Package net.sf.basedb.core

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:

• VirtualColumn
• Dynamic

Last modified

$Date: 2019-03-12 07:53:27 +0100 (tis, 12 mars 2019) $

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum

Enum.EnumDesc<E extends Enum<E>>

Enum Constant Summary

Enum Constants

Enum Constant	Description
CLONED_REPORTERS	Table that holds cloned reporter information for an experiment.
COLUMN	Table that maps columns coordinates in a data cube to raw bioassays.
COLUMN_EXTRA_FLOAT	Table that stores float column extra values.
COLUMN_EXTRA_INT	Table that stores integer column extra values.
COLUMN_EXTRA_STRING	Table that stores string column extra values.
FILTER	Table that holds column/position coordinates that remains after a filtering operation has been applied to a data cube layer.
POSITION	Table that maps position coordinates in a data cube to reporters.
POSITION_EXTRA_FLOAT	Table that stores float position extra values.
POSITION_EXTRA_INT	Table that stores integer position extra values.
POSITION_EXTRA_STRING	Table that stores string position extra values.
RAWPARENTS	Table that maps column/position coordinates in a data cube to the id's of the raw spots their intensities where calculated from.
SPOT	Table that stores spot intensities for each spot in a data cube.
SPOT_EXTRA_FLOAT	Table that stores float spot extra values.
SPOT_EXTRA_INT	Table that stores integer spot extra values.
SPOT_EXTRA_STRING	Table that stores string spot extra values.

Field Summary

Fields

Modifier and Type	Field	Description
private final String	alias	The alias to use in queries for this table.
private final VirtualColumn[]	columns	The columns in the table.
private final String	nameTemplate	The name template, # is replaced by the ID of the VirtualDb item.

Constructor Summary

Constructors

Modifier	Constructor	Description
private	VirtualTable(String nameTemplate, String alias, VirtualColumn... columns)	Creates a new virtual table.

Method Summary

Modifier and Type	Method	Description
String	getAlias()	Get the alias of this table.
final long	getBytesPerRow(Experiment experiment)
long	getBytesPerRow(VirtualDb vdb)	Get the number of bytes a single row in the database occupies.
final VirtualColumn[]	getColumns(Experiment exp)	Get all columns in this table.
VirtualColumn[]	getColumns(VirtualDb vdb)	Get all columns in this table.
String	getQualifiedTableName(VirtualDb vdb)	Get the real table name of this table in the database, quoted and with catalog/schema information prepended to it.
String	getTableName(VirtualDb vdb)	Get the real table name of this table in the database.
boolean	hasColumn(VirtualColumn column)	Check if the specified column is part of the virtual table or not.
static VirtualTable	valueOf(String name)	Returns the enum constant of this class with the specified name.
static VirtualTable[]	values()	Returns an array containing the constants of this enum class, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

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(VirtualDb)

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