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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.
opt to this group
AlreadySelectedException
with the specified detail message.
CyAttributesUtils.traverseAttributeValues().GraphViewHandler that simply reflects GraphPerspective
changes on a given GraphViewflatten method.BirdsEyeViewHandler and initialized in CytoscapeDesktop
This class will be removed 5/2008.token into its constituent parts
using the following algorithm.
CytoscapeProgressMonitor when the user
click on the Cancel button.
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.
Options descriptor.CommandLineParser interface
can parse a String array according to the Options specified
and return a CommandLine.get method.
giny.view.GraphView is kept synchronized
with its giny.model.GraphPerspective member by this
GraphViewController.
char.
char.
Attribute
Bookmarks
Category
Child
str.
Cysession
Cytopanel
Cytopanels
DataSource
str.
JAXBElement<String>}
Desktop
DesktopSize
Edge
str.
str.
HiddenEdges
HiddenNodes
Network
NetworkFrame
NetworkFrames
NetworkTree
Node
Ontology
OntologyServer
len.
Panel
Panels
JAXBElement<String>}
Parent
Plugin
Plugins
SelectedEdges
SelectedNodes
JAXBElement<String>}
Server
JAXBElement<String>}
SessionState
str.
Object of type obj
with the value of str.
Object of type clazz
with the value of str.
ViewableNodes
CyCommands and CyCommandNamespaces.CyCommands.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.
startPos for the
text in text with the column width width.
construct method has returned.
Parser's abstract
flatten method.
Option exists for the first character of
the arguments entry AND an Option
does not exist for the whole argument then
add the first character as an option to the processed tokens
list e.g.
arguments that have been passed to the parse
method.
Parser's abstract
flatten method.
FontChooser
JList or JComboBox in the face specified.construct method.
CLOption with specified id, or
null if no command line option is found.
CLOption with specified name, or
null if no command line option is found.
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.
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
getDescriptor().getId() instead
CLOptionDescriptor.getIncompatible() instead.
Option
opt
belongs to.
Object type of this Option.
Object type of this Option.
Options.
java.util.Collection.
DownloadableInfo.getType()
DownloadableInfo.getType()
null if there is no value.
null if there is no value.
defaultValue if there is no value.
node,
at column number column.
ch represents.
flatten method.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.
hasArg is true.
num
argument values.
Option is a member
of this Options.
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.
required
is true.
ch is a value code, i.e.
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.
MissingArgumentException
with the specified detail message.
MissingSelectedException
with the specified detail message.
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.
arguments
based on the specifed Options.
arguments
based on the specifed Options.
ParseException
with the specified detail message.
Options instance represented by
pattern.
Parser creates CommandLines.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.flatten method.options with the specified
command line syntax.
options with the specified
command line syntax.
options with the specified
command line syntax.
options with the specified
command line syntax.
options with the specified
command line syntax.
options with the specified
command line syntax.
options with the specified
command line syntax.
options with the specified
command line syntax.
opt using the values retrieved from the
specified iterator iter.
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.
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.
PluginManager#inquireThread(String, PluginInquireAction)
it will be set here.
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.
Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)
Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)
CyNetwork.setSelectedEdgeState(Collection, boolean)
CyNetwork.setSelectedEdgeState(Collection, boolean)
name.
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().CLOption.getId() when the option is a text argument.
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().
UnrecognizedArgumentException
with the specified detail message.
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 )).type.
sep as a means to
separate argument values.
=' as a means to
separate argument values.
' '.
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