytoscape.util.swing | CytoScape |
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| UndoAction | An action that calls undo for the most recent edit in the undoable edit stack. | Class | cytoscape.util.undo | CytoScape |
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| URLUtil | | Class | cytoscape.util | CytoScape |
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| WidestStringComboBoxModel | This ComboBoxModel tracks the widest string getLabel(Object anObject) should be overridden to derive the String from | Class | cytoscape.util.swing | CytoScape |
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| WidestStringComboBoxPopupMenuListener | Listener that can be attached to a JComboBox. | Class | cytoscape.util.swing | CytoScape |
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| WidestStringProvider | Marker interface to decouple WidestStringComboBoxPopupMenuListener from WidestStringComboBoxModel. | Interface | cytoscape.util.swing | CytoScape |
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| 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 |
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| XGMMLFileFilter | FileFilter for Reading in XGMML Files. | Class | cytoscape.util | CytoScape |
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| ZipUtil | Compression-related methods mainly for Session Writer. | Class | cytoscape.util | CytoScape |