Index (gov.usda.gdpc API)

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A

ACCESSION - Static variable in class gov.usda.gdpc.TaxonProperty: Accession of taxon (data type: java.lang.String).
ACCESSION - Static variable in class gov.usda.gdpc.xml.PropertyTag: TAXON PROPERTIES
ALIGNEXP - Static variable in class gov.usda.gdpc.panzea.PanzeaPropertyMap
ALIGNMENT - Static variable in class gov.usda.gdpc.panzea.PanzeaPropertyMap
ALIGN_INDEX - Static variable in class gov.usda.gdpc.panzea.PanzeaGenotypeExperimentDatabaseMapping
ALIGN_PROGRAM - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: Align Program associated with genotype experiment (data type: java.lang.String).
ALIGN_PROGRAM - Static variable in class gov.usda.gdpc.xml.PropertyTag: GENOTYPE EXPERIMENT PROPERTIES
ALLELE_LIST - Static variable in class gov.usda.gdpc.GenotypeProperty: Value of genotype (data type: gov.usda.gdpc.AlleleList).
ALLELE_LIST - Static variable in class gov.usda.gdpc.xml.PropertyTag: GENOTYPE PROPERTIES
ALLELE_LIST_ALLELE - Static variable in class gov.usda.gdpc.xml.PropertyTag
ALTITUDE - Static variable in class gov.usda.gdpc.LocalityProperty: Altitude of locality (data type: java.lang.Double).
ALTITUDE - Static variable in class gov.usda.gdpc.xml.PropertyTag: LOCALITY PROPERTIES
AboutAction - class gov.usda.gdpc.browser.AboutAction.
AbstractDBConnection - class gov.usda.gdpc.AbstractDBConnection.: This class provides a skeletal implementation of the DBConnection interface, to minimize the effort required to implement this interface.
AbstractDBConnection(String, String) - Constructor for class gov.usda.gdpc.AbstractDBConnection: AbstractDBConnection Constructor.
AbstractDBElement - class gov.usda.gdpc.AbstractDBElement.: This class provides a skeletal implementation of the DBElement interface to minimize the effort required to implement this interface.
AbstractDBElement(Map, String) - Constructor for class gov.usda.gdpc.AbstractDBElement: AbstractDBElement constructor.
AbstractDBElement(Property[], Map, String) - Constructor for class gov.usda.gdpc.AbstractDBElement
AbstractDBElementGroup - class gov.usda.gdpc.AbstractDBElementGroup.: This class provides a skeletal implementation of the DBElementGroup interface to minimize the effort required to implement this interface.
AbstractDBElementGroup(DBElement[]) - Constructor for class gov.usda.gdpc.AbstractDBElementGroup: AbstractDBElementGroup constructor.
AbstractDBElementGroup(Object[], boolean) - Constructor for class gov.usda.gdpc.AbstractDBElementGroup: AbstractDBElementGroup constructor.
AbstractDBElementGroup() - Constructor for class gov.usda.gdpc.AbstractDBElementGroup: AbstractDBElementGroup constructor.
AbstractDBElementGroup(List) - Constructor for class gov.usda.gdpc.AbstractDBElementGroup: AbstractDBElementGroup constructor.
AbstractDBElementGroup(List, boolean) - Constructor for class gov.usda.gdpc.AbstractDBElementGroup: AbstractDBElementGroup constructor.
AbstractDBElementGroup(DBElementGroup[]) - Constructor for class gov.usda.gdpc.AbstractDBElementGroup: AbstractDBElementGroup constructor.
AbstractDBElementGroup(Group[], boolean) - Constructor for class gov.usda.gdpc.AbstractDBElementGroup: AbstractDBElementGroup constructor.
AbstractDBGateway - class gov.usda.gdpc.AbstractDBGateway.: This class provides a skeletal implementation of the DBGateway interface to minimize the effort required to implement this interface.
AbstractDBGateway() - Constructor for class gov.usda.gdpc.AbstractDBGateway: AbstractDBGateway constructor.
AbstractDatabaseMapping - class gov.usda.gdpc.database.AbstractDatabaseMapping.: This class provides a skeletal implementation of the DatabaseMapping interface, to minimize the effort required to implement this interface.
AbstractDatabaseMapping(Property) - Constructor for class gov.usda.gdpc.database.AbstractDatabaseMapping: AbstractDatabaseMapping Constructor.
AbstractDatabaseMappingIndex - class gov.usda.gdpc.database.AbstractDatabaseMappingIndex.: This class provides a skeletal implementation of the IndexDatabaseMapping interface, to minimize the effort required to implement this interface.
AbstractDatabaseMappingIndex() - Constructor for class gov.usda.gdpc.database.AbstractDatabaseMappingIndex: AbstractDatabaseMappingIndex Constructor.
AbstractDatabaseMappingIndex(int) - Constructor for class gov.usda.gdpc.database.AbstractDatabaseMappingIndex: AbstractDatabaseMappingIndex Constructor.
AbstractEnvironmentExperimentGroup - class gov.usda.gdpc.AbstractEnvironmentExperimentGroup.: This class provides a skeletal implementation of the EnvironmentExperimentGroup interface to minimize the effort required to implement this interface.
AbstractEnvironmentExperimentGroup(EnvironmentExperiment[]) - Constructor for class gov.usda.gdpc.AbstractEnvironmentExperimentGroup: AbstractEnvironmentExperimentGroup constructor.
AbstractEnvironmentExperimentGroup() - Constructor for class gov.usda.gdpc.AbstractEnvironmentExperimentGroup: AbstractEnvironmentExperimentGroup constructor.
AbstractEnvironmentExperimentGroup(List) - Constructor for class gov.usda.gdpc.AbstractEnvironmentExperimentGroup: AbstractEnvironmentExperimentGroup constructor.
AbstractEnvironmentExperimentGroup(EnvironmentExperimentGroup[]) - Constructor for class gov.usda.gdpc.AbstractEnvironmentExperimentGroup: AbstractEnvironmentExperimentGroup constructor.
AbstractFilter - class gov.usda.gdpc.AbstractFilter.: This class provides a skeletal implementation of the Filter interface to minimize the effort required to implement this interface.
