Deprecated API

Contents

• Deprecated Interfaces
• Deprecated Classes
• Deprecated Fields
• Deprecated Methods
• Deprecated Constructors

Deprecated Interfaces

cytoscape.layout.LayoutAlgorithm
Use CyLayoutAlgorithm instead. Will be removed June, 2008

Deprecated Classes

cytoscape.actions.AnimatedLayoutAction
Not apparently used. Shout if you are. Will be removed 5/2008.

cytoscape.data.annotation.Annotation
Use regular CyAttributes for annotation.

cytoscape.data.annotation.AnnotationDescription
Use regular CyAttributes for annotation.

cytoscape.actions.BackgroundColorAction
Use vizmapper gui to edit background color. Will be removed 5/2008

cytoscape.actions.BirdsEyeViewAction
This class is no longer used since the BirdsEyeView is now always part of the NetworkPanel. BirdsEyeView creation and event handling is done by the BirdsEyeViewHandler and initialized in CytoscapeDesktop This class will be removed 5/2008.

cytoscape.actions.CheckBoxFileChooser
This isn't apparently used anywhere. If you are using it, let us know! If you need a file use FileUtil.getFile(). Will be removed 5/2008.

cytoscape.actions.ExpFileChooser
Not apparently used anywhere. Shout if you are. Will be removed 5/2008.

cytoscape.data.attr.util.ExtensibleMultiHashMapModel
Use MultiHashMapFactory instead.

cytoscape.data.annotation.FlattenIntVectors
Use regular CyAttributes for annotation.

cytoscape.visual.ui.LabelPlacerGraphic

cytoscape.visual.LabelPosition

cytoscape.visual.parsers.LabelPositionParser

cytoscape.visual.parsers.ObjectToString
will be removed in May 2011. Use ValueToStringConverterManager.manager.toString(obj) instead.

cytoscape.data.annotation.Ontology
Use regular CyAttributes for annotation.

cytoscape.data.annotation.OntologyDescription
Use regular CyAttributes for annotation.

cytoscape.data.annotation.OntologyTerm
Use regular CyAttributes for annotation.

cytoscape.dialogs.preferences.PluginsTableModel
This class is no longer used in cytoscape. If you are using it, let us know and we'll figure something out. Otherwise, this will be removed December 2007.

Deprecated Fields

cytoscape.data.Semantics.BIOLOGICAL_PROCESS

cytoscape.data.Semantics.CELLULAR_COMPONENT

cytoscape.data.Semantics.DNA

cytoscape.visual.mappings.ObjectMapping.EDGE_MAPPING

cytoscape.data.Semantics.GO_ALIASES

cytoscape.data.Semantics.GO_COMMON_NAME

cytoscape.plugin.InstallablePlugin.MATCH_JAR_REGEXP
This was only ever used internally, so now it is package protected and part of JarUtil. Use that one as an alternative. Will be removed Jan 2010.

cytoscape.data.Semantics.MOLECULAR_FUNCTION

cytoscape.data.Semantics.MOLECULE_TYPE

cytoscape.visual.mappings.ObjectMapping.NODE_MAPPING

cytoscape.data.Semantics.PROTEIN

cytoscape.data.Semantics.RNA

cytoscape.data.Semantics.SPECIES

Deprecated Methods

cytoscape.view.CytoscapeDesktop.addEdit(UndoableEdit)
Use CyUndo.getUndoableEditSupport().postEdit(edit) instead. Will be removed March 2008.

cytoscape.data.Semantics.applyNamingServices(CyNetwork)

cytoscape.visual.VisualProperty.applyToEdgeView(EdgeView, Object)
Use other the applyToNodeView method with the VisualPropertyDependency arg as null. Will be removed Jan 2011.

cytoscape.visual.VisualProperty.applyToNodeView(NodeView, Object)
Use other the applyToNodeView method with the VisualPropertyDependency arg as null. Will be removed Jan 2011.

cytoscape.data.Semantics.areSynonyms(String, String, CyNetwork)

cytoscape.data.Semantics.assignCommonNames(CyNetwork, BioDataServer)

cytoscape.data.Semantics.assignNodeAliases(CyNode, String, BioDataServer)

cytoscape.data.Semantics.assignSpecies(CyNetwork)

cytoscape.actions.DestroyNetworkAction.destroyCurrentNetwork()
Use Cytoscape.destroyNetwork(Cytoscape.getCurrentNetwork()) instead. Will be gone 11/2008.

