Package net.sf.basedb.core

Class DynamicQuery

java.lang.Object

net.sf.basedb.core.AbstractQuery

net.sf.basedb.core.AbstractSqlQuery

net.sf.basedb.core.DynamicQuery

All Implemented Interfaces:

ClonableReporterQuery, Query, SqlQuery

Direct Known Subclasses:

DataCube.RawMappingQuery, DynamicExtraValueQuery, DynamicPositionQuery, DynamicSpotQuery

public abstract class DynamicQuery
extends AbstractSqlQuery
implements ClonableReporterQuery

Represents a query against the dynamic database. A single query object may query against data in one data cube at a time. Most of the times however, this is limited to data in a single bioassayset. A query usually has the VirtualTable.SPOT or VirtualTable.POSITION as the root table for the query. Use factory methods in the Dynamic class to join other tables and create restrictions based on the data in those tables.

This type of query is executed by the AbstractSqlQuery.iterate(DbControl) method and returns the result as a DynamicResultIterator.

Version:

2.0

Author:

Nicklas

See Also:

• BioAssaySet.getSpotData()
• BioAssaySet.getPositionData()
• ExtraValue.getValues()

Last modified

$Date: 2017-12-08 14:18:12 +0100 (fr, 08 dec 2017) $

Nested Class Summary

Nested classes/interfaces inherited from class net.sf.basedb.core.AbstractSqlQuery

AbstractSqlQuery.CountWork

Field Summary

Fields

Modifier and Type	Field	Description
private final DataCube	cube
private final boolean	hasClonedReporters
private final VirtualTable	rootTable
private final IntensityTransform	transform
private boolean	useClonedReporters
private final VirtualDb	virtualDb

Constructor Summary

Constructors

Constructor	Description
DynamicQuery(DataCube cube, VirtualTable rootTable, IntensityTransform transform)	Create a new dynamic query.
DynamicQuery(VirtualDb vdb, VirtualTable rootTable)	Create a new non-restricted dynamic query.

Method Summary

Modifier and Type	Method	Description
(package private) DataCube	getDataCube()
IntensityTransform	getIntensityTransform()	Get the intensity transform that was used to store spot intensities for the root bioassay set in this query.
String	getRootAlias()	The alias of the item that is returned by this query.
(package private) VirtualTable	getRootTable()
VirtualDb	getVirtualDb()	Get the virtual database that this query is using.
boolean	hasClonedReporters()	Check if the virtual database that this query is using has cloned reporter annotations or not.
void	setUseClonedReporters(boolean useClonedReporters)	Set if cloned reporters should be used by default or not.
boolean	useClonedReporters()	Checks if this query is using cloned reporter or not by default.

Methods inherited from class net.sf.basedb.core.AbstractSqlQuery

closeResultSet, closeStatement, count, getDefaultSelects, getJepFunctions, getLimitHandler, getQueryType, getRowSelectionForLimitHandler, iterate, parseParameters, releaseSavepoint, rollbackToSavepoint, setParameters

Methods inherited from class net.sf.basedb.core.AbstractQuery

addAutoJoiner, getCountQuery, getFirstResult, getIdQuery, getMainQuery, getMaxResults, getParameterNames, getParameters, getParameterType, getParameterValue, getPermanentSelects, getQueryParameter, getQuerySection, getSelects, group, groupPermanent, hasParameterValue, having, havingPermanent, isCounting, isDistinct, isFailSafe, isReadonly, isReturningTotalCount, join, joinPermanent, order, orderPermanent, postProcessQuery, reset, resetTemporary, restrict, restrictPermanent, select, selectPermanent, setCounting, setDistinct, setFailSafe, setFirstResult, setMaxResults, setParameter, setPermanentParameter, setReturnTotalCount, temporaryJoin, temporarySelect, toQl, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface net.sf.basedb.core.query.Query

addAutoJoiner, getFirstResult, getMaxResults, getParameterNames, getQueryParameter, getQuerySection, group, groupPermanent, hasParameterValue, having, havingPermanent, isCounting, isDistinct, isFailSafe, isReadonly, isReturningTotalCount, join, joinPermanent, order, orderPermanent, reset, restrict, restrictPermanent, select, selectPermanent, setDistinct, setFailSafe, setFirstResult, setMaxResults, setParameter, setPermanentParameter, setReturnTotalCount, toQl

Field Details

cube

private final DataCube cube

virtualDb

private final VirtualDb virtualDb

rootTable

private final VirtualTable rootTable

transform

private final IntensityTransform transform

hasClonedReporters

private final boolean hasClonedReporters

useClonedReporters

private boolean useClonedReporters

Constructor Details

DynamicQuery

DynamicQuery(DataCube cube,
 VirtualTable rootTable,
 IntensityTransform transform)

Create a new dynamic query.

Parameters:

cube - The cube to query against

rootTable - The root table of the query

DynamicQuery

DynamicQuery(VirtualDb vdb,
 VirtualTable rootTable)

Create a new non-restricted dynamic query.

Parameters:

vdb - The virtual database to use

rootTable - The root table of the query

Since:

3.1

Method Details

getRootAlias

public String getRootAlias()

The alias of the item that is returned by this query.

Specified by:

getRootAlias in interface Query

See Also:

• Item.getAlias()

hasClonedReporters

public boolean hasClonedReporters()

Check if the virtual database that this query is using has cloned reporter annotations or not.

Specified by:

hasClonedReporters in interface ClonableReporterQuery

Since:

3.1

useClonedReporters

public boolean useClonedReporters()

Checks if this query is using cloned reporter or not by default. The default setting is to use cloned reporters if they are available in the experiment.

Specified by:

useClonedReporters in interface ClonableReporterQuery

Returns:

TRUE if this query is using cloned reporters, FALSE if not

Since:

3.1

setUseClonedReporters

public void setUseClonedReporters(boolean useClonedReporters)

Set if cloned reporters should be used by default or not.

Specified by:

setUseClonedReporters in interface ClonableReporterQuery

Parameters:

useClonedReporters - TRUE to use cloned reporters by default, FALSE to use the master reporters

Since:

3.1

getVirtualDb

public VirtualDb getVirtualDb()

Get the virtual database that this query is using.

Specified by:

getVirtualDb in interface ClonableReporterQuery

Returns:

A virtual database item

Since:

3.1

getDataCube

DataCube getDataCube()

getRootTable

VirtualTable getRootTable()

getIntensityTransform

public IntensityTransform getIntensityTransform()

Get the intensity transform that was used to store spot intensities for the root bioassay set in this query.

Since:

2.12