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java.lang.Object net.sf.basedb.core.AbstractQuery net.sf.basedb.core.AbstractSqlQuery net.sf.basedb.core.DynamicQuery net.sf.basedb.core.DynamicPositionQuery
public class DynamicPositionQuery
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
.
BioAssaySet.getPositionData()
Field Summary | |
---|---|
private BioAssaySet |
bioAssaySet
|
private Select[] |
defaultSelects
|
private Set<Object> |
joinedItems
|
Constructor Summary | |
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DynamicPositionQuery(BioAssaySet bioAssaySet)
Create a new dynamic query. |
Method Summary | |
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(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 |
joinReporters(JoinType joinType)
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 |
Methods inherited from class net.sf.basedb.core.AbstractSqlQuery |
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bindLimits, count, getQueryType, iterate, parseParameters, setParameters |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface net.sf.basedb.core.query.Query |
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addAutoJoiner, getFirstResult, getMaxResults, getParameterNames, getQueryParameter, getQuerySection, group, groupPermanent, hasParameterValue, having, havingPermanent, isCounting, isDistinct, isReadonly, isReturningTotalCount, join, joinPermanent, order, orderPermanent, restrict, restrictPermanent, select, selectPermanent, setDistinct, setFirstResult, setMaxResults, setParameter, setPermanentParameter, setReturnTotalCount, toQl |
Field Detail |
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private final BioAssaySet bioAssaySet
private Select[] defaultSelects
private Set<Object> joinedItems
Constructor Detail |
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DynamicPositionQuery(BioAssaySet bioAssaySet)
bioAssaySet
- The bioAssaySet to query againstMethod Detail |
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Select[] getDefaultSelects()
getDefaultSelects
in class AbstractSqlQuery
public void reset()
reset
in interface Query
reset
in class AbstractQuery
public JepFunction[] getJepFunctions(DbControl dc, boolean restrictions)
PositionFunction
ReporterFunction
ScoreFunction
ExtraValueFunction
(if a bioassay set
has been specified)
InReporterListFunction
(only if restrictions=true)
NotInReporterListFunction
(only if restrictions=true)
getJepFunctions
in class DynamicQuery
restrictions
- If FALSE the metod should only return functions
that can be used as Expression
:s, otherwise it should return
both expression and restriction functionspublic void joinReporters(JoinType joinType) throws InvalidDataException, BaseException
joinType
- The type of join. Can not be null.
InvalidDataException
- If joinType is null.
BaseException
- If anything else goes wrong.Dynamic.selectReporter(String)
,
Dynamic.reporter(String)
public void joinExtraValue(ExtraValue extraValue, JoinType joinType) throws InvalidDataException, BaseException
extraValue
- The extra values to join. Can not be null.joinType
- The type of join. Can not be null.
InvalidDataException
- If any of the required parameters are null.
BaseException
- If something else fails.Dynamic.select(ExtraValue, String)
,
Dynamic.extraValue(ExtraValue)
public void setAutoJoinType(JoinType joinType)
JoinType.LEFT
. This setting doesn't affect joins that has been made
directly to the query.
joinType
- The type of the automatic joins
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