AbstractFilter() - Constructor for class gov.usda.gdpc.AbstractFilter: AbstractFilter constructor.
AbstractFilterValue - class gov.usda.gdpc.AbstractFilterValue.: This class provides a skeletal implementation of the DBConnection interface, to minimize the effort required to implement this interface.
AbstractFilterValue(Property) - Constructor for class gov.usda.gdpc.AbstractFilterValue: AbstractFilterValue Constructor.
AbstractGenotypeExperimentGroup - class gov.usda.gdpc.AbstractGenotypeExperimentGroup.: This class provides a skeletal implementation of the GenotypeExperimentGroup interface to minimize the effort required to implement this interface.
AbstractGenotypeExperimentGroup(GenotypeExperiment[]) - Constructor for class gov.usda.gdpc.AbstractGenotypeExperimentGroup: AbstractGenotypeExperimentGroup constructor.
AbstractGenotypeExperimentGroup() - Constructor for class gov.usda.gdpc.AbstractGenotypeExperimentGroup: AbstractGenotypeExperimentGroup constructor.
AbstractGenotypeExperimentGroup(List) - Constructor for class gov.usda.gdpc.AbstractGenotypeExperimentGroup: AbstractGenotypeExperimentGroup constructor.
AbstractGenotypeExperimentGroup(GenotypeExperimentGroup[]) - Constructor for class gov.usda.gdpc.AbstractGenotypeExperimentGroup: AbstractGenotypeExperimentGroup constructor.
AbstractGenotypeGroup - class gov.usda.gdpc.AbstractGenotypeGroup.: This class provides a skeletal implementation of the GenotypeGroup interface to minimize the effort required to implement this interface.
AbstractGenotypeGroup(Genotype[]) - Constructor for class gov.usda.gdpc.AbstractGenotypeGroup: AbstractGenotypeGroup constructor.
AbstractGenotypeGroup() - Constructor for class gov.usda.gdpc.AbstractGenotypeGroup: AbstractGenotypeGroup constructor.
AbstractGenotypeGroup(List) - Constructor for class gov.usda.gdpc.AbstractGenotypeGroup: AbstractGenotypeGroup constructor.
AbstractGenotypeGroup(GenotypeGroup[]) - Constructor for class gov.usda.gdpc.AbstractGenotypeGroup: AbstractGenotypeGroup constructor.
AbstractGroup - class gov.usda.gdpc.AbstractGroup.: This class provides a skeletal implementation of the Group interface to minimize the effort required to implement this interface.
AbstractGroup(Object[]) - Constructor for class gov.usda.gdpc.AbstractGroup: AbstractGroup constructor.
AbstractGroup(Object[], boolean) - Constructor for class gov.usda.gdpc.AbstractGroup: AbstractGroup constructor.
AbstractGroup() - Constructor for class gov.usda.gdpc.AbstractGroup: AbstractGroup constructor.
AbstractGroup(List) - Constructor for class gov.usda.gdpc.AbstractGroup: AbstractGroup constructor.
AbstractGroup(List, boolean) - Constructor for class gov.usda.gdpc.AbstractGroup: AbstractGroup constructor.
AbstractGroup(Group[]) - Constructor for class gov.usda.gdpc.AbstractGroup: AbstractGroup constructor.
AbstractGroup(Group[], boolean) - Constructor for class gov.usda.gdpc.AbstractGroup: AbstractGroup constructor.
AbstractJDBCConnection - class gov.usda.gdpc.database.AbstractJDBCConnection.: This class provides a skeletal implementation of the DBConnection interface which should be used as a connection to a database via JDBC.
AbstractJDBCConnection(String, String, String, String, String, String) - Constructor for class gov.usda.gdpc.database.AbstractJDBCConnection: AbstractJDBCConnection Constructor.
AbstractJDBCConnection(String, String, String, String, String, char[]) - Constructor for class gov.usda.gdpc.database.AbstractJDBCConnection: AbstractJDBCConnection Constructor.
AbstractLocalityGroup - class gov.usda.gdpc.AbstractLocalityGroup.: This class provides a skeletal implementation of the LocalityGroup interface to minimize the effort required to implement this interface.
AbstractLocalityGroup(Locality[]) - Constructor for class gov.usda.gdpc.AbstractLocalityGroup: AbstractLocalityGroup constructor.
AbstractLocalityGroup() - Constructor for class gov.usda.gdpc.AbstractLocalityGroup: AbstractLocalityGroup constructor.
AbstractLocalityGroup(List) - Constructor for class gov.usda.gdpc.AbstractLocalityGroup: AbstractLocalityGroup constructor.
AbstractLocalityGroup(LocalityGroup[]) - Constructor for class gov.usda.gdpc.AbstractLocalityGroup: AbstractLocalityGroup constructor.
AbstractLocusGroup - class gov.usda.gdpc.AbstractLocusGroup.: This class provides a skeletal implementation of the LocusGroup interface to minimize the effort required to implement this interface.
AbstractLocusGroup(Locus[]) - Constructor for class gov.usda.gdpc.AbstractLocusGroup: AbstractLocusGroup constructor.
AbstractLocusGroup() - Constructor for class gov.usda.gdpc.AbstractLocusGroup: AbstractLocusGroup constructor.
AbstractLocusGroup(List) - Constructor for class gov.usda.gdpc.AbstractLocusGroup: AbstractLocusGroup constructor.
AbstractLocusGroup(LocusGroup[]) - Constructor for class gov.usda.gdpc.AbstractLocusGroup: AbstractLocusGroup constructor.
AbstractPhenotypeGroup - class gov.usda.gdpc.AbstractPhenotypeGroup.: This class provides a skeletal implementation of the PhenotypeGroup interface to minimize the effort required to implement this interface.
AbstractPhenotypeGroup(Phenotype[]) - Constructor for class gov.usda.gdpc.AbstractPhenotypeGroup: AbstractPhenotypeGroup constructor.
AbstractPhenotypeGroup() - Constructor for class gov.usda.gdpc.AbstractPhenotypeGroup: AbstractPhenotypeGroup constructor.
AbstractPhenotypeGroup(List) - Constructor for class gov.usda.gdpc.AbstractPhenotypeGroup: AbstractPhenotypeGroup constructor.
