Uses of Interface
org.cytoscape.model.CyTable

Packages that use CyTable

Package	Description
org.cytoscape.application	This package provides Cytoscape version number, application-wide setting, basic access to current network, selected networks, views and rendering engines.
org.cytoscape.command	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.
org.cytoscape.command.util	Tunable classes useful for command applications
org.cytoscape.equations	Various types and utility methods relating to attribute equations.
org.cytoscape.group.data	An api for configuring CyGroups.
org.cytoscape.io.read	Handle importing Cytoscape data (network, attributes, session, properties, etc) from files/URLs.
org.cytoscape.io.write	This package provides factory interfaces to be used by anyone wishing to provide export or writing capabilities to the rest of Cytoscape.
org.cytoscape.jobs	This package provides a mechanism for executing remote jobs from within Cytoscape.
org.cytoscape.model	This package has the core interfaces of network and table data structures that are foundational to Cytoscape.
org.cytoscape.model.events	This package contains the event interfaces necessary for communicating with the classes in org.cytoscape.model.
org.cytoscape.model.subnetwork	This package contains rootnetwork and subnetwork extensions to the CyNetwork interface that provide a more complex meta-network data model.
org.cytoscape.task	This package provides base classes for common task factory types as well as their associated task types found in Cytoscape.
org.cytoscape.task.edit	This package include a set of task factory interfaces that allow the modification or editing of various objects within Cytoscape.
org.cytoscape.task.write	This package contains a set of task factory interfaces used for exporting or writing a variety of Cytoscape objects to files.
org.cytoscape.util.json

Uses of CyTable in org.cytoscape.application

Methods in org.cytoscape.application that return CyTable

Modifier and Type	Method and Description
CyTable	CyApplicationManager.getCurrentTable() Returns the currently active table.

Methods in org.cytoscape.application with parameters of type CyTable

Modifier and Type	Method and Description
void	CyApplicationManager.setCurrentTable(CyTable table) Sets the currently active table.

Uses of CyTable in org.cytoscape.command

Methods in org.cytoscape.command that return CyTable

Modifier and Type	Method and Description
CyTable	StringToModel.getTable(String strTable) Convert a string request for a table into a CyTable.

Methods in org.cytoscape.command with parameters of type CyTable

Modifier and Type	Method and Description
List<CyRow>	StringToModel.getRowList(CyTable table, String rowlist) Convert a string request for a rowlist into a list of CyRows.

Uses of CyTable in org.cytoscape.command.util

Methods in org.cytoscape.command.util that return CyTable

Modifier and Type	Method and Description
CyTable	RowList.getTable() Get the table for this rowlist

Methods in org.cytoscape.command.util with parameters of type CyTable

Modifier and Type	Method and Description
void	RowList.setTable(CyTable table) Set the table for this rowlist

Constructors in org.cytoscape.command.util with parameters of type CyTable

Constructor and Description
RowList(CyTable targetTable) Create a new RowList object with an initial table

Uses of CyTable in org.cytoscape.equations

Methods in org.cytoscape.equations with parameters of type CyTable

Modifier and Type	Method and Description
static void	EquationUtil.refreshEquations(CyTable table, EquationCompiler compiler) Refreshes all the equations in the given CyTable

Uses of CyTable in org.cytoscape.group.data

Methods in org.cytoscape.group.data with parameters of type CyTable

Modifier and Type	Method and Description
<T> T	Aggregator.aggregate(CyTable table, CyGroup group, CyColumn column) Aggregate the column for the members of the specified group into the group.

Uses of CyTable in org.cytoscape.io.read

Methods in org.cytoscape.io.read that return CyTable

Modifier and Type	Method and Description
CyTable[]	CyTableReader.getTables() Return an array of CyTable objects.

Uses of CyTable in org.cytoscape.io.write

Methods in org.cytoscape.io.write with parameters of type CyTable

Modifier and Type	Method and Description
CyWriter	CyTableWriterFactory.createWriter(OutputStream os, CyTable table) Creates a single Task that will write the specified CyTable object to the specified OutputStream.
CyWriter	CyTableWriterManager.getWriter(CyTable table, CyFileFilter filter, File file) Returns the CyWriter Task that will attempt to write the specified table to the specified file of the specified file type.
CyWriter	CyTableWriterManager.getWriter(CyTable table, CyFileFilter filter, OutputStream os) Returns the CyWriter Task that will attempt to write the specified table to the specified output stream of the specified file type.