cytoscape.actions.DestroyNetworkViewAction.destroyViewFromCurrentNetwork()
Use Cytoscape.destroyNetworkView() instead. Will go 11/2008.

cytoscape.data.Semantics.getAllSynonyms(String, CyNetwork)

cytoscape.data.CyAttributes.getAttributeList(String, String)
Use getListAttribute() instead. Will be removed 11/2007.

cytoscape.data.CyAttributes.getAttributeMap(String, String)
Use getMapAttribute() instead. Will be removed 11/2007.

cytoscape.CyNetwork.getClientData(String)
Use CyAttributes directly. This method will be removed in May, 2007.

cytoscape.giny.FingCyNetwork.getClientData(String)
Get Some client data

cytoscape.CyNetwork.getClientDataNames()
Use CyAttributes directly. This method will be removed in May, 2007.

cytoscape.giny.FingCyNetwork.getClientDataNames()
Get a list of all currently available ClientData objects

cytoscape.view.CyMenus.getCytoPanelMenu()
Will be removed April 2008. Cytopanels no longer have a separate menu (they're in View).

cytoscape.view.CytoscapeDesktop.getHelpBroker()
Will be removed April 2008. Use CyHelpBroker.getHelpBroker() instead.

cytoscape.view.CytoscapeDesktop.getHelpSet()
Will be removed April 2008. Use CyHelpBroker.getHelpSet() instead.

cytoscape.visual.mappings.MappingType.getMappingType(String)
Will be removed 5/2008

cytoscape.visual.NodeAppearanceCalculator.getNodeSizeLocked()
Use VisualStyle.getDependency().check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED) instead. Will be removed Jan 2011.

cytoscape.visual.NodeAppearance.getNodeSizeLocked()
Use VisualStyle.getDependency().check(VisualPropertyDependency .Definition.NODE_SIZE_LOCKED) instead. Will be removed Jan 2011.

cytoscape.util.Misc.getRGBText(Color)
Will be removed April, 2011. Use ColorUtil.getColorAsText instead.

cytoscape.data.Semantics.getSpeciesInNetwork(CyNetwork)

cytoscape.visual.parsers.ObjectToString.getStringValue(Object)

cytoscape.view.NetworkViewManager.getTabbedPane()
Tabbed view is no longer used. Will be removed Aug 2008.

cytoscape.visual.calculators.Calculator.getUI(JDialog, CyNetwork)
replaced by new VizMap GUI components. Will be removed in 2.8 or 3.0

cytoscape.visual.calculators.AbstractCalculator.getUI(JDialog, CyNetwork)
Will be removed next release (2.8 or 3.0)

cytoscape.visual.mappings.ObjectMapping.getUI(JDialog, CyNetwork)

cytoscape.visual.mappings.AbstractMapping.getUI(JDialog, CyNetwork)

cytoscape.view.CytoscapeDesktop.getViewType()
View type is no longer used, so just don't use this method. Will be gone August 2008.

cytoscape.view.CyMenus.initCytoPanelMenus()
Will be removed April 2008. Cytopanels are initialized in the Display* actions. Do not use.

cytoscape.visual.CalculatorCatalogFactory.loadCalculatorCatalog(String)
The vmName parameter is no longer used - just use loadCalculatorCatalog(). Will be removed 10/06.

cytoscape.util.Misc.parseRGBText(String)
will be removed in April, 2011. use ColorUtil.parseColorText instead.

cytoscape.view.CytoscapeDesktop.parseViewType(String)
View types are no longer support so stop using this. Will be removed August 2008.

cytoscape.CyNetwork.putClientData(String, Object)
Use CyAttributes directly. This method will be removed in May, 2007.

cytoscape.giny.FingCyNetwork.putClientData(String, Object)
Networks can support client data.

cytoscape.util.ZipUtil.readFile(String, String)

cytoscape.visual.mappings.ObjectMapping.setControllingAttributeName(String, CyNetwork, boolean)
Will be removed in 2.8. Use setControllingAttributeName(final String controllingAttrName) instead.