AbstractPhenotypeGroup(PhenotypeGroup[]) - Constructor for class gov.usda.gdpc.AbstractPhenotypeGroup: AbstractPhenotypeGroup constructor.
AbstractPhenotypeOntologyGroup - class gov.usda.gdpc.AbstractPhenotypeOntologyGroup.: This class provides a skeletal implementation of the PhenotypeOntologyGroup interface to minimize the effort required to implement this interface.
AbstractPhenotypeOntologyGroup(PhenotypeOntology[]) - Constructor for class gov.usda.gdpc.AbstractPhenotypeOntologyGroup: AbstractPhenotypeOntologyGroup constructor.
AbstractPhenotypeOntologyGroup() - Constructor for class gov.usda.gdpc.AbstractPhenotypeOntologyGroup: AbstractPhenotypeOntologyGroup constructor.
AbstractPhenotypeOntologyGroup(List) - Constructor for class gov.usda.gdpc.AbstractPhenotypeOntologyGroup: AbstractPhenotypeOntologyGroup constructor.
AbstractPhenotypeOntologyGroup(PhenotypeOntologyGroup[]) - Constructor for class gov.usda.gdpc.AbstractPhenotypeOntologyGroup: AbstractPhenotypeOntologyGroup constructor.
AbstractProperty - class gov.usda.gdpc.AbstractProperty.
AbstractProperty(String, String, String, String) - Constructor for class gov.usda.gdpc.AbstractProperty: AbstractProperty constructor.
AbstractProperty(String, Class, String, String) - Constructor for class gov.usda.gdpc.AbstractProperty: AbstractProperty constructor.
AbstractPropertyMap - class gov.usda.gdpc.database.AbstractPropertyMap.: This class provides a skeletal implementation of the PropertyMap interface, to minimize the effort required to implement this interface.
AbstractPropertyMap() - Constructor for class gov.usda.gdpc.database.AbstractPropertyMap: AbstractPropertyMap Constructor.
AbstractTable - class gov.usda.gdpc.util.AbstractTable.: This class provides a skeletal implementation of the Table interface to minimize the effort required to implement this interface.
AbstractTable() - Constructor for class gov.usda.gdpc.util.AbstractTable
AbstractTable(List, List, Object[][]) - Constructor for class gov.usda.gdpc.util.AbstractTable: AbstractTable constructor.
AbstractTaxonGroup - class gov.usda.gdpc.AbstractTaxonGroup.: This class provides a skeletal implementation of the TaxonGroup interface to minimize the effort required to implement this interface.
AbstractTaxonGroup(Taxon[]) - Constructor for class gov.usda.gdpc.AbstractTaxonGroup: AbstractTaxonGroup constructor.
AbstractTaxonGroup() - Constructor for class gov.usda.gdpc.AbstractTaxonGroup: AbstractTaxonGroup constructor.
AbstractTaxonGroup(List) - Constructor for class gov.usda.gdpc.AbstractTaxonGroup: AbstractTaxonGroup constructor.
AbstractTaxonGroup(TaxonGroup[]) - Constructor for class gov.usda.gdpc.AbstractTaxonGroup: AbstractTaxonGroup constructor.
AbstractXMLDocument - class gov.usda.gdpc.xml.AbstractXMLDocument.
AbstractXMLDocument(String) - Constructor for class gov.usda.gdpc.xml.AbstractXMLDocument: AbstractXMLDocument Constructor.
AbstractXMLDocument(File) - Constructor for class gov.usda.gdpc.xml.AbstractXMLDocument: AbstractXMLDocument Constructor.
AbstractXMLDocument(boolean) - Constructor for class gov.usda.gdpc.xml.AbstractXMLDocument: AbstractXMLDocument Constructor.
AbstractXMLDocument() - Constructor for class gov.usda.gdpc.xml.AbstractXMLDocument: AbstractXMLDocument Constructor.
AddDBConnectionAction - class gov.usda.gdpc.browser.AddDBConnectionAction.
AddSOAPConnectionAction - class gov.usda.gdpc.browser.AddSOAPConnectionAction.
AlleleList - class gov.usda.gdpc.AlleleList.: List of alleles.
AlleleList(Collection) - Constructor for class gov.usda.gdpc.AlleleList: AlleleList constructor.
AlleleList(String[]) - Constructor for class gov.usda.gdpc.AlleleList: AlleleList constructor.
AlleleListDeserializer - class gov.usda.gdpc.axis.AlleleListDeserializer.
AlleleListDeserializer() - Constructor for class gov.usda.gdpc.axis.AlleleListDeserializer: AlleleListDeserializer Constructor.
ArrayUtils - class gov.usda.gdpc.util.ArrayUtils.: Utilities class that provides array handling functions.
accept(File) - Method in class gov.usda.gdpc.browser.FileFilter: Return whether file accepted.
actionPerformed(ActionEvent) - Method in class gov.usda.gdpc.browser.AboutAction
actionPerformed(ActionEvent) - Method in class gov.usda.gdpc.browser.AddDBConnectionAction
actionPerformed(ActionEvent) - Method in class gov.usda.gdpc.browser.AddSOAPConnectionAction
actionPerformed(ActionEvent) - Method in class gov.usda.gdpc.browser.DeselectAction
actionPerformed(ActionEvent) - Method in class gov.usda.gdpc.browser.DoubleArrowAction: Invoked when action performed.
actionPerformed(ActionEvent) - Method in class gov.usda.gdpc.browser.ExitAction
actionPerformed(ActionEvent) - Method in class gov.usda.gdpc.browser.GetStartedAction
actionPerformed(ActionEvent) - Method in class gov.usda.gdpc.browser.HelpAction
actionPerformed(ActionEvent) - Method in class gov.usda.gdpc.browser.RemoveAllFromTreeAction: Invoked when action performed.
actionPerformed(ActionEvent) - Method in class gov.usda.gdpc.browser.RemoveDBConnectionAction
actionPerformed(ActionEvent) - Method in class gov.usda.gdpc.browser.RemoveFromTreeAction
actionPerformed(ActionEvent) - Method in class gov.usda.gdpc.browser.RightArrowAction
actionPerformed(ActionEvent) - Method in class gov.usda.gdpc.browser.UpdateAction
add(Object) - Method in class gov.usda.gdpc.AbstractGroup: This operation is not supported.
