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java.lang.Objectnet.sf.basedb.core.AbstractQuery
net.sf.basedb.core.AbstractSqlQuery
net.sf.basedb.core.DynamicQuery
public abstract class DynamicQuery
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
.
BioAssaySet.getSpotData()
,
BioAssaySet.getPositionData()
,
ExtraValue.getValues()
Nested Class Summary |
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Nested classes/interfaces inherited from class net.sf.basedb.core.AbstractSqlQuery |
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AbstractSqlQuery.CountWork |
Field Summary | |
---|---|
private DataCube |
cube
|
private boolean |
hasClonedReporters
|
private VirtualTable |
rootTable
|
private IntensityTransform |
transform
|
private boolean |
useClonedReporters
|
private VirtualDb |
virtualDb
|
Constructor Summary | |
---|---|
DynamicQuery(DataCube cube,
VirtualTable rootTable,
IntensityTransform transform)
Create a new dynamic query. |
|
DynamicQuery(VirtualDb vdb,
VirtualTable rootTable)
Create a new non-restricted 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()
|
VirtualDb |
getVirtualDb()
Get the virtual database that this query is using. |
boolean |
hasClonedReporters()
Check if the virtual database that this query is using has cloned reporter annotations or not. |
void |
setUseClonedReporters(boolean useClonedReporters)
Set if cloned reporters should be used by default or not. |
boolean |
useClonedReporters()
Checks if this query is using cloned reporter or not by default. |
Methods inherited from class net.sf.basedb.core.AbstractSqlQuery |
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bindLimits, closeResultSet, closeStatement, count, getDefaultSelects, getQueryType, iterate, parseParameters, releaseSavepoint, rollbackToSavepoint, 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, isFailSafe, isReadonly, isReturningTotalCount, join, joinPermanent, order, orderPermanent, reset, restrict, restrictPermanent, select, selectPermanent, setDistinct, setFailSafe, setFirstResult, setMaxResults, setParameter, setPermanentParameter, setReturnTotalCount, toQl |
Field Detail |
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private final DataCube cube
private final VirtualDb virtualDb
private final VirtualTable rootTable
private final IntensityTransform transform
private final boolean hasClonedReporters
private boolean useClonedReporters
Constructor Detail |
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DynamicQuery(DataCube cube, VirtualTable rootTable, IntensityTransform transform)
cube
- The cube to query againstrootTable
- The root table of the queryDynamicQuery(VirtualDb vdb, VirtualTable rootTable)
vdb
- The virtual database to userootTable
- The root table of the queryMethod Detail |
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public String getRootAlias()
getRootAlias
in interface Query
Item.getAlias()
public boolean hasClonedReporters()
hasClonedReporters
in interface ClonableReporterQuery
public boolean useClonedReporters()
useClonedReporters
in interface ClonableReporterQuery
public void setUseClonedReporters(boolean useClonedReporters)
setUseClonedReporters
in interface ClonableReporterQuery
useClonedReporters
- TRUE to use cloned reporters by default, FALSE
to use the master reporterspublic VirtualDb getVirtualDb()
getVirtualDb
in interface ClonableReporterQuery
public abstract JepFunction[] getJepFunctions(DbControl dc, boolean restrictions)
JepExpressionFunction
or JepRestrictionFunction
.
restrictions
- If FALSE the metod should only return functions
that can be used as Expression
:s, otherwise it should return
both expression and restriction functionsDataCube getDataCube()
VirtualTable getRootTable()
public IntensityTransform getIntensityTransform()
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