Enum Class VirtualTable

java.lang.Object
java.lang.Enum<VirtualTable>
net.sf.basedb.core.VirtualTable
All Implemented Interfaces:
Serializable, Comparable<VirtualTable>, Constable

public enum VirtualTable extends Enum<VirtualTable>
This enumeration defines constants that are used to specify different virtual tables in the dynamic part of the database used for analysis. For each VirtualDb it is possible to create one real table for each VirtualTable constant.

The information in these objects are used by HibernateUtil.createVirtualTable(VirtualDb, VirtualTable) to create the extra tables needed by an experiment to store analysed data. These objects are also used in query elements by DynamicQuery:s when it needs to reference a certain column in one of the dynamic tables.

Version:
2.0
Author:
Nicklas
See Also:
Last modified
$Date: 2019-03-12 07:53:27 +0100 (tis, 12 mars 2019) $
  • Enum Constant Details

    • SPOT

      public static final VirtualTable SPOT
      Table that stores spot intensities for each spot in a data cube. The number of intensity columns are the same as the number of channels in the experiment.
    • SPOT_EXTRA_INT

      public static final VirtualTable SPOT_EXTRA_INT
      Table that stores integer spot extra values. One value can be stored for each spot.
    • SPOT_EXTRA_FLOAT

      public static final VirtualTable SPOT_EXTRA_FLOAT
      Table that stores float spot extra values. One value can be stored for each spot.
    • SPOT_EXTRA_STRING

      public static final VirtualTable SPOT_EXTRA_STRING
      Table that stores string spot extra values. One value can be stored for each spot.
    • POSITION

      public static final VirtualTable POSITION
      Table that maps position coordinates in a data cube to reporters. Each position may map to one reporter or null.
    • POSITION_EXTRA_INT

      public static final VirtualTable POSITION_EXTRA_INT
      Table that stores integer position extra values. One value can be stored for each position.
    • POSITION_EXTRA_FLOAT

      public static final VirtualTable POSITION_EXTRA_FLOAT
      Table that stores float position extra values. One value can be stored for each position.
    • POSITION_EXTRA_STRING

      public static final VirtualTable POSITION_EXTRA_STRING
      Table that stores string position extra values. One value can be stored for each position.
    • COLUMN

      public static final VirtualTable COLUMN
      Table that maps columns coordinates in a data cube to raw bioassays. Each column may map to any number of raw bioassays.
    • COLUMN_EXTRA_INT

      public static final VirtualTable COLUMN_EXTRA_INT
      Table that stores integer column extra values. One value can be stored for each column.
    • COLUMN_EXTRA_FLOAT

      public static final VirtualTable COLUMN_EXTRA_FLOAT
      Table that stores float column extra values. One value can be stored for each column.
    • COLUMN_EXTRA_STRING

      public static final VirtualTable COLUMN_EXTRA_STRING
      Table that stores string column extra values. One value can be stored for each column.
    • RAWPARENTS

      public static final VirtualTable RAWPARENTS
      Table that maps column/position coordinates in a data cube to the id's of the raw spots their intensities where calculated from. Each column/position coordinate may map to any number of raw spots.
    • FILTER

      public static final VirtualTable FILTER
      Table that holds column/position coordinates that remains after a filtering operation has been applied to a data cube layer.
    • CLONED_REPORTERS

      public static final VirtualTable CLONED_REPORTERS
      Table that holds cloned reporter information for an experiment. The reporter id, version and external id are mandatory columns. Additional columns will be added according to what is defined by the ReporterCloneTemplate attached to an experiment.
      Since:
      3.1
  • Field Details

    • nameTemplate

      private final String nameTemplate
      The name template, # is replaced by the ID of the VirtualDb item.
    • alias

      private final String alias
      The alias to use in queries for this table.
    • columns

      private final VirtualColumn[] columns
      The columns in the table.
  • Constructor Details

    • VirtualTable

      private VirtualTable(String nameTemplate, String alias, VirtualColumn... columns)
      Creates a new virtual table.
      Parameters:
      nameTemplate - The template for generating table names
      alias - The alias of the table used in queries
      columns - The columns that are part of the table
  • Method Details

    • values

      public static VirtualTable[] values()
      Returns an array containing the constants of this enum class, in the order they are declared.
      Returns:
      an array containing the constants of this enum class, in the order they are declared
    • valueOf

      public static VirtualTable valueOf(String name)
      Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)
      Parameters:
      name - the name of the enum constant to be returned.
      Returns:
      the enum constant with the specified name
      Throws:
      IllegalArgumentException - if this enum class has no constant with the specified name
      NullPointerException - if the argument is null
    • getTableName

      public String getTableName(VirtualDb vdb)
      Get the real table name of this table in the database.
      Parameters:
      vdb - The virtual database
    • getQualifiedTableName

      public String getQualifiedTableName(VirtualDb vdb)
      Get the real table name of this table in the database, quoted and with catalog/schema information prepended to it.
      Parameters:
      vdb - The virtual database
    • getAlias

      public String getAlias()
      Get the alias of this table. Used in queries: SELECT ... FROM table AS alias ...
    • getColumns

      public VirtualColumn[] getColumns(VirtualDb vdb)
      Get all columns in this table.
      Parameters:
      vdb - The virtual database this table belongs to
      Since:
      3.1
    • getColumns

      public final VirtualColumn[] getColumns(Experiment exp)
      Get all columns in this table.
      Parameters:
      exp - The experiment this table belongs to
      Since:
      3.1
    • hasColumn

      public boolean hasColumn(VirtualColumn column)
      Check if the specified column is part of the virtual table or not. This method doesn't check columns that depends on the raw data type, ie. the number of intensity columns in the SPOT table.
      Parameters:
      column - The column to check
      Returns:
      TRUE if the column is part of the table, FALSE otherwise
    • getBytesPerRow

      public final long getBytesPerRow(Experiment experiment)
      Since:
      3.1
      See Also:
    • getBytesPerRow

      public long getBytesPerRow(VirtualDb vdb)
      Get the number of bytes a single row in the database occupies. The number doesn't include any variable length columns, ie. string columns. The caller should add the string length to the value returned from this method.
      Parameters:
      vdb - The virtual database where the table is stored
      Since:
      3.1