add(int, Object) - Method in class gov.usda.gdpc.AbstractGroup: This operation is not supported.
add(List) - Method in class gov.usda.gdpc.gui.DBElementTree: Adds given list of elements to this tree.
add(DBElement) - Method in class gov.usda.gdpc.gui.DBElementTree: Adds given element to the tree.
add(DBElement) - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: Adds a DBElement to this property node tree.
add(List) - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: Adds a list of DBElements to this property node tree.
add(DBElement) - Method in class gov.usda.gdpc.gui.dbetree.HeadNode: Adds a DBElement to this property node tree.
add(List) - Method in class gov.usda.gdpc.gui.dbetree.HeadNode: Adds a list of DBElements to this property node tree.
add(DBElement) - Method in interface gov.usda.gdpc.gui.dbetree.Node: Adds the given DBElement to this value node tree.
add(DBElement) - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode: Adds a DBElement to this property node tree.
add(List) - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode: Adds a list of DBElements to this property node tree.
add(DBElement) - Method in class gov.usda.gdpc.gui.dbetree.ValueNode: Adds the given DBElement to this value node tree.
add(Object) - Method in class gov.usda.gdpc.util.ReadOnlyCollection
add(Object) - Method in class gov.usda.gdpc.util.ReadOnlyList
add(int, Object) - Method in class gov.usda.gdpc.util.ReadOnlyList
add(Object) - Method in class gov.usda.gdpc.util.ReadOnlySet
add(Object) - Method in class gov.usda.gdpc.util.SortedList: Add specified object to this sorted list.
add(int, Object) - Method in class gov.usda.gdpc.util.SortedList: Unsupported Operation.
add(Object) - Method in class gov.usda.gdpc.util.TreeSetPlusNull
addAll(Collection) - Method in class gov.usda.gdpc.AbstractGroup: This operation is not supported.
addAll(int, Collection) - Method in class gov.usda.gdpc.AbstractGroup: This operation is not supported.
addAll(Collection) - Method in class gov.usda.gdpc.util.ReadOnlyCollection
addAll(Collection) - Method in class gov.usda.gdpc.util.ReadOnlyList
addAll(int, Collection) - Method in class gov.usda.gdpc.util.ReadOnlyList
addAll(Collection) - Method in class gov.usda.gdpc.util.ReadOnlySet
addAll(Collection) - Method in class gov.usda.gdpc.util.SortedList
addAll(int, Collection) - Method in class gov.usda.gdpc.util.SortedList: Unsupported Operation.
addAll(Collection) - Method in class gov.usda.gdpc.util.TreeSetPlusNull
addConstant(Object) - Method in class gov.usda.gdpc.database.SQLStatements: Adds a constant value that will be added to the final list of distinct values.
addDBConnection(DBConnection) - Method in class gov.usda.gdpc.AbstractDBGateway: Adds a database connection to this gateway.
addDBConnection(DBConnection) - Method in interface gov.usda.gdpc.DBGateway: Adds a database connection to this gateway.
addDistinctProperty(Property) - Method in class gov.usda.gdpc.browser.FilterValuesPanel: Adds the distinct values for the given property.
addDistinctProperty(Property[]) - Method in class gov.usda.gdpc.browser.FilterValuesPanel: Adds the distinct values to the panel for the given properties.
addElement(Object) - Method in class gov.usda.gdpc.gui.GenericList: Adds the given element to this list.
addElements(Object[]) - Method in class gov.usda.gdpc.gui.GenericList
addElements(Vector) - Method in class gov.usda.gdpc.gui.GenericList
addElements(List) - Method in class gov.usda.gdpc.gui.GenericList
addInfo(Property, Object) - Method in class gov.usda.gdpc.database.ExtraInfo: Add extra information for a particular property.
addMapping(DatabaseMapping) - Method in class gov.usda.gdpc.database.AbstractPropertyMap: Adds the specified database mapping.
addMapping(DatabaseMapping) - Method in interface gov.usda.gdpc.database.PropertyMap: Adds the specified database mapping.
addNotify(TreeModelEvent) - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: This notifies this model that nodes have been added.
addNotify(TreeModelEvent) - Method in class gov.usda.gdpc.gui.dbetree.HeadNode
addNotify(TreeModelEvent) - Method in interface gov.usda.gdpc.gui.dbetree.Node
addNotify(TreeModelEvent) - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode
addNotify(TreeModelEvent) - Method in class gov.usda.gdpc.gui.dbetree.ValueNode
addRefPanes(String[], ListModel[], Property[]) - Method in class gov.usda.gdpc.browser.FilterValuesPanel: Adds the reference panels for the given properties.
addSQLStatements(SQLStatements) - Method in class gov.usda.gdpc.database.SQLStatements: Adds another SQL statements instance to this one.
addStatement(String, ExtraInfo) - Method in class gov.usda.gdpc.database.SQLStatements: Add a SQL statement with its extra information.
addTreeModelListener(TreeModelListener) - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: Adds given listener to this model.
addValue(FilterValue) - Method in class gov.usda.gdpc.AbstractFilter: Adds a value for a particular property for this filter.
addValue(FilterValue) - Method in class gov.usda.gdpc.EnvironmentExperimentFilter: Adds a value for a particular environment experiment property for this filter.
addValue(FilterValue) - Method in interface gov.usda.gdpc.Filter: Adds a value for a particular property for this filter.
addValue(FilterValue) - Method in class gov.usda.gdpc.GenotypeExperimentFilter: Adds a value for a particular genotype experiment property for this filter.
addValue(FilterValue) - Method in class gov.usda.gdpc.GenotypeFilter: Adds a value for a particular genotype property for this filter.
addValue(FilterValue) - Method in class gov.usda.gdpc.LocalityFilter: Adds a value for a particular locality property for this filter.
addValue(FilterValue) - Method in class gov.usda.gdpc.LocusFilter: Adds a value for a particular locus property for this filter.
addValue(FilterValue) - Method in class gov.usda.gdpc.PhenotypeFilter: Adds a value for a particular phenotype property for this filter.
addValue(FilterValue) - Method in class gov.usda.gdpc.PhenotypeOntologyFilter: Adds a value for a particular phenotype ontology property for this filter.
addValue(FilterValue) - Method in class gov.usda.gdpc.TaxonFilter: Adds a value for a particular taxon property for this filter.
addValues(Property, List) - Method in class gov.usda.gdpc.DistinctPropertyValues: This adds the given values for the given property.
addValues(DistinctPropertyValues) - Method in class gov.usda.gdpc.DistinctPropertyValues: This adds the given values to this instance.
asString() - Method in class gov.usda.gdpc.Identifier: Returns string representation of this identifier.

