Package net.sf.basedb.core

Class DynamicPositionQuery

java.lang.Object

net.sf.basedb.core.AbstractQuery

net.sf.basedb.core.AbstractSqlQuery

net.sf.basedb.core.DynamicQuery

net.sf.basedb.core.DynamicPositionQuery

All Implemented Interfaces:

ClonableReporterQuery, Query, SqlQuery

public class DynamicPositionQuery
extends DynamicQuery

Represents a query for position information against the dynamic database. A single query object may query against data in one bioassayset at a time. Use factory methods in the Dynamic class to join other tables and create restrictions based on the data in those tables. You may of course also use the regular expressions and restrictions from the Expressions, Restrictions and other classes.

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.getPositionData()

Last modified

$Date: 2012-09-14 09:28:35 +0200 (fr, 14 sep 2012) $

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 BioAssaySet	bioAssaySet
private Select[]	defaultSelects
private Set<Object>	joinedItems

Constructor Summary

Constructors

Constructor	Description
DynamicPositionQuery(BioAssaySet bioAssaySet)	Create a new dynamic query.
DynamicPositionQuery(Experiment experiment)

Method Summary

Modifier and Type	Method	Description
(package private) Select[]	getDefaultSelects()	Default selection: position
JepFunction[]	getJepFunctions(DbControl dc, boolean restrictions)	The following JEP function can be used: pos(): PositionFunction rep(property): ReporterFunction score(reporter-list-id): ScoreFunction xtra(extra-value-id): ExtraValueFunction (if a bioassay set has been specified) inList(reporter-list-id): InReporterListFunction (only if restrictions=true) notInList(reporter-list-id): NotInReporterListFunction (only if restrictions=true)
void	joinExtraValue(ExtraValue extraValue, JoinType joinType)	Join extra values in the query.
void	joinReporterList(ReporterList reporterList, JoinType joinType)	Makes a join with a ReporterList
void	joinReporters(JoinType joinType)	Join information about reporters in the query.
void	joinReporters(JoinType joinType, boolean useCloned)	Join information about reporters in the query.
void	reset()	Reset join information.
void	setAutoJoinType(JoinType joinType)	Specify the join type of automatic joins.

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

getDataCube, getIntensityTransform, getRootAlias, getRootTable, getVirtualDb, hasClonedReporters, setUseClonedReporters, useClonedReporters

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

closeResultSet, closeStatement, count, 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, 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, restrict, restrictPermanent, select, selectPermanent, setDistinct, setFailSafe, setFirstResult, setMaxResults, setParameter, setPermanentParameter, setReturnTotalCount, toQl

Field Details

bioAssaySet

private final BioAssaySet bioAssaySet

defaultSelects

private Select[] defaultSelects

joinedItems

private Set<Object> joinedItems

Constructor Details

DynamicPositionQuery

DynamicPositionQuery(BioAssaySet bioAssaySet)

Create a new dynamic query.

Parameters:

bioAssaySet - The bioAssaySet to query against

DynamicPositionQuery

DynamicPositionQuery(Experiment experiment)

Method Details

getDefaultSelects

Select[] getDefaultSelects()

Default selection: position

Specified by:

getDefaultSelects in class AbstractSqlQuery

reset

public void reset()

Reset join information.

Specified by:

reset in interface Query

Overrides:

reset in class AbstractQuery

getJepFunctions

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

The following JEP function can be used:

• pos(): PositionFunction
• rep(property): ReporterFunction
• score(reporter-list-id): ScoreFunction
• xtra(extra-value-id): ExtraValueFunction (if a bioassay set has been specified)
• inList(reporter-list-id): InReporterListFunction (only if restrictions=true)
• notInList(reporter-list-id): NotInReporterListFunction (only if restrictions=true)

Specified by:

getJepFunctions in class AbstractSqlQuery

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

joinReporters

public void joinReporters(JoinType joinType)
                   throws InvalidDataException,
BaseException

Join information about reporters in the query. Now it becomes possible to select reporter data or restrict the results based on reporter information.

NOTE! Since BASE 3.1 this method automatically join to the cloned reporter table if available. Use joinReporters(JoinType, boolean), or DynamicQuery.setUseClonedReporters(boolean) with a FALSE value to force using the master reporters table.

Parameters:

joinType - The type of join. Can not be null.

Throws:

InvalidDataException - If joinType is null.

BaseException - If anything else goes wrong.

See Also:

• Dynamic.selectReporter(String)
• Dynamic.reporter(String)

joinReporters

public void joinReporters(JoinType joinType,
 boolean useCloned)

Join information about reporters in the query. If the useCloned parameter is TRUE cloned reporter annotations are used if available, otherwise the master reporter annotations are used.

Parameters:

joinType - The type of join. Can not be null.

Throws:

InvalidDataException - If joinType parameter is null.

Since:

3.1

See Also:

• Dynamic.selectReporter(String)
• Dynamic.reporter(String)

joinReporterList

public void joinReporterList(ReporterList reporterList,
 JoinType joinType)

Makes a join with a ReporterList

Parameters:

reporterList - To do the join on.

joinType - The join type to use.

Since:

3.0

See Also:

• JoinType

joinExtraValue

public void joinExtraValue(ExtraValue extraValue,
 JoinType joinType)
                    throws InvalidDataException,
BaseException

Join extra values in the query. Now it becomes possible to select those extra values or use them for restrictions.

Parameters:

extraValue - The extra values to join. Can not be null.

joinType - The type of join. Can not be null.

Throws:

InvalidDataException - If any of the required parameters are null.

BaseException - If something else fails.

See Also:

• Dynamic.select(ExtraValue, String)
• Dynamic.extraValue(ExtraValue)

setAutoJoinType

public void setAutoJoinType(JoinType joinType)

Specify the join type of automatic joins. The default join type is JoinType.LEFT. This setting doesn't affect joins that has been made directly to the query.

Parameters:

joinType - The type of the automatic joins

Since:

2.12