Package net.sf.basedb.core
Enum VirtualTable
- java.lang.Object
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- java.lang.Enum<VirtualTable>
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- net.sf.basedb.core.VirtualTable
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- All Implemented Interfaces:
Serializable
,Comparable<VirtualTable>
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 eachVirtualDb
it is possible to create one real table for eachVirtualTable
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 byDynamicQuery
: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) $
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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.
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Field Summary
Fields Modifier and Type Field Description private String
alias
The alias to use in queries for this table.private VirtualColumn[]
columns
The columns in the table.private String
nameTemplate
The name template, # is replaced by the ID of theVirtualDb
item.
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Constructor Summary
Constructors Modifier Constructor Description private
VirtualTable(String nameTemplate, String alias, VirtualColumn... columns)
Creates a new virtual table.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description String
getAlias()
Get the alias of this table.long
getBytesPerRow(Experiment experiment)
long
getBytesPerRow(VirtualDb vdb)
Get the number of bytes a single row in the database occupies.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 type with the specified name.static VirtualTable[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
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Enum Constant Detail
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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 theReporterCloneTemplate
attached to an experiment.- Since:
- 3.1
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Field Detail
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nameTemplate
private final String nameTemplate
The name template, # is replaced by the ID of theVirtualDb
item.
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alias
private final String alias
The alias to use in queries for this table.
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columns
private final VirtualColumn[] columns
The columns in the table.
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Constructor Detail
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VirtualTable
private VirtualTable(String nameTemplate, String alias, VirtualColumn... columns)
Creates a new virtual table.- Parameters:
nameTemplate
- The template for generating table namesalias
- The alias of the table used in queriescolumns
- The columns that are part of the table
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Method Detail
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values
public static VirtualTable[] values()
Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:for (VirtualTable c : VirtualTable.values()) System.out.println(c);
- Returns:
- an array containing the constants of this enum type, in the order they are declared
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valueOf
public static VirtualTable valueOf(String name)
Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (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 type has no constant with the specified nameNullPointerException
- if the argument is null
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getTableName
public String getTableName(VirtualDb vdb)
Get the real table name of this table in the database.- Parameters:
vdb
- The virtual database
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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
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getAlias
public String getAlias()
Get the alias of this table. Used in queries:SELECT ... FROM table AS alias ...
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getColumns
public VirtualColumn[] getColumns(VirtualDb vdb)
Get all columns in this table.- Parameters:
vdb
- The virtual database this table belongs to- Since:
- 3.1
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getColumns
public final VirtualColumn[] getColumns(Experiment exp)
Get all columns in this table.- Parameters:
exp
- The experiment this table belongs to- Since:
- 3.1
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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 theSPOT
table.- Parameters:
column
- The column to check- Returns:
- TRUE if the column is part of the table, FALSE otherwise
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getBytesPerRow
public final long getBytesPerRow(Experiment experiment)
- Since:
- 3.1
- See Also:
getBytesPerRow(VirtualDb)
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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
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