B

BasicWindowMonitor - class gov.usda.gdpc.browser.BasicWindowMonitor.
BasicWindowMonitor() - Constructor for class gov.usda.gdpc.browser.BasicWindowMonitor
Browser - class gov.usda.gdpc.browser.Browser.
Browser() - Constructor for class gov.usda.gdpc.browser.Browser: Browser constructor.
buildKey(Map) - Static method in class gov.usda.gdpc.EnvironmentExperiment: This builds the unique key for this environment experiment based on the EnvironmentExperimentProperty.ID and EnvironmentExperimentProperty.DATA_SOURCE.
buildKey(String, Identifier) - Static method in class gov.usda.gdpc.EnvironmentExperiment: This builds the unique key for this environment experiment based on the EnvironmentExperimentProperty.ID and EnvironmentExperimentProperty.DATA_SOURCE.
buildKey(Map) - Static method in class gov.usda.gdpc.Genotype: This builds the unique key for this phenotype based on the GenotypeProperty.DATA_SOURCE, GenotypeProperty.TAXON, and GenotypeProperty.GENOTYPE_EXPERIMENT.
buildKey(String, Taxon, GenotypeExperiment) - Static method in class gov.usda.gdpc.Genotype: This builds the unique key for this phenotype based on the GenotypeProperty.DATA_SOURCE, GenotypeProperty.TAXON, and GenotypeProperty.GENOTYPE_EXPERIMENT.
buildKey(Map) - Static method in class gov.usda.gdpc.GenotypeExperiment: This builds the unique key for this genotype experiment based on the GenotypeExperimentProperty.ID and GenotypeExperimentProperty.DATA_SOURCE.
buildKey(String, Identifier) - Static method in class gov.usda.gdpc.GenotypeExperiment: This builds the unique key for this environment experiment based on the GenotypeExperimentProperty.ID and GenotypeExperimentProperty.DATA_SOURCE.
buildKey(Map) - Static method in class gov.usda.gdpc.Locality: This builds the unique key for this locality based on the LocalityProperty.ID and LocalityProperty.DATA_SOURCE.
buildKey(String, Identifier) - Static method in class gov.usda.gdpc.Locality: This builds the unique key for this locality based on the LocalityProperty.ID and LocalityProperty.DATA_SOURCE.
buildKey(Map) - Static method in class gov.usda.gdpc.Locus: This builds the unique key for this locus based on the LocusProperty.ID and LocusProperty.DATA_SOURCE.
buildKey(String, Identifier) - Static method in class gov.usda.gdpc.Locus: This builds the unique key for this locus based on the LocusProperty.ID and LocusProperty.DATA_SOURCE.
buildKey(Map) - Static method in class gov.usda.gdpc.Phenotype: This builds the unique key for this phenotype based on the PhenotypeProperty.DATA_SOURCE, PhenotypeProperty.TAXON, PhenotypeProperty.ENVIRONMENT_EXPERIMENT, and PhenotypeProperty.ONTOLOGY.
buildKey(String, Taxon, EnvironmentExperiment, PhenotypeOntology) - Static method in class gov.usda.gdpc.Phenotype: This builds the unique key for this phenotype based on the PhenotypeProperty.DATA_SOURCE, PhenotypeProperty.TAXON, PhenotypeProperty.ENVIRONMENT_EXPERIMENT, and PhenotypeProperty.ONTOLOGY.
buildKey(Map) - Static method in class gov.usda.gdpc.PhenotypeOntology: This builds the unique key for this phenotype ontology based on the PhenotypeOntologyPropery.ID and PhenotypeOntologyProperty.DATA_SOURCE.
buildKey(String, Identifier) - Static method in class gov.usda.gdpc.PhenotypeOntology: This builds the unique key for this phenotype ontology based on the PhenotypeOntologyPropery.ID and PhenotypeOntologyProperty.DATA_SOURCE.
buildKey(Map) - Static method in class gov.usda.gdpc.Taxon: This builds the unique key for this taxon based on the TaxonPropery.ID and TaxonProperty.DATA_SOURCE.
buildKey(String, Identifier) - Static method in class gov.usda.gdpc.Taxon: This builds the unique key for this taxon based on the TaxonPropery.ID and TaxonProperty.DATA_SOURCE.

C

CALENDAR - Static variable in class gov.usda.gdpc.Convert
CHROMOSOME_NUMBER - Static variable in class gov.usda.gdpc.LocusProperty: Chromosome where locus exist (data type: java.lang.Integer).
CHROMOSOME_NUMBER - Static variable in class gov.usda.gdpc.xml.PropertyTag: LOCUS PROPERTIES
CITY - Static variable in class gov.usda.gdpc.LocalityProperty: City of locality (data type: java.lang.String).
COLLECTOR - Static variable in class gov.usda.gdpc.TaxonProperty: Collector of taxon (data type: java.lang.String).
COLLECTOR - Static variable in class gov.usda.gdpc.xml.PropertyTag
COL_PROPERTY - Static variable in class gov.usda.gdpc.browser.GenericPropTableModel
COL_PROPERTY - Static variable in class gov.usda.gdpc.browser.PropertiesTableModel
COL_VALUE - Static variable in class gov.usda.gdpc.browser.GenericPropTableModel
COL_VALUE - Static variable in class gov.usda.gdpc.browser.PropertiesTableModel
COMMENTS - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: Comments associated with genotype experiment (data type: java.lang.String).
COMMENTS - Static variable in class gov.usda.gdpc.LocusProperty: Comments about locus (data type: java.lang.String).
