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:

Query, SqlQuery

Direct Known Subclasses:

DataCube.RawMappingQuery, DynamicExtraValueQuery, DynamicPositionQuery, DynamicSpotQuery

public abstract class DynamicQuery
extends AbstractSqlQuery

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: 2010-04-20 10:02:16 +0200 (Tue, 20 Apr 2010) $

Field Summary

private DataCube	cube
private VirtualTable	rootTable
private IntensityTransform	transform
private VirtualDb	virtualDb

Constructor Summary

DynamicQuery(DataCube cube, VirtualTable rootTable, IntensityTransform transform)
Create a new dynamic query.

Method Summary

(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.
abstract JepFunction[]	getJepFunctions(DbControl dc, boolean restrictions) Create custom JEP function that can be used with the current query.
String	getRootAlias() The alias of the item that is returned by this query.
(package private) VirtualTable	getRootTable()
(package private) VirtualDb	getVirtualDb()

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

bindLimits, count, getDefaultSelects, getQueryType, iterate, parseParameters, setParameters

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

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

Field Detail

cube

private final DataCube cube

virtualDb

private final VirtualDb virtualDb

rootTable

private final VirtualTable rootTable

transform

private final IntensityTransform transform

Constructor Detail

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

Method Detail

getRootAlias

public String getRootAlias()

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

See Also:

Item.getAlias()

getJepFunctions

public abstract JepFunction[] getJepFunctions(DbControl dc,
                                              boolean restrictions)

Create custom JEP function that can be used with the current query. The actual function need to implement either JepExpressionFunction or JepRestrictionFunction.

Parameters:

restrictions - If FALSE the metod should only return functions that can be used as Expression:s, otherwise it should return both expression and restriction functions

Since:

2.15

getDataCube

DataCube getDataCube()

getVirtualDb

VirtualDb getVirtualDb()

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