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UnmarshallingEventHandler
to minimize code generation.UnmarshallingEventHandler
to minimize code generation.CyAttributes.
CyAttributes.setAttribute(String, String, Double) instead.
FingCyNetwork.addSelectEventListener(SelectEventListener)
giny.view.GraphView objects that this
GraphViewController keeps synchronized with their
giny.model.GraphPerspective objects.
giny.view.GraphView objects that this
GraphViewController keeps synchronized to their
giny.model.GraphPerspective objects.
CyNode.getIdentifier() instead.
This attribute will be removed in April, 2007.
CyAttributes.setAttributeList(String, String, java.util.List)
for equivalent functionality.
GraphViewHandler that simply reflects GraphPerspective
changes on a given GraphViewThe argument is simply a String that is useful for identifying the caller of this method. This is provided for debugging purposes, in case an algorithm forgets to provide a matching end method for each begin.
CytoscapeProgressMonitor when the user
click on the Cancel button.
CyNode.getIdentifier() instead.
This attribute will be removed in April, 2007.
ChangeEvent is needed per catalog instance since
the event's only state is the source property.
ChangeEvent is needed per calculator instance
since the event's only state is the source property.
CyNode.getIdentifier() instead.
This attribute will be removed in April, 2007.
get method.
giny.view.GraphView is kept synchronized
with its giny.model.GraphPerspective member by this
GraphViewController.
XMLSerializerXMLSerializerMarshaller object that can be used to convert a
java content-tree into XML data.
Marshaller object that can be used to convert a
java content-tree into XML data.
Unmarshaller object that can be used to convert XML
data into a java content-tree.
Unmarshaller object that can be used to convert XML
data into a java content-tree.
Validator object that can be used to validate a
java content-tree.
Validator object that can be used to validate a
java content-tree.
CytoscapeToolBar.initializeCytoscapeToolBar().
CyAttributes.deleteAttribute(String) instead.
CyAttributes.deleteAttribute(String, String) instead.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
MappingFactory to construct a new
ObjectMapping based on the supplied arguments.
The argument is a String for identifying the caller of this method.
ErrorHandler and reports to the
SAXUnmarshallerHandler.ErrorHandler and reports to the
SAXUnmarshallerHandler.construct method has returned.
CyNetwork.selectAllEdges()
FingCyNetwork.selectAllEdges()
CyNetwork.selectAllNodes()
FingCyNetwork.selectAllNodes()
SelectEventSelectFilterFontChooser
JList or JComboBox in the face specified.If the current state is clear (i.e., there are no calls to beginActivity without matching endActivity calls), then this method does nothing.
The argument is a String for identifying the caller of this method.
CyAttributes instead. It provides several
getter methods for retrieving Boolean, Integer, Double and String values.
construct method.
CyAttributes that provides
this functionality, but it can be recreated via several calls.
CyAttributesUtils.getAttribute(String, CyAttributes)
instead.
CyAttributes.getAttributeNames() instead.
CyAttributeUtils.getAttributes(String,CyAttributes).
CyNode.getIdentifier() or
CyEdge.getIdentifier() instead.
CyAttributesUtils.getClass(String,CyAttributes) instead.
CyAttributes directly. This method will be
removed in May, 2007.
CyAttributes directly. This method will be
removed in May, 2007.
column.
column.
CyAttributes.getDoubleAttribute(String, String) instead.
Cytoscape.getEdgeAttributes() instead. This
method will be removed in September, 2006.
Cytoscape.getEdgeAttributes() instead. This
method will be removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
Cytoscape.getEdgeAttributes() instead. This
method will be removed in September, 2006.
CyNetwork.getSelectedEdges()
FingCyNetwork.getSelectedEdges()
CyNetwork.getSelectedEdges()
FingCyNetwork.getSelectedEdges()
CyNetwork.getSelectedNodes()
FingCyNetwork.getSelectedNodes()
CyNetwork.getSelectedNodes()
FingCyNetwork.getSelectedNodes()
CyNetwork.getSelectFilter()
FingCyNetwork.getSelectFilter()
Cytoscape.getCyNode(String) or
Cytoscape.getCyEdge(String, String, String, String) instead.
cytoscape.view.GraphViewHandler for the given
giny.view.GraphView
Map with giny.view.GraphView
objects as keys, and cytoscape.view.GraphViewHandler objects
as values, two or more different keys can share the same value.
giny.view.GraphView objects
that this GraphViewController will keep synchronized with
their corresponding giny.model.GraphPerspective objects
available through their getGraphPerspective() method
CyAttributes.getIntegerAttribute(String, String)
instead.
CyAttributes.getAttributeList(String, String)
instead.
GraphPerspective.nodesIterator() or
GraphPerspective.edgesIterator() instead.
Cytoscape.getNodeAttributes() instead. This
method will be removed in September, 2006.
Cytoscape.getNodeAttributes() instead. This
method will be removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
Cytoscape.getNodeAttributes() instead. This
method will be removed in September, 2006.
CyAttributes that provides
this functionality, but it can be recreated via several calls.
MultiHashMap.getObjectKeys(String)
instead.
CyAttributes.getAttributeList(String, String)
instead.
CyAttributes.getStringAttribute(String, String)
instead.
CyAttributes that provides
this functionality, but it can be recreated via several calls.
CyAttributes that provides
this functionality, but it can be recreated via several calls.
CyAttributes instead. It provides several
getter methods for retrieving Boolean, Integer, Double and String values.
node,
at column number column.
