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java.lang.Objectgov.nih.nci.caarray.services.bioassaydata.IlluminaDbDataHanderDataSource
public class IlluminaDbDataHanderDataSource
Constructor Summary | |
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IlluminaDbDataHanderDataSource()
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Method Summary | |
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void |
close(java.sql.Connection connection)
Closes a JDBC connection. |
void |
close(java.sql.Statement statement)
Closes a JDBC statement. |
protected gov.nih.nci.caarray.services.bioassaydata.DataHandlerDataSourceManagerDB |
createDataHandlerDataSourceManagerDB()
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CompositeSequenceDimension |
getCompositeSequenceDimension(ArrayDesign arrayDesign)
Looks up an existing CompositeSequenceDimension for this array design. |
java.util.List<CompositeSequence> |
getCompositeSequences(CompositeGroup compositeGroup)
Retrieve partial attributes of Feature only (id & identifier fields) |
java.util.List<CompositeSequence> |
getCompositeSequences(CompositeSequenceDimension dimension)
Retrieve partial attributes of CompositeSequence only (id & identifier fields) |
java.sql.Connection |
getConnection()
Returns a JDBC database connection to use to store raw data. |
java.util.List<Feature> |
getContainedFeatures(FeatureDimension dimension)
Retrieve partial attributes of Feature only (id) |
FeatureDimension |
getFeatureDimension(ArrayDesign arrayDesign)
Looks up an existing FeatureDimension for this array design. |
java.util.List<Feature> |
getFeatures(FeatureGroup featureGroup)
Retrieve partial attributes of Feature only (id & identifier fields) |
java.util.List<Feature> |
getFeaturesWithLoacationAndZone(FeatureGroup featureGroup)
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QuantitationType |
getQuantitationType(QuantitationTypeDescriptor descriptor)
Returns the quantitation type corresponding to the identifier provided. |
ReporterDimension |
getReporterDimension(ArrayDesign arrayDesign)
Looks up an existing ReporterDimension for this array design. |
java.util.List<Reporter> |
getReporters(ReporterDimension dimension)
Retrieve partial attributes of Reporter only (id ) |
QuantitationType |
instantiate(QuantitationTypeDescriptor descriptor)
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void |
linkToExperiment(BioAssayData bioAssayData,
Experiment experiment)
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void |
linkToExperiment(BioAssay bioAssay,
Experiment experiment)
Associates a BioAssay to an Experiment |
QuantitationType |
lookupQuantitationType(QuantitationTypeDescriptor descriptor)
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void |
save(BioAssay bioAssay)
Saves the given BioAssay and its related elements. |
void |
save(DesignElement designElement)
Saves the given DesignElement and its related elements. |
void |
setNewDesignElementDimensionOnCreateManagerDBForNextCreateOnly(boolean newDesignElementDimensionOnCreateManagerDBForNextCreateOnly)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public IlluminaDbDataHanderDataSource()
Method Detail |
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protected gov.nih.nci.caarray.services.bioassaydata.DataHandlerDataSourceManagerDB createDataHandlerDataSourceManagerDB()
public void setNewDesignElementDimensionOnCreateManagerDBForNextCreateOnly(boolean newDesignElementDimensionOnCreateManagerDBForNextCreateOnly)
public QuantitationType getQuantitationType(QuantitationTypeDescriptor descriptor) throws DataHandlerDataSourceException
descriptor
- the quantitation type identifier.
DataHandlerDataSourceException
public QuantitationType instantiate(QuantitationTypeDescriptor descriptor)
public QuantitationType lookupQuantitationType(QuantitationTypeDescriptor descriptor) throws DataHandlerDataSourceException
DataHandlerDataSourceException
public java.sql.Connection getConnection() throws DataHandlerDataSourceException
DataHandlerDataSourceException
public void save(BioAssay bioAssay) throws DataHandlerDataSourceException
BioAssay
and its related elements.
bioAssay
- the BioAssay to save.
DataHandlerDataSourceException
public void close(java.sql.Connection connection)
connection
- the connection to close.public void close(java.sql.Statement statement)
statement
- the statement to close.public void save(DesignElement designElement) throws DataHandlerDataSourceException
DesignElement
and its related elements.
DataHandlerDataSourceException
public FeatureDimension getFeatureDimension(ArrayDesign arrayDesign) throws DataHandlerDataSourceException
DataHandlerDataSourceException
public ReporterDimension getReporterDimension(ArrayDesign arrayDesign) throws DataHandlerDataSourceException
DataHandlerDataSourceException
public CompositeSequenceDimension getCompositeSequenceDimension(ArrayDesign arrayDesign) throws DataHandlerDataSourceException
DataHandlerDataSourceException
public void linkToExperiment(BioAssay bioAssay, Experiment experiment) throws DataHandlerDataSourceException
DataHandlerDataSourceException
public void linkToExperiment(BioAssayData bioAssayData, Experiment experiment) throws DataHandlerDataSourceException
DataHandlerDataSourceException
public java.util.List<Feature> getFeatures(FeatureGroup featureGroup) throws DataHandlerDataSourceException
DataHandlerDataSourceException
public java.util.List<CompositeSequence> getCompositeSequences(CompositeGroup compositeGroup) throws DataHandlerDataSourceException
DataHandlerDataSourceException
public java.util.List<Feature> getContainedFeatures(FeatureDimension dimension) throws DataHandlerDataSourceException
DataHandlerDataSourceException
public java.util.List<Reporter> getReporters(ReporterDimension dimension) throws DataHandlerDataSourceException
DataHandlerDataSourceException
public java.util.List<CompositeSequence> getCompositeSequences(CompositeSequenceDimension dimension) throws DataHandlerDataSourceException
DataHandlerDataSourceException
public java.util.List<Feature> getFeaturesWithLoacationAndZone(FeatureGroup featureGroup) throws DataHandlerDataSourceException
DataHandlerDataSourceException
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