gov.usda.gdpc.panzea
Class PanzeaDBConnection

java.lang.Object
  gov.usda.gdpc.AbstractDBConnection
      gov.usda.gdpc.database.AbstractJDBCConnection
          gov.usda.gdpc.panzea.PanzeaDBConnection

All Implemented Interfaces:

DBConnection

Direct Known Subclasses:

GrameneConnection

public class PanzeaDBConnection

extends AbstractJDBCConnection

Author:

terryc

Field Summary

Fields inherited from class gov.usda.gdpc.database.AbstractJDBCConnection

myConnection, myDriver, myPassword, myUID, myURL

Fields inherited from class gov.usda.gdpc.AbstractDBConnection

myDataSource, myDescription

Constructor Summary

PanzeaDBConnection()

PanzeaDBConnection(java.lang.String dataSource, java.lang.String description, java.lang.String driver, java.lang.String url, java.lang.String uid, char[] passwd)
PanzeaDBConnection Constructor.

PanzeaDBConnection(java.lang.String dataSource, java.lang.String description, java.lang.String driver, java.lang.String url, java.lang.String uid, java.lang.String passwd)
PanzeaDBConnection Constructor.

Method Summary

DistinctPropertyValues	getDistinctProperties(java.util.List properties) Returns list(s) of distinct property values for the given properties.
EnvironmentExperimentGroup	getEnvironmentExperimentGroup(EnvironmentExperimentFilter filter) Gets an environment experiment group based on the given environment experiment filter.
GenotypeExperimentGroup	getGenotypeExperimentGroup(GenotypeExperimentFilter filter) Gets a genotype experiment group based on the given genotype experiment filter.
GenericTable	getGenotypeGenericTable(GenotypeExperimentGroup experimentGroup, TaxonGroup taxonGroup) Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups.
GenotypeGroup	getGenotypeGroup(GenotypeExperimentGroup experimentGroup, TaxonGroup taxonGroup) Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups.
LocalityGroup	getLocalityGroup(LocalityFilter filter) Gets a locality group based on the given locality filter.
LocusGroup	getLocusGroup(LocusFilter filter) Gets a locus group based on the given locus filter.
PhenotypeGroup	getPhenotypeGroup(EnvironmentExperimentGroup experimentGroup, TaxonGroup taxonGroup, PhenotypeOntologyGroup ontologyGroup) Gets the phenotypes for all combinations of environment experiments, taxa, and phenotype ontologys defined by the respective groups.
PhenotypeOntologyGroup	getPhenotypeOntologyGroup(PhenotypeOntologyFilter filter) Get a phenotype ontology group based on the given pheotype ontology filter.
PhenotypeOntologyGroup	getPhenotypeOntologyGroupFromDB(PhenotypeOntologyFilter filter)
TaxonGroup	getTaxonGroup(TaxonFilter filter) Gets a taxon group based on the given taxon filter.

Methods inherited from class gov.usda.gdpc.database.AbstractJDBCConnection

close, equals, executeQuery, executeQueryNoScroll, getDriver, getInString, getInString, getInStringWithQuotes, getMultiInStringWithQuotes, getUID, getURL, isClosed, makeConnection

Methods inherited from class gov.usda.gdpc.AbstractDBConnection

getDataSource, getDescription, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface gov.usda.gdpc.DBConnection

getDataSource, getDescription

Constructor Detail

PanzeaDBConnection

public PanzeaDBConnection(java.lang.String dataSource,
                          java.lang.String description,
                          java.lang.String driver,
                          java.lang.String url,
                          java.lang.String uid,
                          java.lang.String passwd)

PanzeaDBConnection Constructor.

Parameters:

dataSource - the data source of this connection

description - description of the connection

driver - the jdbc driver

url - a database url of the form jdbc:subprotocol:subname

uid - the database user on whose behalf the connection is being made

passwd - the user's password

PanzeaDBConnection

public PanzeaDBConnection(java.lang.String dataSource,
                          java.lang.String description,
                          java.lang.String driver,
                          java.lang.String url,
                          java.lang.String uid,
                          char[] passwd)

PanzeaDBConnection Constructor.

Parameters:

dataSource - the data source of this connection

description - description of the connection

driver - the jdbc driver

url - a database url of the form jdbc:subprotocol:subname

uid - the database user on whose behalf the connection is being made

passwd - the user's password

PanzeaDBConnection

public PanzeaDBConnection()

Method Detail

getEnvironmentExperimentGroup

public EnvironmentExperimentGroup getEnvironmentExperimentGroup(EnvironmentExperimentFilter filter)

Gets an environment experiment group based on the given environment experiment filter.