Uses of CyTable in org.cytoscape.jobs

Methods in org.cytoscape.jobs that return CyTable

Modifier and Type	Method and Description
default CyTable	CyJobDataService.getTableData(CyJobData data, String key) Optional method to extract table data (usually not model associated tables) from a CyJobData object.

Methods in org.cytoscape.jobs with parameters of type CyTable

Modifier and Type	Method and Description
default CyJobData	CyJobDataService.addData(CyJobData data, String key, CyTable table, List<CyRow> rows, List<String> columns) An optional method to add table data to a CyJobData item.

Uses of CyTable in org.cytoscape.model

Methods in org.cytoscape.model that return CyTable

Modifier and Type	Method and Description
CyTable	CyTableFactory.createTable(String title, String primaryKey, Class<?> primaryKeyType, boolean pub, boolean isMutable) Creates a CyTable object with the specified name, primary key, visibility, and mutability.
CyTable	CyTableFactory.createTable(String title, String primaryKey, Class<?> primaryKeyType, boolean pub, boolean isMutable, CyTableFactory.InitialTableSize initialSize) Creates a CyTable object with the specified name, primary key, visibility, and mutability.
CyTable	CyNetwork.getDefaultEdgeTable() A convenience method returns the default attribute table for the edges of this network.
CyTable	CyNetwork.getDefaultNetworkTable() A convenience method returns the default attribute table for this network.
CyTable	CyNetwork.getDefaultNodeTable() A convenience method returns the default attribute table for the nodes of this network.
CyTable	VirtualColumnInfo.getSourceTable() Returns the originating table for this column if this column is virtual.
CyTable	CyTableMetadata.getTable() Returns the table whose metadata is described by this instance.
CyTable	CyRow.getTable() Returns the CyTable that this row belongs to.
CyTable	CyColumn.getTable() Returns the table for this column.
CyTable	CyNetwork.getTable(Class<? extends CyIdentifiable> type, String namespace) Returns the table with the specified namespace and type from this network.
CyTable	CyNetworkTableManager.getTable(CyNetwork network, Class<? extends CyIdentifiable> type, String namespace) Returns the table with the specified namespace and type from the network.
CyTable	CyTableManager.getTable(long suid) Returns the table with the specified SUID.

Methods in org.cytoscape.model that return types with arguments of type CyTable

Modifier and Type	Method and Description
Set<CyTable>	CyTableManager.getAllTables(boolean includePrivate) Returns a Set of all tables with the specified visibility.
Set<CyTable>	CyTableManager.getGlobalTables() Returns a set of all global tables.
Set<CyTable>	CyTableManager.getLocalTables(Class<? extends CyIdentifiable> type) Returns set of all local tables for the given data type.
Map<String,CyTable>	CyNetworkTableManager.getTables(CyNetwork network, Class<? extends CyIdentifiable> type) Returns a read-only map of all of the tables for the specified type from the network.

Methods in org.cytoscape.model with parameters of type CyTable

Modifier and Type	Method and Description
void	CyTableManager.addTable(CyTable table) Registers a new table with the manager and fires a TableAddedEvent event.
String	CyTable.addVirtualColumn(String virtualColumn, String sourceColumn, CyTable sourceTable, String targetJoinKey, boolean isImmutable) Adds a "virtual" column to the the current table.
void	CyTable.addVirtualColumns(CyTable sourceTable, String targetJoinKey, boolean isImmutable) Adds all columns in another table as "virtual" columns to the the current table.
static Set<String>	CyTableUtil.getColumnNames(CyTable table) Returns all the column names of a given table.
CyNetwork	CyNetworkTableManager.getNetworkForTable(CyTable table) Returns the network this table is registered with.
String	CyNetworkTableManager.getTableNamespace(CyTable table) Returns the namespace of this table.
Class<? extends CyIdentifiable>	CyNetworkTableManager.getTableType(CyTable table) Returns the type of this table (either CyNetwork.class, CyNode.class, or CyEdge.class.
void	CyNetworkTableManager.setTable(CyNetwork network, Class<? extends CyIdentifiable> type, String namespace, CyTable table) Associates the given table to the network using the specified namespace and type.
void	CyTable.swap(CyTable otherTable) Swaps the contents and properties (such as mutability) of "otherTable" with this table.

