Uses of Interface
org.cytoscape.model.CyTable
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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 applicationsorg.cytoscape.equations Various types and utility methods relating to attribute equations.org.cytoscape.group.data An api for configuringCyGroup
s.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 -
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Uses of CyTable in org.cytoscape.application
Methods in org.cytoscape.application that return CyTable Modifier and Type Method Description CyTable
CyApplicationManager. getCurrentTable()
Returns the currently active table.Methods in org.cytoscape.application with parameters of type CyTable Modifier and Type Method 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 Description CyTable
StringToModel. getTable(String strTable)
Convert a string request for a table into aCyTable
.Methods in org.cytoscape.command with parameters of type CyTable Modifier and Type Method Description List<CyRow>
StringToModel. getRowList(CyTable table, String rowlist)
Convert a string request for a rowlist into a list ofCyRow
s. -
Uses of CyTable in org.cytoscape.command.util
Methods in org.cytoscape.command.util that return CyTable Modifier and Type Method Description CyTable
RowList. getTable()
Get the table for this rowlistMethods in org.cytoscape.command.util with parameters of type CyTable Modifier and Type Method Description void
RowList. setTable(CyTable table)
Set the table for this rowlistConstructors in org.cytoscape.command.util with parameters of type CyTable Constructor 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 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 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 Description CyTable[]
CyTableReader. getTables()
Return an array ofCyTable
objects. -
Uses of CyTable in org.cytoscape.io.write
Methods in org.cytoscape.io.write with parameters of type CyTable Modifier and Type Method Description CyWriter
CyTableWriterFactory. createWriter(OutputStream os, CyTable table)
Creates a single Task that will write the specifiedCyTable
object to the specified OutputStream.CyWriter
CyTableWriterManager. getWriter(CyTable table, CyFileFilter filter, File file)
Returns theCyWriter
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 theCyWriter
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 Description default CyTable
CyJobDataService. getTableData(CyJobData data, String key)
Optional method to extract table data (usually not model associated tables) from aCyJobData
object.Methods in org.cytoscape.jobs with parameters of type CyTable Modifier and Type Method 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 aCyJobData
item. -
Uses of CyTable in org.cytoscape.model
Methods in org.cytoscape.model that return CyTable Modifier and Type Method 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
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
CyRow. getTable()
Returns theCyTable
that this row belongs to.CyTable
CyTableManager. getTable(long suid)
Returns the table with the specified SUID.CyTable
CyTableMetadata. getTable()
Returns the table whose metadata is described by this instance.Methods in org.cytoscape.model that return types with arguments of type CyTable Modifier and Type Method 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 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)
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 Description CyTable
TableAboutToBeDeletedEvent. getTable()
Returns the table that is about to be deleted from the table manager.CyTable
TableAddedEvent. getTable()
Returns the table added to the table manager.Constructors in org.cytoscape.model.events with parameters of type CyTable Constructor 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)
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Uses of CyTable in org.cytoscape.model.subnetwork
Methods in org.cytoscape.model.subnetwork that return CyTable Modifier and Type Method 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 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 Description TaskIterator
TableTaskFactory. createTaskIterator(CyTable table)
Used to provision this factory with aCyTable
that will be used to create tasks.boolean
AbstractTableTaskFactory. isReady(CyTable table)
Returns true if the supplied table is not null.boolean
TableTaskFactory. isReady(CyTable table)
Returns true if this task factory is ready to produce a TaskIterator.Constructors in org.cytoscape.task with parameters of type CyTable Constructor Description AbstractTableTask(CyTable table)
Initializes a Task that needs to operate on aCyTable
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Uses of CyTable in org.cytoscape.task.edit
Methods in org.cytoscape.task.edit with parameters of type CyTable Modifier and Type Method 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
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
MapTableToNetworkTablesTaskFactory. createTaskIterator(CyTable globalTable, boolean selectedNetworksOnly, List<CyNetwork> networkList, Class<? extends CyIdentifiable> tableType)
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 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 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 Description String
CyJSONUtil. toJson(CyTable cyTable, boolean includeDefinition, boolean includeRows)
Returns a JSON representation of a CyTable.
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