Package net.sf.basedb.core

Class DynamicSpotQuery

java.lang.Object

net.sf.basedb.core.AbstractQuery

net.sf.basedb.core.AbstractSqlQuery

net.sf.basedb.core.DynamicQuery

net.sf.basedb.core.DynamicSpotQuery

All Implemented Interfaces:

ClonableReporterQuery, Query, SqlQuery

public class DynamicSpotQuery
extends DynamicQuery

Represents a query for spot information in 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.getSpotData()

Last modified

$Date: 2014-06-04 14:41:12 +0200 (on, 04 jun 2014) $

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 boolean	disableRawJoinOnMergedData
private Set<Object>	joinedItems

Constructor Summary

Constructors

Constructor	Description
DynamicSpotQuery(BioAssaySet bioAssaySet)	Create a new dynamic query.

Method Summary

Modifier and Type	Method	Description
(package private) Select[]	getDefaultSelects()	Default selection: column, postion, ch1, ch2, ...
boolean	getDisableRawJoinOnMergedData()
JepFunction[]	getJepFunctions(DbControl dc, boolean restrictions)	The following JEP functions can be used: ch(n): ChannelFunction rawCh(n): RawChannelFunction pos(): PositionFunction rep(property): ReporterFunction score(reporter-list-id): ScoreFunction xtra(extra-value-id): ExtraValueFunction (if a bioassay set has been specified) raw(property): RawFunction inList(reporter-list-id): InReporterListFunction (only if restrictions=true) notInList(reporter-list-id): NotInReporterListFunction (only if restrictions=true)
boolean	hasDisabledRawJoin()	Check if joining to raw data has been disabled.
void	joinExtraValue(ExtraValue extraValue, JoinType joinType)	Join extra values in the query.
void	joinRawData(JoinType joinType)	Join information about raw data 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.
void	setDisableRawJoinOnMergedData(boolean disable)	Disable automatic and manual joining of raw data if the bioassay set contains merged data.

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

disableRawJoinOnMergedData

private boolean disableRawJoinOnMergedData

defaultSelects

private Select[] defaultSelects

joinedItems

private Set<Object> joinedItems

Constructor Details

DynamicSpotQuery

DynamicSpotQuery(BioAssaySet bioAssaySet)

Create a new dynamic query.

Parameters:

bioAssaySet - The bioassay set to query against

Method Details

getDefaultSelects

Select[] getDefaultSelects()

Default selection: column, postion, ch1, ch2, ...

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 functions can be used:

• ch(n): ChannelFunction
• rawCh(n): RawChannelFunction
• pos(): PositionFunction
• rep(property): ReporterFunction
• score(reporter-list-id): ScoreFunction
• xtra(extra-value-id): ExtraValueFunction (if a bioassay set has been specified)
• raw(property): RawFunction
• 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

setDisableRawJoinOnMergedData

public void setDisableRawJoinOnMergedData(boolean disable)

Disable automatic and manual joining of raw data if the bioassay set contains merged data. Eg. if the BioAssaySet.getMaxRawMappingsForSpot() returns a value != 1. Note! Joins that have already been applied before this method is called are not disabled.

Since:

2.15

getDisableRawJoinOnMergedData

public boolean getDisableRawJoinOnMergedData()

Returns:

TRUE if joining raw data has been disabled for merged data

hasDisabledRawJoin

public boolean hasDisabledRawJoin()

Check if joining to raw data has been disabled. It is disabled only if BioAssaySet.getMaxRawMappingsForSpot() != 1 and getDisableRawJoinOnMergedData() == true

Returns:

TRUE if raw data join has been disabled, FALSE if not

joinReporters

public void joinReporters(JoinType joinType)
                   throws InvalidDataException

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 parameter is null.

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.

See Also:

• JoinType

joinRawData

public void joinRawData(JoinType joinType)
                 throws InvalidDataException

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

Parameters:

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

Throws:

InvalidDataException - If joinType parameter is null.

See Also:

• Dynamic.selectRawData(String)
• Dynamic.rawData(String)

joinExtraValue

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

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.

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