cytoscape.visual.mappings.AbstractMapping.setControllingAttributeName(String, CyNetwork, boolean)

cytoscape.visual.NodeAppearanceCalculator.setNodeSizeLocked(boolean)
Use VisualStyle.getDependency().set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED,b) instead. Will be removed Jan 2011.

cytoscape.visual.NodeAppearance.setNodeSizeLocked(boolean)
Use VisualStyle.getDependency().set(VisualPropertyDependency.Definition .NODE_SIZE_LOCKED,b) instead. Will be removed Jan 2011.

cytoscape.view.CyMenus.setNodesRequiredItemsEnabled()
Will be removed April 2008. Item state is now handled by Actions directly. Don't use this.

cytoscape.view.CyMenus.setOverviewEnabled(boolean)
Will be removed April 2008. Item state is now handled by Actions directly. Don't use this.

cytoscape.view.CyNetworkView.setSelected(CyEdge[])
this method is not working, use CyNetwork.setSelectedEdgeState(Collection, boolean)

cytoscape.view.CyNetworkView.setSelected(CyNode[])
this method is not working, use Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)

cytoscape.view.CyNetworkView.setSelected(EdgeView[])
this method is not working, use CyNetwork.setSelectedEdgeState(Collection, boolean)

cytoscape.view.CyNetworkView.setSelected(NodeView[])
this method is not working, use Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)

cytoscape.view.CyMenus.setVisualMapperItemsEnabled(boolean)
Will be removed April 2008. Item state is now handled by Actions directly. Don't use this.

cytoscape.view.CytoscapeDesktop.setVisualStyle(VisualStyle)
use VisualMappingManager.setVisualStyle(VisualStyle style) instead.

cytoscape.view.NetworkViewManager.stateChanged(ChangeEvent)
Will no longer support ChangeListener. Will be removed August 2008.

cytoscape.dialogs.preferences.PreferenceValueDialog.validatedPluginData(Component, String)
no longer used by anyting. Will leave this world Dec 2007.

cytoscape.view.NetworkViewManager.windowGainedFocus(WindowEvent)
Will no longer support WindowFocusListener. Will be removed August 2008.

cytoscape.view.NetworkViewManager.windowLostFocus(WindowEvent)
Will no longer support WindowFocusListener. Will be removed August 2008.

Deprecated Constructors

cytoscape.visual.mappings.continuous.ContinuousLegend(String, List, Object, VisualPropertyType)

cytoscape.visual.mappings.ContinuousMapping(Object, byte)

cytoscape.visual.mappings.DiscreteMapping(Object, byte)

cytoscape.visual.mappings.DiscreteMapping(Object, String, byte)

cytoscape.visual.EdgeAppearanceCalculator()
Use VisualStyle.getEdgeAppearanceCalculator() or new EdgeAppearanceCalculator( VisualStyle.getDependency() ); Will be removed Jan 2010.

cytoscape.dialogs.ExportAsGraphicsFileChooser(CyFileFilter[])

cytoscape.view.NetworkViewManager(CytoscapeDesktop, int)
view_type is no longer used. Use the other constructor. Will be removed Aug 2008.

cytoscape.visual.NodeAppearanceCalculator()
Use VisualStyle.getNodeAppearanceCalculator() or new NodeAppearancCalculator( VisualStyle.getDependency() ) instead. Will be removed January 2011.

cytoscape.visual.mappings.PassThroughMapping(Object)

cytoscape.visual.mappings.PassThroughMapping(Object, byte)

cytoscape.visual.mappings.PassThroughMapping(Object, String)

cytoscape.dialogs.preferences.PreferenceValueDialog(Dialog, String, String, PreferencesDialog, TableModel, String, boolean)
includeBrowse is not longer supported. Use the other constructor instead. Will be removed 5/2008.

cytoscape.layout.Tunable(String, String, int, Object, Object, Object, int, boolean)
Use the IMMUTABLE flag directly rather than this special constructor.

cytoscape.data.readers.VisualStyleBuilder(String, Map, Map, Map)
this should no longer be used and is not functional. Use VisualStyleBuilder(String) instead and then call addProperty for each value