COMMENTS - Static variable in class gov.usda.gdpc.TaxonProperty: Comments about taxon (data type: java.lang.String).
COMMENTS - Static variable in class gov.usda.gdpc.xml.PropertyTag
CONNECTIONS_TAB - Static variable in class gov.usda.gdpc.browser.Browser
COUNTRY - Static variable in class gov.usda.gdpc.LocalityProperty: Country of locality (data type: java.lang.String).
COUNTRY - Static variable in class gov.usda.gdpc.xml.PropertyTag
Calendar - class gov.usda.gdpc.util.Calendar.
Calendar() - Constructor for class gov.usda.gdpc.util.Calendar: Constructs a default Calendar using the current time in the default time zone with the default locale.
Calendar(int, int, int) - Constructor for class gov.usda.gdpc.util.Calendar: Constructs a Calendar with the given date set in the default time zone with the default locale.
Calendar(int, int, int, int, int) - Constructor for class gov.usda.gdpc.util.Calendar: Constructs a Calendar with the given date and time set for the default time zone with the default locale.
Calendar(int, int, int, int, int, int) - Constructor for class gov.usda.gdpc.util.Calendar: Constructs a Calendar with the given date and time set for the default time zone with the default locale.
Calendar(Locale) - Constructor for class gov.usda.gdpc.util.Calendar: Constructs a Calendar based on the current time in the default time zone with the given locale.
Calendar(TimeZone) - Constructor for class gov.usda.gdpc.util.Calendar: Constructs a Calendar based on the current time in the given time zone with the default locale.
Calendar(TimeZone, Locale) - Constructor for class gov.usda.gdpc.util.Calendar: Constructs a GregorianCalendar based on the current time in the given time zone with the given locale.
Chromosome - class gov.usda.gdpc.Chromosome.
Chromosome(int, Locus[]) - Constructor for class gov.usda.gdpc.Chromosome: Chromosome Constructor
Chromosome(int) - Constructor for class gov.usda.gdpc.Chromosome: Chromosome constructor.
Chromosome(int, List) - Constructor for class gov.usda.gdpc.Chromosome: Chromosome constructor.
Chromosome(int, LocusGroup[]) - Constructor for class gov.usda.gdpc.Chromosome: Chromosome constructor.
ColumnData - class gov.usda.gdpc.browser.ColumnData.
ColumnData(String, int, int) - Constructor for class gov.usda.gdpc.browser.ColumnData
ConnectionsMenu - class gov.usda.gdpc.browser.ConnectionsMenu.
ConnectionsMenu(Browser) - Constructor for class gov.usda.gdpc.browser.ConnectionsMenu: ConnectionsMenu constructor comment.
ConstantDatabaseMapping - class gov.usda.gdpc.database.ConstantDatabaseMapping.
ConstantDatabaseMapping(Property, Object) - Constructor for class gov.usda.gdpc.database.ConstantDatabaseMapping: ConstantDatabaseMapping Constructor.
Convert - class gov.usda.gdpc.Convert.
changeTable(Table) - Method in class gov.usda.gdpc.browser.MatrixTableModel: Changes the table backing this matrix table model.
children() - Method in class gov.usda.gdpc.gui.dbetree.HeadNode
children() - Method in interface gov.usda.gdpc.gui.dbetree.Node
children() - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode
children() - Method in class gov.usda.gdpc.gui.dbetree.ValueNode
clear() - Method in class gov.usda.gdpc.AbstractDBElement: This operation is not supported.
clear() - Method in class gov.usda.gdpc.AbstractGroup: This operation is not supported.
clear() - Method in class gov.usda.gdpc.util.ReadOnlyCollection
clear() - Method in class gov.usda.gdpc.util.ReadOnlyList
clear() - Method in class gov.usda.gdpc.util.ReadOnlySet
clear() - Method in class gov.usda.gdpc.util.SortedList
clear() - Method in class gov.usda.gdpc.util.TreeSetPlusNull
clearItems() - Method in class gov.usda.gdpc.gui.DBElementTree: Clears all items in this tree.
close() - Method in class gov.usda.gdpc.AbstractDBConnection: This method is unsupported by this class.
close() - Method in interface gov.usda.gdpc.DBConnection: This method is used to tell the connection to close or generally release any resources and shutdown.
close() - Method in class gov.usda.gdpc.axis.DBConnectionProxy: This method is used to tell the connection to close or generally release any resources and shutdown.
close() - Method in class gov.usda.gdpc.database.AbstractJDBCConnection: Close the database connection.
compareTo(Object) - Method in class gov.usda.gdpc.AbstractDBElement: Compares two database elements to determine there order based on the alphabetical order of the string returned by getName().
compareTo(Object) - Method in class gov.usda.gdpc.AbstractProperty: Compares two properties to determine there order based on the alphabetical order of the property name.
compareTo(Object) - Method in class gov.usda.gdpc.Identifier: Compares this object with the specified object for order.
compareTo(Object) - Method in class gov.usda.gdpc.util.Calendar: Compares this object with the specified object for order.
componentShown(ComponentEvent) - Method in class gov.usda.gdpc.browser.DistinctComponentAdapter
contains(Object) - Method in class gov.usda.gdpc.AbstractGroup: Returns true if this collection contains the specified element.
contains(Object) - Method in class gov.usda.gdpc.util.ReadOnlyCollection
contains(Object) - Method in class gov.usda.gdpc.util.ReadOnlyList
contains(Object) - Method in class gov.usda.gdpc.util.ReadOnlySet
contains(Object) - Method in class gov.usda.gdpc.util.SortedList
contains(Object) - Method in class gov.usda.gdpc.util.TreeSetPlusNull
containsAll(Collection) - Method in class gov.usda.gdpc.AbstractGroup: Returns true if this collection contains all of the elements in the specified collection.
containsAll(Collection) - Method in class gov.usda.gdpc.util.ReadOnlyCollection
containsAll(Collection) - Method in class gov.usda.gdpc.util.ReadOnlyList
containsAll(Collection) - Method in class gov.usda.gdpc.util.ReadOnlySet
containsAll(Collection) - Method in class gov.usda.gdpc.util.SortedList
containsAll(Collection) - Method in class gov.usda.gdpc.util.TreeSetPlusNull
containsKey(Object) - Method in class gov.usda.gdpc.AbstractDBElement: Returns true if this map contains a mapping for the specified key.
