Package net.sf.basedb.core

Class VirtualColumn

java.lang.Object
net.sf.basedb.core.VirtualColumn
public class VirtualColumn extends Object
This class is used to define columns in the virtual tables in the dynamic part of the database that are storing analysed data. 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: 2015-04-20 11:08:18 +0200 (må, 20 apr 2015) $

  • Field Details

    • INDEXED

      public static final boolean INDEXED
      Used in constructor to tell that the column should be indexed.
      See Also:

    • UNIQUE

      public static final boolean UNIQUE
      Used in constructor to tell that the column must contain only unique values.
      Since:
      3.1
      See Also:

    • NULLABLE

      public static final boolean NULLABLE
      Used in constructor to tell that the column should be nullable.
      See Also:

    • PRIMARY_KEY

      public static final boolean PRIMARY_KEY
      Used in constructor to tell that the column is part of the primary key.
      See Also:

    • CUBE

      public static final VirtualColumn CUBE
      This column stores the data cube number.
      See Also:

    • LAYER

      public static final VirtualColumn LAYER
      This column stores the data cube layer coordinate.
      See Also:

    • COLUMN

      public static final VirtualColumn COLUMN
      This column stores the data cube column coordinate.
      See Also:

    • POSITION

      public static final VirtualColumn POSITION
      This column stores the data cube position coordinate.

    • FILTER

      public static final VirtualColumn FILTER
      This column stores the data cube filter number.
      See Also:

    • EXTRA

      public static final VirtualColumn EXTRA
      This column stores the data cube extra value number.
      See Also:

    • REPORTER_ID

      public static final VirtualColumn REPORTER_ID
      This column stores the id of a reporter. For perfomance reasons it is not linked with a foreign key to the Reporters table.
      See Also:

    • REPORTER_ID_PK

      public static final VirtualColumn REPORTER_ID_PK
      Column for storing the id of a reporter when it is part of the primary key. For perfomance reasons it is not linked with a foreign key to the Reporters table.
      Since:
      3.1

    • REPORTER_VERSION

      public static final VirtualColumn REPORTER_VERSION
      Column for storing the original version of a reporter that is cloned to a virtual table.
      Since:
      3.1

    • REPORTER_EXTERNAL_ID

      public static final VirtualColumn REPORTER_EXTERNAL_ID
      Column for storing the external reporter id.
      Since:
      3.1

    • RAWDATA_ID

      public static final VirtualColumn RAWDATA_ID
      This column stores the id of a raw date object. For perfomance reasons it is not linked with a foreign key to the raw date table.
      See Also:

    • RAWBIOASSAY_ID

      public static final VirtualColumn RAWBIOASSAY_ID
      This column stores the id of a raw bioassay. For perfomance reasons it is not linked with a foreign key to the RawBioAssays table.
      See Also:

    • EXTRA_INT

      public static final VirtualColumn EXTRA_INT
      This column stores extra integer values.

    • EXTRA_FLOAT

      public static final VirtualColumn EXTRA_FLOAT
      This column stores extra float values.

    • EXTRA_STRING

      public static final VirtualColumn EXTRA_STRING
      This column stores extra string values.

    • extraValueColumns

      private static final Map<Type,VirtualColumn> extraValueColumns
      A cache of virtual column objects for extra value types.

    • name

      private final String name
      The name of the column.

    • column

      private final String column
      The column name in the database of the column.

    • typeWrapper

      private final TypeWrapper<?> typeWrapper
      The data type of the column.

    • size

      private final int size
      The size of the column if it is a string.

    • indexed

      private final boolean indexed
      If the column should be indexed or not.

    • unique

      private final boolean unique
      If the column must contain unique values or not.

    • nullable

      private final boolean nullable
      If the column should be nullable or not.

    • primaryKey

      private final boolean primaryKey
      If the column should be part of the primary key or not.

    • untransformIntensities

      private final boolean untransformIntensities

  • Constructor Details

    • VirtualColumn

      private VirtualColumn(String name, String column, TypeWrapper<?> type, int size, boolean indexed, boolean unique, boolean nullable, boolean primaryKey, boolean untransformIntensities)
      Create a new virtual column.

  • Method Details

    • channelRaw

      public static VirtualColumn channelRaw(int channel)
      Get a column that stores the raw spot value for a channel. This may be an intensity value or a transformed value as given by the BioAssaySet.getIntensityTransform() for the current bioassay set.
      Parameters:
      channel - The channel number
      Returns:
      a VirtualColumn object.
      Since:
      2.12
      See Also:

    • channelIntensity

      public static VirtualColumn channelIntensity(int channel)
      Get a column that returns the intensity values for a channel. Transformed intensity values (as given by the BioAssaySet.getIntensityTransform() setting for the current bioassay set), are untransformed automatically.
      Parameters:
      channel - The channel number
      Returns:
      a VirtualColumn object
      Since:
      2.12
      See Also:

    • extraValue

      public static VirtualColumn extraValue(Type valueType)
      Get a column that stores the calculated extra values for a value type. Only one VirtualColumn object per type exists. Only Type.INT, Type.FLOAT and Type.STRING are supported.
      Parameters:
      valueType - The type to get the column for.
      Returns:
      a VirtualColumn object.

    • clonableProperty

      public static VirtualColumn clonableProperty(ClonableProperty property)
      Get a virtual column view of a cloned reporter property.
      Parameters:
      property - The cloned reporter property
      Returns:
      A virtual column representation of the cloned property
      Since:
      3.1

    • equals

      public boolean equals(Object other)
      A virtual column is equal to another if both have the same name.
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • getName

      public String getName()
      Get the name of the column. This is the name that is used as an alias in SQL SELECT statements by default.
      Returns:
      a String

    • getColumn

      public String getColumn()
      Get the database column name of the column.
      Returns:
      a String

    • getTypeWrapper

      public TypeWrapper<?> getTypeWrapper()
      Get a wrapper for accessing underlying type information from Hibernate.
      Since:
      2.16

    • getSize

      public int getSize()
      Get the maximum size of data in the column if it is a string. Ie. getType() == Hibernate.STRING
      Returns:
      The size as an int.

    • isIndexed

      public boolean isIndexed()
      If the column is indexed or not.
      Returns:
      TRUE if indexed, FALSE otherwise.

    • isUnique

      public boolean isUnique()
      If the column must contain unique values or not.
      Returns:
      TRUE if unique, FALSE otherwise.

    • isNullable

      public boolean isNullable()
      If null values are allowed in the column or not.
      Returns:
      TRUE if null is allowed, FALSE otherwise

    • isPrimaryKey

      public boolean isPrimaryKey()
      If the column is part of the primary key or not.
      Returns:
      TRUE if it's part of, FALSE otherwise.

    • untransformIntensities

      public boolean untransformIntensities()
      A flag indicating if transformed intensity valus belonging to a bioassay set should be untransformed as part of a query.
      Since:
      2.12
      See Also: