gov.nih.nci.caarray.services.bioassaydata
Class IlluminaDataHandlerDataSourceManagerDB
java.lang.Object
gov.nih.nci.caarray.services.util.db.ManagerDB
gov.nih.nci.caarray.services.bioassaydata.IlluminaDataHandlerDataSourceManagerDB
public class IlluminaDataHandlerDataSourceManagerDB
- extends ManagerDB
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 |
IlluminaDataHandlerDataSourceManagerDB
public IlluminaDataHandlerDataSourceManagerDB()
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