CyAttributes instead.giny.model.GraphPerspective
objects accessed through giny.view.GraphView.getGraphPerspective() of
this object's graphViews is made.
GraphViewController.DEFAULT_GRAPH_VIEW_HANDLER
to all the given giny.view.GraphView objects in the array.
cytoscape.view.GraphViewHandler objects
for the given giny.view.GraphView objects in the arrays.
giny.mode.GraphPerspective by updating one of its
giny.view.GraphViews.giny.view.GraphView.
giny.view.GraphView.
CyAttributes.getType(String) instead.
CyAttributes.hasAttribute(String, String) instead.
CyNode.getIdentifier() instead.
This attribute will be removed in April, 2007.
node,
at column number column is editable.
CyNetwork.isSelected(Node)
CyNetwork.isSelected(Edge)
FingCyNetwork.isSelected(Node)
FingCyNetwork.isSelected(Edge)
Marshaller interface for JAXB RI.Marshaller interface for JAXB RI.MappingFactory to construct a new
ObjectMapping based on the supplied arguments.
CyAttributes.getAttributeNames().length instead.
CyAttributesReader instead.
CyAttributes directly. This method will be
removed in May, 2007.
CyAttributesReader instead.
giny.view.GraphView objects that this
GraphViewController keeps synchronized to their corresponding
giny.model.GraphPerspective members.
CyNetwork.removeSelectEventListener(SelectEventListener)
FingCyNetwork.removeSelectEventListener(SelectEventListener)
GraphViewController contains the given
giny.view.GraphView, then it is removed from it, and it no longer listens
for change events from the removed giny.view.GraphView's
giny.model.GraphPerspective.
giny.view.GraphView
object.
giny.view.GraphView
object.
giny.view.GraphView object,
it also removes the connected edges to these nodes (an edge without a connecting node makes
no mathematical sense).
giny.view.GraphView object, it also removes the connected edges to
these nodes (an edge without a connecting node makes no mathematical sense).
SAXException or reported through this method.
SAXException or reported through this method.
giny.view.GraphView
object
giny.view.GraphView object
giny.view.GraphView object
giny.view.GraphView object
GraphViewController as a listener for
all giny.model.GraphPerspective that were temporarily
"removed" by calling stopListening(), it updates the GraphViews
of the GraphPerspectives so that they are synchronized to reflect changes that
may have occured while not listening.
GraphViewController listener to the
giny.model.GraphPerspective of the given giny.view.GraphView
that was temporarily "removed" by a call to stopListening(GraphView), it updates
graph_view so that it's synchronized to its GraphPerspective
due to changes that may have occured while not listening.
UnmarshallerHandler.UnmarshallerHandler.giny.view.GraphView object.
giny.view.GraphView object.
CyAttributes.
CyAttributes.setAttribute(String, String, Double) instead.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyNetwork.setSelectedNodeState(Collection,boolean)
CyNetwork.setSelectedEdgeState(Collection,boolean)
FingCyNetwork.setSelectedNodeState(Collection,boolean)
FingCyNetwork.setSelectedEdgeState(Collection,boolean)
CyNetwork.setSelectedEdgeState(Collection,boolean)
CyNetwork.setSelectedEdgeState(Collection,boolean)
FingCyNetwork.setSelectedEdgeState(Collection,boolean)
FingCyNetwork.setSelectedEdgeState(Collection,boolean)
CyNetwork.setSelectedNodeState(Collection,boolean)
CyNetwork.setSelectedNodeState(Collection,boolean)
FingCyNetwork.setSelectedNodeState(Collection,boolean)
FingCyNetwork.setSelectedNodeState(Collection,boolean)
giny.view.GraphView object belongs to this
GraphViewController, then its GraphViewHandler
is set to the given one.
giny.view.GraphView objects
that this GraphViewController will keep synchronized with
their corresponding giny.model.GraphPerspective objects
available through their getGraphPerspective() method, the
DEFAULT_GRAPH_VIEW_HANDLER is set for all the views.
giny.view.GraphView objects
that this GraphViewController will keep synchronized with
their corresponding giny.model.GraphPerspective objects
available through their getGraphPerspective() method, the
cytoscape.view.GraphViewHandler objects for the
GraphViews are obtained from the given Map,
if a GraphView in the array is not a key in the Map
then DEFAULT_GRAPH_VIEW_HANDLER is used.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
CyAttributes directly. This method will be
removed in September, 2006.
Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)
Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)
CyNetwork.setSelectedEdgeState(Collection, boolean)
CyNetwork.setSelectedEdgeState(Collection, boolean)
node,
at column number column.
GraphViewController as a listener for
all giny.model.GraphPerspective objects that it currently
listens to
GraphViewController listener
from the giny.model.GraphPerspective object that the given
giny.view.GraphView views.
construct method
and then exit.
CytoscapeMenuBar.getIdentifier().
CyNetwork.unselectAllEdges()
FingCyNetwork.unselectAllEdges()
CyNetwork.unselectAllNodes()
FingCyNetwork.unselectAllNodes()
giny.view.GraphView object
giny.view.GraphView object
layout must be an object previously returned
by GraphConverter.getGraphCopy().
GraphPerspective
giny.model.GraphPerspective
Useful if GraphPerspectiveChangeEvents haven't been handled,
and a graph_view must be made synchronized with its GraphPerspective.
VisualMappingManager
vizMapper.
#setExitJVMWhenAllWindowsClose
and #addPrimaryWindow( Window )).
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