Uses of CyTable in org.cytoscape.model.events

Methods in org.cytoscape.model.events that return CyTable

Modifier and Type	Method and Description
CyTable	TableAddedEvent.getTable() Returns the table added to the table manager.
CyTable	TableAboutToBeDeletedEvent.getTable() Returns the table that is about to be deleted from the table manager.

Constructors in org.cytoscape.model.events with parameters of type CyTable

Constructor and Description
ColumnCreatedEvent(CyTable source, String columnName) Constructs event.
ColumnDeletedEvent(CyTable source, String columnName) Constructs event.
ColumnNameChangedEvent(CyTable source, String oldColumnName, String newColumnName) Constructs event.
RowsCreatedEvent(CyTable source, Collection<Object> primaryKeys) Constructs event.
RowsDeletedEvent(CyTable source, Collection<Object> primaryKeys) Constructs event.
RowsSetEvent(CyTable source, Collection<RowSetRecord> rows) Constructs Event.
TableAboutToBeDeletedEvent(CyTableManager source, CyTable table) Constructs the event.
TableAddedEvent(CyTableManager source, CyTable table) Constructs the table added event.
TablePrivacyChangedEvent(CyTable source) Constructor method for TablePrivacyChangedEvent.
TableTitleChangedEvent(CyTable source, String oldTitle)

Uses of CyTable in org.cytoscape.model.subnetwork

Methods in org.cytoscape.model.subnetwork that return CyTable

Modifier and Type	Method and Description
CyTable	CyRootNetwork.getSharedEdgeTable() Returns the edge table shared by all subnetworks.
CyTable	CyRootNetwork.getSharedNetworkTable() Returns the network table shared by all subnetworks.
CyTable	CyRootNetwork.getSharedNodeTable() Returns the node table shared by all subnetworks.

Uses of CyTable in org.cytoscape.task

Fields in org.cytoscape.task declared as CyTable

Modifier and Type	Field and Description
protected CyTable	AbstractTableTask.table The table that descendants of this class will operate on.

Methods in org.cytoscape.task with parameters of type CyTable

Modifier and Type	Method and Description
TaskIterator	TableTaskFactory.createTaskIterator(CyTable table) Used to provision this factory with a CyTable that will be used to create tasks.
boolean	TableTaskFactory.isReady(CyTable table) Returns true if this task factory is ready to produce a TaskIterator.
boolean	AbstractTableTaskFactory.isReady(CyTable table) Returns true if the supplied table is not null.

Constructors in org.cytoscape.task with parameters of type CyTable

Constructor and Description
AbstractTableTask(CyTable table) Initializes a Task that needs to operate on a CyTable.

Uses of CyTable in org.cytoscape.task.edit

Methods in org.cytoscape.task.edit with parameters of type CyTable

Modifier and Type	Method and Description
TaskIterator	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.
TaskIterator	MapTableToNetworkTablesTaskFactory.createTaskIterator(CyTable globalTable, boolean selectedNetworksOnly, List<CyNetwork> networkList, Class<? extends CyIdentifiable> tableType)
TaskIterator	JoinTablesTaskTaskFactory.createTaskIterator(CyTable globalTable, boolean selectedNetworksOnly, List<CyNetwork> networkList, CyRootNetwork rootNetwork, CyColumn targetJoinColumn, Class<? extends CyIdentifiable> tableType)
TaskIterator	MapGlobalToLocalTableTaskFactory.createTaskIterator(CyTable globalTable, Collection<CyTable> localTables) Creates a task iterator for mapping a selected global table to a selected local table.
TaskIterator	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.

Method parameters in org.cytoscape.task.edit with type arguments of type CyTable

Modifier and Type	Method and Description
TaskIterator	MapGlobalToLocalTableTaskFactory.createTaskIterator(CyTable globalTable, Collection<CyTable> localTables) Creates a task iterator for mapping a selected global table to a selected local table.

Uses of CyTable in org.cytoscape.task.write

Methods in org.cytoscape.task.write with parameters of type CyTable

Modifier and Type	Method and Description
TaskIterator	ExportTableTaskFactory.createTaskIterator(CyTable table, File file) Returns a task factory that write the specified table to the specified file.

Uses of CyTable in org.cytoscape.util.json

Methods in org.cytoscape.util.json with parameters of type CyTable

Modifier and Type	Method and Description
String	CyJSONUtil.toJson(CyTable cyTable, boolean includeDefinition, boolean includeRows) Returns a JSON representation of a CyTable.