gov.nih.nci.caarray.services.bioassaydata
Class IlluminaDataHandlerDataSourceManagerDB

java.lang.Object
  extended by gov.nih.nci.caarray.services.util.db.ManagerDB
      extended by gov.nih.nci.caarray.services.bioassaydata.IlluminaDataHandlerDataSourceManagerDB

public class IlluminaDataHandlerDataSourceManagerDB
extends ManagerDB


Field Summary
 
Fields inherited from class gov.nih.nci.caarray.services.util.db.ManagerDB
CASCADE_LINK, CASCADE_NONE, CASCADE_OBJECT, ID_UNSET
 
Constructor Summary
IlluminaDataHandlerDataSourceManagerDB()
           
 
Method Summary
 void close(java.sql.Connection connection)
           
 CompositeSequenceDimension getCompositeSequenceDimension(ArrayDesign arrayDesign)
           
 java.util.List<CompositeSequence> getCompositeSequences(CompositeGroup compositeGroup)
          select ID, IDENTIFIER from compositesequence where COMPOSITE_GROUP_ID = ?
 java.util.List<CompositeSequence> getCompositeSequences(CompositeSequenceDimension dimension)
           
 java.util.List<Feature> getContainedFeatures(FeatureDimension dimension)
          select ID, IDENTIFIER from compositesequence where COMPOSITE_GROUP_ID = ?
 FeatureDimension getFeatureDimension(ArrayDesign arrayDesign)
           
 java.util.List<Feature> getFeatures(FeatureGroup featureGroup)
          select ID, IDENTIFIER from feature where FEATURE_GROUP_ID = ?
 java.util.List<Feature> getFeaturesWithLocationAndZone(FeatureGroup featureGroup)
           select f.id, f.identifier, f.feature_location_id, fl.location_row, fl.location_column, f.zone_id, z.name from feature f left outer join featurelocation fl on f.feature_location_id = fl.id left outer join zone z on f.zone_id = z.id where feature_group_id = ?
protected  org.apache.ojb.broker.PersistenceBroker getPersistenceBroker()
          Gets a PersistenceBroker from the pool for the default profile.
 ReporterDimension getReporterDimension(ArrayDesign arrayDesign)
           
 java.util.List<Reporter> getReporters(ReporterDimension dimension)
           
protected  boolean isNewDesignElementDimension(DerivedBioAssay derivedBioAssay)
           
protected  boolean isNewDesignElementDimension(MeasuredBioAssay measuredBioAssay)
           
 void save(DesignElement designElement)
           
 void setNewDesignElementDimension(boolean newDesignElementDimension)
           
 
Methods inherited from class gov.nih.nci.caarray.services.util.db.ManagerDB
clearCache, close, countObjects, countObjects, deleteByQuery, deleteMtoNRelation, deleteObject, deleteObject, deleteObject, deleteObjectByQuery, exists, getIdentifiable, getObject, getObject, getObject, getObject, getObject, getObject, getObjectIterator, getObjectIterator, getObjects, getObjects, getObjects, getSqlInLimit, insertMtoNRelation, insertMtoNRelation, insertObject, insertObject, link, link, removeFromCache, retrieveReference, retrieveReferences, setCascadeDelete, setCascadeRetrieve, setCascadeStore, storeObject, storeObject, unlink, unlink, updateObject, updateObject
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

IlluminaDataHandlerDataSourceManagerDB

public IlluminaDataHandlerDataSourceManagerDB()
Method Detail

setNewDesignElementDimension

public void setNewDesignElementDimension(boolean newDesignElementDimension)

isNewDesignElementDimension

protected boolean isNewDesignElementDimension(DerivedBioAssay derivedBioAssay)

isNewDesignElementDimension

protected boolean isNewDesignElementDimension(MeasuredBioAssay measuredBioAssay)

getPersistenceBroker

protected org.apache.ojb.broker.PersistenceBroker getPersistenceBroker()
Description copied from class: ManagerDB
Gets a PersistenceBroker from the pool for the default profile.

Overrides:
getPersistenceBroker in class ManagerDB
Returns:
A PersistenceBroker instance.

save

public void save(DesignElement designElement)
          throws java.lang.Exception
Throws:
java.lang.Exception

close

public void close(java.sql.Connection connection)

getCompositeSequenceDimension

public CompositeSequenceDimension getCompositeSequenceDimension(ArrayDesign arrayDesign)
                                                         throws java.lang.Exception
Throws:
java.lang.Exception

getReporterDimension

public ReporterDimension getReporterDimension(ArrayDesign arrayDesign)
                                       throws java.lang.Exception
Throws:
java.lang.Exception

getFeatureDimension

public FeatureDimension getFeatureDimension(ArrayDesign arrayDesign)
                                     throws java.lang.Exception
Throws:
java.lang.Exception

getFeatures

public java.util.List<Feature> getFeatures(FeatureGroup featureGroup)
                                    throws DataHandlerDataSourceException
select ID, IDENTIFIER from feature where FEATURE_GROUP_ID = ?

Parameters:
featureGroup -
Returns:
Throws:
DataHandlerDataSourceException
DataHandlerDataSourceException

getCompositeSequences

public java.util.List<CompositeSequence> getCompositeSequences(CompositeGroup compositeGroup)
                                                        throws DataHandlerDataSourceException
select ID, IDENTIFIER from compositesequence where COMPOSITE_GROUP_ID = ?

Parameters:
compositeGroup -
Returns:
Throws:
DataHandlerDataSourceException

getContainedFeatures

public java.util.List<Feature> getContainedFeatures(FeatureDimension dimension)
                                             throws DataHandlerDataSourceException
select ID, IDENTIFIER from compositesequence where COMPOSITE_GROUP_ID = ?

Parameters:
compositeGroup -
Returns:
Throws:
DataHandlerDataSourceException

getReporters

public java.util.List<Reporter> getReporters(ReporterDimension dimension)
                                      throws DataHandlerDataSourceException
Throws:
DataHandlerDataSourceException

getCompositeSequences

public java.util.List<CompositeSequence> getCompositeSequences(CompositeSequenceDimension dimension)
                                                        throws DataHandlerDataSourceException
Throws:
DataHandlerDataSourceException

getFeaturesWithLocationAndZone

public java.util.List<Feature> getFeaturesWithLocationAndZone(FeatureGroup featureGroup)
                                                       throws DataHandlerDataSourceException
 select f.id, f.identifier, f.feature_location_id, fl.location_row,
 fl.location_column, f.zone_id, z.name 
 from feature f left outer join featurelocation fl on f.feature_location_id = fl.id 
 left outer join zone z on f.zone_id = z.id 
 where feature_group_id = ?
 

Parameters:
featureGroup - to limit
Returns:
Throws:
DataHandlerDataSourceException