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Cytoscape 2.6.1 (c) 2006,2007 ISB, MSKCC, UCSD | ||||||||
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addCustomGraphic(Shape,Paint,byte).
The entire index-based custom graphic API has been deprecated. This includes all the methods that refer to custom graphics using indices:
public int addCustomGraphic(Shape s, Paint p, int index); public void removeCustomGraphic(int index); public Paint getCustomGraphicPaint(int index); public Shape getCustomGraphicShape(int index); public int getCustomGraphicCount();To keep things completetly backwards compatible and to avoid introducing bugs, the new API methods are completely independent from the the old API methods. Thus, a custom graphic added using the new API will not be accessible from the old API and visa versa.
The reason for the deprecation is:
In order for multiple plugins to use the old API, each must monitor deletions to custom graphics and update their saved indices, since the indices will shift down as graphics are deleted. This management isn't even possible with the old API because there's no event mechanism to inform plugins when the indices change. Also, each plugin must keep a list of all indices for all graphics added, since the indices may not be contiguous.
Using indices forces the need for a locking mechanism to ensure you are guaranteed a unique and correct index independent of any other plugins.
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.
CyAttributesUtils.traverseAttributeValues().GraphViewHandler that simply reflects GraphPerspective
changes on a given GraphViewBirdsEyeViewHandler and initialized in
This class will be removed 5/2008.CytoscapeProgressMonitor when the user
click on the Cancel button.
get method.
giny.view.GraphView is kept synchronized
with its giny.model.GraphPerspective member by this
GraphViewController.
CytoscapeToolBar.initializeCytoscapeToolBar().
Tunable.USESLIDER is set,
and the caller provides both lower and upper bounds,
the user is presented with a slider interface.
Tunable.NUMERICATTRIBUTE is set, only
integer or double attributes are shown, and if
the Tunable.MULTISELECT flag is set, the user
is presented with a list from which multiple
values can be selected, otherwise, the user
is presented with a combo box.
construct method has returned.
FontChooser
JList or JComboBox in the face specified.construct method.
getListAttribute() instead. Will be removed 11/2007.
getMapAttribute() instead. Will be removed 11/2007.
CyAttributes directly. This method will be
removed in May, 2007.
CyAttributes directly. This method will be
removed in May, 2007.
column.
column.
getNumCustomGraphics().
Note that the new API methods work independent of the old API methods.
See addCustomGraphic(Shape,Paint,int)
for details.
cytoscape.render.stateful.CustomGraphic.getPaint().
Note that the new API methods work independent of the old API methods.
See addCustomGraphic(Shape,Paint,int)
for details.
cytoscape.render.stateful.CustomGraphic.getShape().
Note that the new API methods work independent of the old API methods.
See addCustomGraphic(Shape,Paint,int)
for details.
DownloadableInfo.getDownloadableURL()} will be removed June 2008
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
DownloadableInfo.getLicenseText() will be removed June 2008
DownloadableInfo.getObjectVersion() will be removed June 2008
DownloadableInfo.getType()
DownloadableInfo.getType()
DownloadableInfo.getObjectUrl()} will be removed June 2008
node,
at column number column.
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.halt() is a non-blocking request to halt the task, and
is called by an external entity.
giny.view.GraphView.
giny.view.GraphView.
CyAttributesUtils.copyAttributes().
Tunable.USESLIDER is set,
and the caller provides both lower and upper bounds,
the user is presented with a slider interface.
node,
at column number column is editable.
DownloadableInfo.isLicenseRequired() will be removed June 2008
DownloadableInfo.isNewerObjectVersion(DownloadableInfo)} will be removed June 2008
Compare the version of the object to the given object.
Tunable.MULTISELECT flag is
set, the user is presented with a list
from which multiple values can be selected,
otherwise, the user is presented with a
combo box.
Tunable.NUMERICATTRIBUTE is set, only
integer or double attributes are shown, and if
the Tunable.MULTISELECT flag is set, the user
is presented with a list from which multiple
values can be selected, otherwise, the user
is presented with a combo box.
DownloadableInfo.DownloadableInfo()
Initializes a PluginInfo object with the following defaults:
setName("Unknown"); setDescription("No description");
setObjectVersion("0.1"); setCytoscapeVersion(
cytoscape.cytoscapeVersion.version ); setCategory("Uncategorized");
DownloadableInfo.DownloadableInfo(String)
DownloadableInfo.DownloadableInfo(String)
PluginManager#inquireThread(String, PluginInquireAction)
method to get plugins from a given site.CyAttributes directly. This method will be
removed in May, 2007.
giny.view.GraphView objects that this
GraphViewController keeps synchronized to their corresponding
giny.model.GraphPerspective members.
removeCustomGraphic(CustomGraphic).
Note that the new API methods work independent of the old API methods.
See addCustomGraphic(Shape,Paint,int)
for details.
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).
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.
run() executes the task, and is called by an
external entity.
giny.view.GraphView object.
giny.view.GraphView object.
setListAttribute() instead. Will be removed 11/2007.
setMapAttribute() instead. Will be removed 11/2007.
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.
DownloadableInfo#setLicense(String) will be removed June 2008
Sets the license information for the plugin. Not required.
DownloadableInfo.setLicense(String, boolean) will be removed June 2008
Sets the license information for the plugin. Not required.
DownloadableInfo.setObjectVersion(double)} will be removed June 2008
Sets the version of the plugin. Defaults to 0.1
Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)
Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)
CyNetwork.setSelectedEdgeState(Collection, boolean)
CyNetwork.setSelectedEdgeState(Collection, boolean)
Task know who it should report to regarding
task progress, errors, status description, etc.
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.
Task.run() and tasks are terminated prematurely
[and asynchronously] with Task.halt().DownloadableInfo.DownloadableInfo()
Initializes a ThemeInfo object with the following defaults:
setName("Unknown"); setDescription("No description");
setObjectVersion("0.1"); setCytoscapeVersion(
cytoscape.cytoscapeVersion.version ); setCategory("Theme");
DownloadableInfo.DownloadableInfo(String)
CytoscapeMenuBar.getIdentifier().
giny.view.GraphView object
giny.view.GraphView object
GraphPerspective
giny.model.GraphPerspective
Useful if GraphPerspectiveChangeEvents haven't been handled,
and a graph_view must be made synchronized with its GraphPerspective.
#setExitJVMWhenAllWindowsClose
and #addPrimaryWindow( Window )).' '.
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