Specified by:

getEnvironmentExperimentGroup in interface DBConnection

Overrides:

getEnvironmentExperimentGroup in class AbstractDBConnection

Parameters:

filter - filter containing criteria.

Returns:

the environment experiment group

getGenotypeExperimentGroup

public GenotypeExperimentGroup getGenotypeExperimentGroup(GenotypeExperimentFilter filter)

Gets a genotype experiment group based on the given genotype experiment filter.

Specified by:

getGenotypeExperimentGroup in interface DBConnection

Overrides:

getGenotypeExperimentGroup in class AbstractDBConnection

Parameters:

filter - filter containing criteria.

Returns:

the genotype experiment group

getPhenotypeGroup

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

Gets the phenotypes for all combinations of environment experiments, taxa, and phenotype ontologys defined by the respective groups.

Specified by:

getPhenotypeGroup in interface DBConnection

Overrides:

getPhenotypeGroup in class AbstractDBConnection

Parameters:

experimentGroup - environment experiment group

taxonGroup - taxon group

ontologyGroup - phenotype ontology group

Returns:

phenotype group

getLocusGroup

public LocusGroup getLocusGroup(LocusFilter filter)

Gets a locus group based on the given locus filter.

Specified by:

getLocusGroup in interface DBConnection

Overrides:

getLocusGroup in class AbstractDBConnection

Parameters:

filter - filter containing criteria to build locus group.

Returns:

the locus group

getLocalityGroup

public LocalityGroup getLocalityGroup(LocalityFilter filter)

Gets a locality group based on the given locality filter.

Specified by:

getLocalityGroup in interface DBConnection

Overrides:

getLocalityGroup in class AbstractDBConnection

Parameters:

filter - filter containing criteria.

Returns:

the locality group

getTaxonGroup

public TaxonGroup getTaxonGroup(TaxonFilter filter)

Gets a taxon group based on the given taxon filter.

Specified by:

getTaxonGroup in interface DBConnection

Overrides:

getTaxonGroup in class AbstractDBConnection

Parameters:

filter - filter containing criteria.

Returns:

the taxon group

getPhenotypeOntologyGroup

public PhenotypeOntologyGroup getPhenotypeOntologyGroup(PhenotypeOntologyFilter filter)

Get a phenotype ontology group based on the given pheotype ontology filter.

Specified by:

getPhenotypeOntologyGroup in interface DBConnection

Overrides:

getPhenotypeOntologyGroup in class AbstractDBConnection

Parameters:

filter - phenotype ontology filter

Returns:

phenotype ontology group

getPhenotypeOntologyGroupFromDB

public PhenotypeOntologyGroup getPhenotypeOntologyGroupFromDB(PhenotypeOntologyFilter filter)

getDistinctProperties

public DistinctPropertyValues getDistinctProperties(java.util.List properties)

Returns list(s) of distinct property values for the given properties. The list(s) are values retrieved from this database connection. If null returned, this connection does not support the properties or the values could not be retrieved.

Specified by:

getDistinctProperties in interface DBConnection

Overrides:

getDistinctProperties in class AbstractDBConnection

Parameters:

properties - list of properties

Returns:

list(s) of distinct property values

getGenotypeGroup

public GenotypeGroup getGenotypeGroup(GenotypeExperimentGroup experimentGroup,
                                      TaxonGroup taxonGroup)

Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups.

Specified by:

getGenotypeGroup in interface DBConnection

Overrides:

getGenotypeGroup in class AbstractDBConnection

Parameters:

experimentGroup - genotype experiment group

taxonGroup - taxon group

Returns:

genotype group

getGenotypeGenericTable

public GenericTable getGenotypeGenericTable(GenotypeExperimentGroup experimentGroup,
                                            TaxonGroup taxonGroup)

Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups. Since the return type of this method does not include experiment or taxon information, neither input parameter can be empty or null. This method returns an empty table in that event.

Specified by:

getGenotypeGenericTable in interface DBConnection

Overrides:

getGenotypeGenericTable in class AbstractDBConnection

Parameters:

experimentGroup - genotype experiment group

taxonGroup - taxon group

Returns:

generic table