containsValue(Object) - Method in class gov.usda.gdpc.AbstractDBElement: Returns true if this map maps one or more keys to the specified value.
convertStringToObject(String, Class) - Static method in class gov.usda.gdpc.Convert
createAnnotationAlignment(GenotypeTable) - Static method in class gov.usda.gdpc.pal.PALUtil: Converts the given GDPC GenotypeTable to a PAL SimpleAnnotatedAlignment.
createAnnotationAlignment(GenotypeTable, int) - Static method in class gov.usda.gdpc.pal.PALUtil
createCharacterAlignment(PhenotypeTable) - Static method in class gov.usda.gdpc.pal.PALUtil
createDBElement(DBElement) - Method in class gov.usda.gdpc.xml.AbstractXMLDocument
createInstanceForTASSEL() - Static method in class gov.usda.gdpc.browser.Browser: Factory method to create Browser instance for TASSEL
createProperties(String, Object, Element) - Method in class gov.usda.gdpc.xml.AbstractXMLDocument
createTableDBElement(DBElement) - Method in class gov.usda.gdpc.xml.AbstractXMLDocument

D

DATA_SOURCE - Static variable in class gov.usda.gdpc.EnvironmentExperimentProperty: Data source of environment experiment (data type: java.lang.String).
DATA_SOURCE - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: Data source of genotype experiment (data type: java.lang.String).
DATA_SOURCE - Static variable in class gov.usda.gdpc.GenotypeProperty: Data source of genotype (data type: java.lang.String).
DATA_SOURCE - Static variable in class gov.usda.gdpc.LocalityProperty: Data source of locality (data type: java.lang.String).
DATA_SOURCE - Static variable in class gov.usda.gdpc.LocusProperty: Data source of locus (data type: java.lang.String).
DATA_SOURCE - Static variable in class gov.usda.gdpc.PhenotypeOntologyProperty: Data source of phenotype ontology (data type: java.lang.String).
DATA_SOURCE - Static variable in class gov.usda.gdpc.PhenotypeProperty: Data source of phenotype (data type: java.lang.String).
DATA_SOURCE - Static variable in class gov.usda.gdpc.TaxonProperty: Data source of taxon (data type: java.lang.String).
DATA_SOURCE - Static variable in class gov.usda.gdpc.xml.PropertyTag
DATE - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: Date of this genotype experiment (data type: gov.usda.gdpc.util.Calendar)
DBConnection - interface gov.usda.gdpc.DBConnection.: Defines the low level interaction with a database.
DBConnectionProperties - class gov.usda.gdpc.browser.DBConnectionProperties.
DBConnectionProperties() - Constructor for class gov.usda.gdpc.browser.DBConnectionProperties: DBConnectionProperties Constructor.
DBConnectionProxy - class gov.usda.gdpc.axis.DBConnectionProxy.
DBConnectionProxy(String, String) - Constructor for class gov.usda.gdpc.axis.DBConnectionProxy: DBConnectionProxy Constructor.
DBConnectionsPanel - class gov.usda.gdpc.browser.DBConnectionsPanel.
DBConnectionsPanel(Browser) - Constructor for class gov.usda.gdpc.browser.DBConnectionsPanel: DBConnectionsPanel Constructor.
DBELEMENT - Static variable in class gov.usda.gdpc.xml.GDPCTag
DBELEMENTS - Static variable in class gov.usda.gdpc.xml.GDPCTag
DBElement - interface gov.usda.gdpc.DBElement.: Element that came from a database.
DBElementDeserializer - class gov.usda.gdpc.axis.DBElementDeserializer.
DBElementDeserializer() - Constructor for class gov.usda.gdpc.axis.DBElementDeserializer: DBElementDeserializer Constructor.
DBElementGroup - interface gov.usda.gdpc.DBElementGroup.: List of database elements.
DBElementPanel - class gov.usda.gdpc.browser.DBElementPanel.
DBElementPanel(Class) - Constructor for class gov.usda.gdpc.browser.DBElementPanel: DBElementPanel Constructor.
DBElementPanel(Class, DBGateway, String[], ListModel[], Property[]) - Constructor for class gov.usda.gdpc.browser.DBElementPanel: DBElementPanel Constructor.
DBElementPanel(Class, DBGateway, Browser, Property[]) - Constructor for class gov.usda.gdpc.browser.DBElementPanel: DBElementPanel Constructor.
DBElementPanel(Class, DBGateway, Browser, Property[], String[], ListModel[], Property[]) - Constructor for class gov.usda.gdpc.browser.DBElementPanel: DBElementPanel Constructor.
DBElementProperties - class gov.usda.gdpc.browser.DBElementProperties.
DBElementProperties() - Constructor for class gov.usda.gdpc.browser.DBElementProperties: DBElementProperties Constructor.
DBElementTree - class gov.usda.gdpc.gui.DBElementTree.
DBElementTree(HeadNode) - Constructor for class gov.usda.gdpc.gui.DBElementTree: DBElementTree Constructor.
DBElementTree() - Constructor for class gov.usda.gdpc.gui.DBElementTree: DBElementTree Constructor.
DBElementTreeModel - class gov.usda.gdpc.gui.dbetree.DBElementTreeModel.
DBElementTreeModel(HeadNode) - Constructor for class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: DBElementTreeModel Constructor.
DBElementTreeModel() - Constructor for class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: DBElementTreeModel Constructor.
DBElementsDeserializer - class gov.usda.gdpc.axis.DBElementsDeserializer.
DBElementsDeserializer() - Constructor for class gov.usda.gdpc.axis.DBElementsDeserializer: DBElementsDeserializer Constructor.
DBGateway - interface gov.usda.gdpc.DBGateway.: The single point of access to retrieve data from the database(s).
DEFAULT_MAX_NUMBER_ENTRIES - Static variable in class gov.usda.gdpc.util.ExceptionUtils: Default maximun number of entries.
DISTINCT_PROPERTY_VALUES - Static variable in class gov.usda.gdpc.xml.GDPCTag
DOUBLE - Static variable in class gov.usda.gdpc.Convert
DatabaseMapping - interface gov.usda.gdpc.database.DatabaseMapping.: This is a database mapping.
