Uses of Class
org.cytoscape.work.TaskIterator
Package
Description
Interface to support execution of tasks as commands, including
the ability to get a list of namespaces, commands, and arguments,
and then execute those commands with a set of arguments.
Handle importing Cytoscape data (network, attributes, session, properties, etc) from files/URLs.
Interfaces for SOAP/REST web service clients, web services that return results as networks or tables, or query results.
This package provides base classes for common task factory types as well as their associated task types found in Cytoscape.
This package provides a variety of task factory interfaces for creating
new instances of network and other objects.
This package include a set of task factory interfaces that allow
the modification or editing of various objects within Cytoscape.
This package includes a set of task factory interfaces showing and hiding
nodes and edges within network views.
This package contains a set of task factory interfaces for reading
various Cytoscape objects from files and URLs.
This package includes a set of task factory interfaces for selecting, de-selecting and inverting selections
of nodes, edges, or combinations of both based on specific criteria.
This package contains a set of task factory interfaces used for
exporting or writing a variety of Cytoscape objects to files.
This package provides access to the available layout algorithms, as well as provides abstract layout
classes and layout information containers for the convenience of implementing other layout algorithms.
This package defines the task framework, where tasks are units of work.
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Uses of TaskIterator in org.cytoscape.command
Modifier and TypeMethodDescriptionCommandExecutorTaskFactory.createTaskIterator(File commandFile, TaskObserver observer)
Creates a task iterator that will execute the specified commands.CommandExecutorTaskFactory.createTaskIterator(String namespace, String command, Map<String,Object> args, TaskObserver observer)
Creates a task iterator that will execute the specified command.CommandExecutorTaskFactory.createTaskIterator(List<String> commands, TaskObserver observer)
Creates a task iterator that will execute the specified commands.CommandExecutorTaskFactory.createTaskIterator(TaskObserver observer, String... commands)
Creates a task iterator that will execute the specified commands. -
Uses of TaskIterator in org.cytoscape.io.read
Modifier and TypeMethodDescriptionInputStreamTaskFactory.createTaskIterator(InputStream is, String inputName)
Sets the input stream that will be read by the Reader created from this factory. -
Uses of TaskIterator in org.cytoscape.io.webservice
Modifier and TypeMethodDescriptionWebServiceClient.createTaskIterator(Object query)
Set query for the tasks to be executed. -
Uses of TaskIterator in org.cytoscape.task
Modifier and TypeMethodDescriptionEdgeViewTaskFactory.createTaskIterator(View<CyEdge> edgeView, CyNetworkView networkView)
Creates a new TaskIterator using the given edge view and network view.NetworkCollectionTaskFactory.createTaskIterator(Collection<CyNetwork> networks)
Provisions this factory with the collection of networks that will be passed into any task created by it.NetworkTaskFactory.createTaskIterator(CyNetwork network)
Provisions this factory with theCyNetwork
that will be passed into any task created by it.NetworkViewCollectionTaskFactory.createTaskIterator(Collection<CyNetworkView> networkViews)
Provisions this factory with the collection of network views that will be passed into any task created by it.NetworkViewLocationTaskFactory.createTaskIterator(CyNetworkView networkView, Point2D javaPt, Point2D xformPt)
Creates a task iterator using the specified network view and points.NetworkViewTaskFactory.createTaskIterator(CyNetworkView networkView)
Creates a new TaskIterator using the givenCyNetworkView
NodeViewTaskFactory.createTaskIterator(View<CyNode> nodeView, CyNetworkView networkView)
Provisions this factory with the node view and its associated network view, both of which will be passed into any task that will be created by this factory.RootNetworkCollectionTaskFactory.createTaskIterator(Collection<CyRootNetwork> networks)
