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
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:
- Last modified
- $Date: 2012-09-14 09:28:35 +0200 (fr, 14 sep 2012) $
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Nested Class Summary
Nested classes/interfaces inherited from class net.sf.basedb.core.AbstractSqlQuery
AbstractSqlQuery.CountWork
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Field Summary
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Constructor Summary
ConstructorDescriptionDynamicPositionQuery
(BioAssaySet bioAssaySet) Create a new dynamic query.DynamicPositionQuery
(Experiment experiment) -
Method Summary
Modifier and TypeMethodDescription(package private) Select[]
Default selection: positiongetJepFunctions
(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 aReporterList
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
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Field Details
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bioAssaySet
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defaultSelects
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joinedItems
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Constructor Details
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DynamicPositionQuery
DynamicPositionQuery(BioAssaySet bioAssaySet) Create a new dynamic query.- Parameters:
bioAssaySet
- The bioAssaySet to query against
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DynamicPositionQuery
DynamicPositionQuery(Experiment experiment)
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Method Details
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getDefaultSelects
Select[] getDefaultSelects()Default selection: position- Specified by:
getDefaultSelects
in classAbstractSqlQuery
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reset
public void reset()Reset join information.- Specified by:
reset
in interfaceQuery
- Overrides:
reset
in classAbstractQuery
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getJepFunctions
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 classAbstractSqlQuery
restrictions
- If FALSE the metod should only return functions that can be used asExpression
:s, otherwise it should return both expression and restriction functions- Since:
- 2.15
- pos():
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joinReporters
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)
, orDynamicQuery.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:
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joinReporters
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:
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joinReporterList
Makes a join with aReporterList
- Parameters:
reporterList
- To do the join on.joinType
- The join type to use.- Since:
- 3.0
- See Also:
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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:
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setAutoJoinType
Specify the join type of automatic joins. The default join type isJoinType.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
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