gov.usda.gdpc
Class AbstractDBConnection

java.lang.Object
  gov.usda.gdpc.AbstractDBConnection

All Implemented Interfaces:

DBConnection

Direct Known Subclasses:

AbstractJDBCConnection

public abstract class AbstractDBConnection

extends java.lang.Object

implements DBConnection

This class provides a skeletal implementation of the DBConnection interface, to minimize the effort required to implement this interface.

To implement a database connection, the programmer needs to extend this class and provide implementations for the following methods defined in the DBConnection interface:

• getGenotypeExperimentGroup
• getEnvironmentExperimentGroup
• getTaxonGroup
• getLocusGroup
• getGenotypeGroup
• getGenotypeGenericTable
• getPhenotypeGroup
• getLocalityGroup
• getDistinctProperties

Author:

terryc

Field Summary

protected java.lang.String	myDataSource
protected java.lang.String	myDescription

Constructor Summary

AbstractDBConnection(java.lang.String dataSource, java.lang.String description)
AbstractDBConnection Constructor.

Method Summary

void	close() This method is unsupported by this class.
java.lang.String	getDataSource() Returns the data source of this connection.
java.lang.String	getDescription() Returns a description of this connection.
DistinctPropertyValues	getDistinctProperties(java.util.List properties) This method is unsupported by this class.
EnvironmentExperimentGroup	getEnvironmentExperimentGroup(EnvironmentExperimentFilter filter) This method is unsupported by this class.
GenotypeExperimentGroup	getGenotypeExperimentGroup(GenotypeExperimentFilter filter) This method is unsupported by this class.
GenericTable	getGenotypeGenericTable(GenotypeExperimentGroup experimentGroup, TaxonGroup taxonGroup) This method is unsupported by this class.
GenotypeGroup	getGenotypeGroup(GenotypeExperimentGroup experimentGroup, TaxonGroup taxonGroup) This method is unsupported by this class.
LocalityGroup	getLocalityGroup(LocalityFilter filter) This method is unsupported by this class.
LocusGroup	getLocusGroup(LocusFilter filter) This method is unsupported by this class.
PhenotypeGroup	getPhenotypeGroup(EnvironmentExperimentGroup experimentGroup, TaxonGroup taxonGroup, PhenotypeOntologyGroup ontologyGroup) This method is unsupported by this class.
PhenotypeOntologyGroup	getPhenotypeOntologyGroup(PhenotypeOntologyFilter filter) This method is unsupported by this class.
TaxonGroup	getTaxonGroup(TaxonFilter filter) This method is unsupported by this class.
java.lang.String	toString() Returns the String representation of this connection.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

myDataSource

protected final java.lang.String myDataSource

myDescription

protected final java.lang.String myDescription

Constructor Detail

AbstractDBConnection

public AbstractDBConnection(java.lang.String dataSource,
                            java.lang.String description)

AbstractDBConnection Constructor.

Parameters:

dataSource - the data source of this connection

description - description of this connection

Method Detail

getDataSource

public final java.lang.String getDataSource()

Returns the data source of this connection. Typically, a URI.

Specified by:

getDataSource in interface DBConnection

Returns:

data source

getDescription

public final java.lang.String getDescription()

Returns a description of this connection.

Specified by:

getDescription in interface DBConnection

Returns:

description

getLocusGroup

public LocusGroup getLocusGroup(LocusFilter filter)

This method is unsupported by this class. It should be implemented by its subclasses.

Specified by:

getLocusGroup in interface DBConnection

Parameters:

filter - filter containing criteria to build locus group.

Returns:

the locus group

getGenotypeExperimentGroup

public GenotypeExperimentGroup getGenotypeExperimentGroup(GenotypeExperimentFilter filter)

This method is unsupported by this class. It should be implemented by its subclasses.

Specified by:

getGenotypeExperimentGroup in interface DBConnection

Parameters:

filter - filter containing criteria.

Returns:

the genotype experiment group

getTaxonGroup

public TaxonGroup getTaxonGroup(TaxonFilter filter)

This method is unsupported by this class. It should be implemented by its subclasses.

Specified by:

getTaxonGroup in interface DBConnection

Parameters:

filter - filter containing criteria.

Returns:

the taxon group

getPhenotypeOntologyGroup

public PhenotypeOntologyGroup getPhenotypeOntologyGroup(PhenotypeOntologyFilter filter)

This method is unsupported by this class. It should be implemented by its subclasses.

Specified by:

getPhenotypeOntologyGroup in interface DBConnection

Parameters:

filter - phenotype ontology filter

Returns:

phenotype ontology group

getEnvironmentExperimentGroup

public EnvironmentExperimentGroup getEnvironmentExperimentGroup(EnvironmentExperimentFilter filter)

This method is unsupported by this class. It should be implemented by its subclasses.

Specified by:

getEnvironmentExperimentGroup in interface DBConnection

Parameters:

filter - filter containing criteria.

Returns:

the environment experiment group

getLocalityGroup

public LocalityGroup getLocalityGroup(LocalityFilter filter)

This method is unsupported by this class. It should be implemented by its subclasses.

Specified by:

getLocalityGroup in interface DBConnection

Parameters:

filter - filter containing criteria.

Returns:

the locality group

getPhenotypeGroup

public PhenotypeGroup getPhenotypeGroup(EnvironmentExperimentGroup experimentGroup,
                                        TaxonGroup taxonGroup,
                                        PhenotypeOntologyGroup ontologyGroup)

This method is unsupported by this class. It should be implemented by its subclasses.

Specified by:

getPhenotypeGroup in interface DBConnection

Parameters:

experimentGroup - environment experiment group

taxonGroup - taxon group

ontologyGroup - phenotype ontology group

Returns:

phenotype group

getDistinctProperties

public DistinctPropertyValues getDistinctProperties(java.util.List properties)

This method is unsupported by this class. It should be implemented by its subclasses.

Specified by:

getDistinctProperties in interface DBConnection

Parameters:

properties - list of properties

Returns:

list(s) of distinct property values

toString

public java.lang.String toString()

Returns the String representation of this connection. More specifically, it returns the data source of this connection.

Returns:

uri

getGenotypeGroup

public GenotypeGroup getGenotypeGroup(GenotypeExperimentGroup experimentGroup,
                                      TaxonGroup taxonGroup)

This method is unsupported by this class. It should be implemented by its subclasses.

Specified by:

getGenotypeGroup in interface DBConnection

Parameters:

experimentGroup - genotype experiment group

taxonGroup - taxon group

Returns:

genotype group

getGenotypeGenericTable

public GenericTable getGenotypeGenericTable(GenotypeExperimentGroup experimentGroup,
                                            TaxonGroup taxonGroup)

This method is unsupported by this class. It should be implemented by its subclasses.

Specified by:

getGenotypeGenericTable in interface DBConnection

Parameters:

experimentGroup - genotype experiment group

taxonGroup - taxon group

Returns:

generic table

close

public void close()

This method is unsupported by this class. It should be implemented by its subclasses.

Specified by:

close in interface DBConnection