Package net.sf.basedb.core

Class DynamicQuery

java.lang.Object
net.sf.basedb.core.AbstractQuery
net.sf.basedb.core.AbstractSqlQuery
net.sf.basedb.core.DynamicQuery
All Implemented Interfaces:
ClonableReporterQuery, Query, SqlQuery
Direct Known Subclasses:
DataCube.RawMappingQuery, DynamicExtraValueQuery, DynamicPositionQuery, DynamicSpotQuery
public abstract class DynamicQuery
extends AbstractSqlQuery
implements ClonableReporterQuery
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.

Version:
2.0
Author:
Nicklas
See Also:
BioAssaySet.getSpotData(), BioAssaySet.getPositionData(), ExtraValue.getValues()
Last modified
$Date: 2017-12-08 14:18:12 +0100 (fr, 08 dec 2017) $

  • Field Details

    • cube

      private final DataCube cube

    • virtualDb

      private final VirtualDb virtualDb

    • rootTable

      private final VirtualTable rootTable

    • transform

      private final IntensityTransform transform

    • hasClonedReporters

      private final boolean hasClonedReporters

    • useClonedReporters

      private boolean useClonedReporters

  • Constructor Details

    • DynamicQuery

      DynamicQuery​(DataCube cube, VirtualTable rootTable, IntensityTransform transform)
      Create a new dynamic query.
      Parameters:
      cube - The cube to query against
      rootTable - The root table of the query

    • DynamicQuery

      DynamicQuery​(VirtualDb vdb, VirtualTable rootTable)
      Create a new non-restricted dynamic query.
      Parameters:
      vdb - The virtual database to use
      rootTable - The root table of the query
      Since:
      3.1

  • Method Details

    • getRootAlias

      public String getRootAlias()
      The alias of the item that is returned by this query.
      Specified by:
      getRootAlias in interface Query
      See Also:
      Item.getAlias()

    • hasClonedReporters

      public boolean hasClonedReporters()
      Check if the virtual database that this query is using has cloned reporter annotations or not.
      Specified by:
      hasClonedReporters in interface ClonableReporterQuery
      Since:
      3.1

    • useClonedReporters

      public boolean useClonedReporters()
      Checks if this query is using cloned reporter or not by default. The default setting is to use cloned reporters if they are available in the experiment.
      Specified by:
      useClonedReporters in interface ClonableReporterQuery
      Returns:
      TRUE if this query is using cloned reporters, FALSE if not
      Since:
      3.1

    • setUseClonedReporters

      public void setUseClonedReporters​(boolean useClonedReporters)
      Set if cloned reporters should be used by default or not.
      Specified by:
      setUseClonedReporters in interface ClonableReporterQuery
      Parameters:
      useClonedReporters - TRUE to use cloned reporters by default, FALSE to use the master reporters
      Since:
      3.1

    • getVirtualDb

      public VirtualDb getVirtualDb()
      Get the virtual database that this query is using.
      Specified by:
      getVirtualDb in interface ClonableReporterQuery
      Returns:
      A virtual database item
      Since:
      3.1

    • getDataCube

      DataCube getDataCube()

    • getRootTable

      VirtualTable getRootTable()

    • getIntensityTransform

      public IntensityTransform getIntensityTransform()
      Get the intensity transform that was used to store spot intensities for the root bioassay set in this query.
      Since:
      2.12