Provisions this factory with the collection of root-networks that will be passed into any task created by it.RowTaskFactory.createTaskIterator(CyRow row)
Provisions this factory with theCyRow
that will be passed into any task created by it.TableCellTaskFactory.createTaskIterator(CyColumn column, Object primaryKeyValue)
Used to provision this factory with aCyColumn
and a primary key that will be used to create tasks.TableColumnTaskFactory.createTaskIterator(CyColumn column)
Used to provision this factory with aCyColumn
that will be used to create tasks.TableTaskFactory.createTaskIterator(CyTable table)
Used to provision this factory with aCyTable
that will be used to create tasks. -
Uses of TaskIterator in org.cytoscape.task.create
Modifier and TypeMethodDescriptionCloneNetworkTaskFactory.createTaskIterator(CyNetwork network)
Returns a TaskIterator that clones the given network.CreateNetworkViewTaskFactory.createTaskIterator(Collection<CyNetwork> networks, CyNetworkViewFactory factory)
Use this method to create a network view for each of the passed networks.NewNetworkSelectedNodesAndEdgesTaskFactory.createTaskIterator(CyNetwork network)
Returns a TaskIterator that creates a new network from the selected nodes and edges in the given network.NewNetworkSelectedNodesOnlyTaskFactory.createTaskIterator(CyNetwork network)
Returns a TaskIterator that creates a new network from the selected nodes in the given network.NewSessionTaskFactory.createTaskIterator(boolean destroyCurrentSession)
Creates a task iterator for creating a new session and destroying the current session based on the input. -
Uses of TaskIterator in org.cytoscape.task.edit
Modifier and TypeMethodDescriptionEditNetworkTitleTaskFactory.createTaskIterator(CyNetwork network, String title)
Creates a task iterator for editing a network's title.ImportDataTableTaskFactory.createTaskIterator(CyTableReader reader)
Creates a task iterator for importing a table data in a network data table.ImportDataTableTaskFactory.createTaskIterator(CyTable globalTable, boolean selectedNetworksOnly, boolean loadToUnassignedTable, List<CyNetwork> networkList, CyRootNetwork rootNetwork, CyColumn targetJoinColumn, Class<? extends CyIdentifiable> tableType)
Creates a task iterator for importing a table data in a network data table.JoinTablesTaskTaskFactory.createTaskIterator(CyTable globalTable, boolean selectedNetworksOnly, List<CyNetwork> networkList, CyRootNetwork rootNetwork, CyColumn targetJoinColumn, Class<? extends CyIdentifiable> tableType)
MapGlobalToLocalTableTaskFactory.createTaskIterator(CyTable globalTable, Collection<CyTable> localTables)
Creates a task iterator for mapping a selected global table to a selected local table.MapTableToNetworkTablesTaskFactory.createTaskIterator(CyTable globalTable, boolean selectedNetworksOnly, List<CyNetwork> networkList, Class<? extends CyIdentifiable> tableType)
MergeTablesTaskFactory.createTaskIterator(CyTable sourceTable, CyTable targetTable, List<String> sourceColumnsList, String sourceKeyColumn, boolean mergeColumnVirtual, boolean mapToNetworks, boolean selectedNetworksOnly, List<CyNetwork> networkList, CyRootNetwork rootNetwork, CyColumn targetJoinColumn, Class<? extends CyIdentifiable> tableType)
Creates a task iterator for merging two data tables.RenameColumnTaskFactory.createTaskIterator(CyColumn column, String newColumnName)
Create a task iterator for renaming a selected column. -
Uses of TaskIterator in org.cytoscape.task.hide
Modifier and TypeMethodDescriptionHideTaskFactory.createTaskIterator(CyNetworkView view, Collection<CyNode> nodes, Collection<CyEdge> edges)
Creates a task iterator that will hide the given nodes and edges.UnHideTaskFactory.createTaskIterator(CyNetworkView view, Collection<CyNode> nodes, Collection<CyEdge> edges)
Creates a task iterator that will show the given nodes and edges. -
Uses of TaskIterator in org.cytoscape.task.read
Modifier and TypeMethodDescriptionLoadMultipleNetworkFilesTaskFactory.createTaskIterator(List<File> files, CyRootNetwork rootNetwork)
Creates a task iterator for loading one or more networks from supported files (e.g.LoadNetworkFileTaskFactory.createTaskIterator(File file)
Creates a task iterator for loading a network from a file.LoadNetworkFileTaskFactory.createTaskIterator(File file, TaskObserver observer)
