Package org.cytoscape.model

Interface CyColumn

All Superinterfaces:
CyIdentifiable
public interface CyColumn extends CyIdentifiable
This class describes a column in a CyTable.

Column Namespaces

A column name can be broken down into two parts, a "namespace" and a "name". The namespace and name can be combined into a String by separating them with a "::", for example: "MyNamespace::MyName". The namespace part is optional, for example the column name "MyName" does not have a namespace. All methods that take a namespace argument will accept null to indicate no namespace. All of the default network columns created by Cytoscape do not have a namespace.

Apps are encouraged to put any columns they create into a namespace. The advantages of doing this are:

  1. Avoid name collision with other apps.
  2. Enable UI features based on namespaces.
  3. Use namespace aware APIs in CyColumn, CyRow and CyTable

Column Naming Rules

Case is ignored when column names are compared, or example "MyColumnName" and "mycolumnname" are equivalent. This also applies to namespaces, for example "MyNamespace::MyName" and "mynamespace::myname" are equivalent.

Whitespace is significant in both the namespace and the name (for historical reasons), for example " mynamespace ::myname" is in the namespace " mynamespace ". The empty string is a valid name for a namespace, for example "::myname" is in the "" namespace. It is highly recommended not to use whitespace in namespace identifiers, stick with alphanumeric characters and underscores.

Pick a namespace identifier that is between 6-15 characters in length that does not contain whitespace or special characters. Good examples are "EnrichmentMap", "clusterMaker" or "WordCloud".

Module: model-api

To use this in your app, include the following dependency in your POM:

<dependency>
    <groupId>org.cytoscape</groupId>
    <artifactId>model-api</artifactId>
</dependency>

Cytoscape Backwards Compatibility (API Interface): We expect that this interface will be used but not implemented by developers using this interface. As such, we reserve the right to add methods to the interface as part of minor version upgrades. We will not remove methods for any changes other than major version upgrades.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static String
    NAMESPACE_SEPARATOR
     

    Fields inherited from interface org.cytoscape.model.CyIdentifiable

    SUID

  • Method Summary

    Modifier and Type
    Method
    Description
    Object
    getDefaultValue()
    Returns the default value for the column, possibly null.
    Class<?>
    getListElementType()
    Returns the data type of the list elements if the column type is List.class otherwise null.
    String
    getName()
    Returns the fully-qualified name of the column.
    default String
    getNameOnly()
    Returns the name portion without the namespace.
    default String
    getNamespace()
    Returns the namespace of the column, or null if the column does not have a namespace.
    CyTable
    getTable()
    Returns the table for this column.
    Class<?>
    getType()
    Returns the data type of the column.
    <T> List<T>
    getValues​(Class<? extends T> type)
    Returns all the values, some of which may be null, for this given column.
    VirtualColumnInfo
    getVirtualColumnInfo()
    Returns information about the virtual column definition of this column.
    boolean
    isImmutable()
    Returns true if the column is immutable i.e.
    boolean
    isPrimaryKey()
    Returns true if the column is the primary key, otherwise false.
    static String
    joinColumnName​(String namespace, String name)
    Joins a namespace and a name string into a fully-qualified column name.
    void
    setName​(String fullyQualifiedName)
    Change the name of this column.
    default void
    setName​(String namespace, String name)
    Change the name of this column.
    static String[]
    splitColumnName​(String fullyQualifiedName)
    Splits a column name into a namespace part and a name part at the first occurrence of a "::".

    Methods inherited from interface org.cytoscape.model.CyIdentifiable

    getSUID

  • Field Details

  • Method Details

    • splitColumnName

      static String[] splitColumnName​(String fullyQualifiedName)
      Splits a column name into a namespace part and a name part at the first occurrence of a "::". If the column name does not contain a "::" then the namespace part will be null. Whitespace is significant. The string "::hello" has "" as the namespace.

    • joinColumnName

      static String joinColumnName​(String namespace, String name)
      Joins a namespace and a name string into a fully-qualified column name. For example: joinColumnName("MyNamespace", "MyName") results in "MyNamespace::MyName".

    • getName

      String getName()
      Returns the fully-qualified name of the column.
      Returns:
      the fully-qualified name of the column.

    • getNamespace

      default String getNamespace()
      Returns the namespace of the column, or null if the column does not have a namespace. Default columns created by Cytoscape do not have a namespace.

    • getNameOnly

      default String getNameOnly()
      Returns the name portion without the namespace.

    • setName

      void setName​(String fullyQualifiedName)
      Change the name of this column. If another column with a matching name already exists in the same namespace, IllegalArgumentException will be thrown. The check for matching column names is case insensitive.
      Parameters:
      newName - the new fully qualified column name
      Throws:
      IllegalArgumentException - if the column is immutable

    • setName

      default void setName​(String namespace, String name)
      Change the name of this column. If another column with a matching name already exists in the same namespace, IllegalArgumentException will be thrown. The check for matching column names is case insensitive.
      Parameters:
      namespace - the new namespace, use null to indicate no namespace
      name - the new name
      Throws:
      IllegalArgumentException - if the column is immutable

    • getType

      Class<?> getType()
      Returns the data type of the column.
      Returns:
      the data type of the column.

    • getListElementType

      Class<?> getListElementType()
      Returns the data type of the list elements if the column type is List.class otherwise null.
      Returns:
      the data type of the list elements if the column type is List.class otherwise null

    • isPrimaryKey

      boolean isPrimaryKey()
      Returns true if the column is the primary key, otherwise false.
      Returns:
      true if the column is the primary key, otherwise false.

    • isImmutable

      boolean isImmutable()
      Returns true if the column is immutable i.e. cannot be deleted or renamed, otherwise false.
      Returns:
      true if the column is immutable i.e. cannot be deleted or renamed, otherwise false. Please note that this does not affect the ability to add or modify values in this column!

    • getTable

      CyTable getTable()
      Returns the table for this column.
      Returns:
      the table that this column is a part of

    • getValues

      <T> List<T> getValues​(Class<? extends T> type)
      Returns all the values, some of which may be null, for this given column. When type is List.class, call getListElementType() get the type of the list elements.
      Type Parameters:
      T - the generic type of the column.
      Parameters:
      type - the datatype of this column. (You can use getType() to obtain it.)
      Returns:
      the values in this column in some arbitrary but consistent order. When type is List.class, a List is returned.

    • getVirtualColumnInfo

      VirtualColumnInfo getVirtualColumnInfo()
      Returns information about the virtual column definition of this column. This method will return an instance even if the column is not virtual.
      Returns:
      an instance of VirtualColumnInfo.

    • getDefaultValue

      Object getDefaultValue()
      Returns the default value for the column, possibly null.
      Returns:
      The default value for the column, possibly null.