Creates a task iterator for loading a network from a file.LoadNetworkURLTaskFactory.createTaskIterator(URL url, TaskObserver observer)
Creates a task iterator for loading a URL into a network.LoadTableFileTaskFactory.createTaskIterator(File file)
Creates the task iterator for importing an attribute file to a table.LoadTableURLTaskFactory.createTaskIterator(URL url)
Creates the task iterator for importing an attribute file to a table.LoadVizmapFileTaskFactory.createTaskIterator(File file)
Creates a task iterator for loading files into visual styles.LoadVizmapFileTaskFactory.createTaskIterator(File file, TaskObserver observer)
Creates a task iterator for loading files into visual styles.OpenSessionTaskFactory.createTaskIterator(File file)
Creates a task iterator for loading a session from a file.OpenSessionTaskFactory.createTaskIterator(File file, boolean confirm)
Creates a task iterator for loading a session from a file, with an option to let the user confirm it before disposing the current session if it is not empty.LoadNetworkURLTaskFactory.loadCyNetworks(URL url)
Creates a task iterator for loading a URL into a network. -
Uses of TaskIterator in org.cytoscape.task.select
Modifier and TypeMethodDescriptionSelectFromFileListTaskFactory.createTaskIterator(CyNetwork network, File file)
Creates a task iterator for selecting items of a network based on a file. -
Uses of TaskIterator in org.cytoscape.task.write
Modifier and TypeMethodDescriptionExportNetworkTaskFactory.createTaskIterator(CyNetwork network, File file)
Creates the task iterator for exporting networks.ExportNetworkViewTaskFactory.createTaskIterator(CyNetworkView view, File file)
Creates the task iterator for exporting network views.ExportSelectedNetworkTaskFactory.createTaskIterator(File file)
Creates the task iterator for exporting the selected network.ExportTableTaskFactory.createTaskIterator(CyTable table, File file)
Returns a task factory that write the specified table to the specified file.ExportVizmapTaskFactory.createTaskIterator(File file)
Creates a task iterator for exporting the vizmap file.SaveSessionAsTaskFactory.createTaskIterator(File file)
Creates a task iterator for saving the session in a specified file. -
Uses of TaskIterator in org.cytoscape.view.layout
Modifier and TypeMethodDescriptionCyLayoutAlgorithm.createTaskIterator(CyNetworkView networkView, Object layoutContext, Set<View<CyNode>> nodesToLayOut, String layoutAttribute)
Creates a task iterator containing the layout tasks. -
Uses of TaskIterator in org.cytoscape.work
Modifier and TypeMethodDescriptionTaskFactory.createTaskIterator()
Returns an iterator containing a sequence ofTask
s.TunableSetter.createTaskIterator(TaskIterator taskIterator, Map<String,Object> tunableValues)
This method takes as input a TaskIterator and a map of tunable names to tunable values and applies those values to any tunables found in the Tasks found in the TaskIterator.TunableSetter.createTaskIterator(TaskIterator taskIterator, Map<String,Object> tunableValues, TaskObserver observer)
This version of createTaskIterator adds a TaskObserver argument.AbstractTask.getTaskIterator()
Modifier and TypeMethodDescriptionvoid
TaskIterator.append(TaskIterator taskIterator)
Adds the tasks in the given TaskIterator to the end of this iterator.TunableSetter.createTaskIterator(TaskIterator taskIterator, Map<String,Object> tunableValues)
This method takes as input a TaskIterator and a map of tunable names to tunable values and applies those values to any tunables found in the Tasks found in the TaskIterator.TunableSetter.createTaskIterator(TaskIterator taskIterator, Map<String,Object> tunableValues, TaskObserver observer)
This version of createTaskIterator adds a TaskObserver argument.void
TaskManager.execute(TaskIterator iterator)
void
TaskManager.execute(TaskIterator iterator, TaskObserver observer)
void
TaskIterator.insertTasksAfter(Task referenceTask, TaskIterator newTasks)
Inserts "newTasks" immediately after "referenceTask".protected void
AbstractTask.insertTasksAfterCurrentTask(TaskIterator newTasks)
Inserts "newTasks" after the current Task, in the TaskIterator that is being managed by this class.void
AbstractTask.setTaskIterator(TaskIterator taskIterator)
This method is used by aTaskIterator
to set itself on the newly added Task.