DatabaseMappingIndex - interface gov.usda.gdpc.database.DatabaseMappingIndex.
DateDatabaseMapping - class gov.usda.gdpc.database.DateDatabaseMapping.
DateDatabaseMapping(Property, String, String) - Constructor for class gov.usda.gdpc.database.DateDatabaseMapping: DateDatabaseMapping Constructor.
DefaultDBGateway - class gov.usda.gdpc.DefaultDBGateway.: This is the default implementation of the database gateway.
DefaultDBGateway() - Constructor for class gov.usda.gdpc.DefaultDBGateway: DefaultDBGateway constructor.
DefaultDatabaseMappingIndex - class gov.usda.gdpc.database.DefaultDatabaseMappingIndex.: This is the default implementation of the IndexDatabaseMapping interface.
DefaultDatabaseMappingIndex() - Constructor for class gov.usda.gdpc.database.DefaultDatabaseMappingIndex: DefaultDatabaseMappingIndex Constructor.
DefaultDatabaseMappingIndex(int) - Constructor for class gov.usda.gdpc.database.DefaultDatabaseMappingIndex: DefaultDatabaseMappingIndex Constructor.
DefaultEnvironmentExperimentGroup - class gov.usda.gdpc.DefaultEnvironmentExperimentGroup.: This is the default implementation of a environment experiment group.
DefaultEnvironmentExperimentGroup(EnvironmentExperiment[]) - Constructor for class gov.usda.gdpc.DefaultEnvironmentExperimentGroup: DefaultEnvironmentExperimentGroup constructor.
DefaultEnvironmentExperimentGroup() - Constructor for class gov.usda.gdpc.DefaultEnvironmentExperimentGroup: DefaultEnvironmentExperimentGroup constructor.
DefaultEnvironmentExperimentGroup(List) - Constructor for class gov.usda.gdpc.DefaultEnvironmentExperimentGroup: DefaultEnvironmentExperimentGroup constructor.
DefaultEnvironmentExperimentGroup(EnvironmentExperimentGroup[]) - Constructor for class gov.usda.gdpc.DefaultEnvironmentExperimentGroup: DefaultEnvironmentExperimentGroup constructor.
DefaultGenotypeExperimentGroup - class gov.usda.gdpc.DefaultGenotypeExperimentGroup.: This is the default implementation of a genotype experiment group.
DefaultGenotypeExperimentGroup(GenotypeExperiment[]) - Constructor for class gov.usda.gdpc.DefaultGenotypeExperimentGroup: DefaultGenotypeExperimentGroup constructor.
DefaultGenotypeExperimentGroup() - Constructor for class gov.usda.gdpc.DefaultGenotypeExperimentGroup: DefaultGenotypeExperimentGroup constructor.
DefaultGenotypeExperimentGroup(List) - Constructor for class gov.usda.gdpc.DefaultGenotypeExperimentGroup: DefaultGenotypeExperimentGroup constructor.
DefaultGenotypeExperimentGroup(GenotypeExperimentGroup[]) - Constructor for class gov.usda.gdpc.DefaultGenotypeExperimentGroup: DefaultGenotypeExperimentGroup constructor.
DefaultGenotypeGroup - class gov.usda.gdpc.DefaultGenotypeGroup.: This is the default implementation of a genotype group.
DefaultGenotypeGroup() - Constructor for class gov.usda.gdpc.DefaultGenotypeGroup: DefaultGenotypeGroup constructor.
DefaultLocalityGroup - class gov.usda.gdpc.DefaultLocalityGroup.: This is the default implementation of a locality group.
DefaultLocalityGroup(Locality[]) - Constructor for class gov.usda.gdpc.DefaultLocalityGroup: DefaultLocalityGroup constructor.
DefaultLocalityGroup() - Constructor for class gov.usda.gdpc.DefaultLocalityGroup: DefaultLocalityGroup constructor.
DefaultLocalityGroup(List) - Constructor for class gov.usda.gdpc.DefaultLocalityGroup: DefaultLocalityGroup constructor.
DefaultLocalityGroup(LocalityGroup[]) - Constructor for class gov.usda.gdpc.DefaultLocalityGroup: DefaultLocalityGroup constructor.
DefaultLocusGroup - class gov.usda.gdpc.DefaultLocusGroup.: This is the default implementation of a locus group.
DefaultLocusGroup(Locus[]) - Constructor for class gov.usda.gdpc.DefaultLocusGroup: DefaultLocusGroup constructor.
DefaultLocusGroup() - Constructor for class gov.usda.gdpc.DefaultLocusGroup: DefaultLocusGroup constructor.
DefaultLocusGroup(List) - Constructor for class gov.usda.gdpc.DefaultLocusGroup: DefaultLocusGroup constructor.
DefaultLocusGroup(LocusGroup[]) - Constructor for class gov.usda.gdpc.DefaultLocusGroup: DefaultLocusGroup constructor.
DefaultPhenotypeGroup - class gov.usda.gdpc.DefaultPhenotypeGroup.: This is the default implementation of a phenotype group.
DefaultPhenotypeGroup(Phenotype[]) - Constructor for class gov.usda.gdpc.DefaultPhenotypeGroup: DefaultPhenotypeGroup constructor.
DefaultPhenotypeGroup() - Constructor for class gov.usda.gdpc.DefaultPhenotypeGroup: DefaultPhenotypeGroup constructor.
DefaultPhenotypeGroup(List) - Constructor for class gov.usda.gdpc.DefaultPhenotypeGroup: DefaultPhenotypeGroup constructor.
DefaultPhenotypeGroup(PhenotypeGroup[]) - Constructor for class gov.usda.gdpc.DefaultPhenotypeGroup: DefaultPhenotypeGroup constructor.
DefaultPhenotypeOntologyGroup - class gov.usda.gdpc.DefaultPhenotypeOntologyGroup.: This is the default implementation of a phenotype ontology group.
DefaultPhenotypeOntologyGroup(PhenotypeOntology[]) - Constructor for class gov.usda.gdpc.DefaultPhenotypeOntologyGroup: DefaultPhenotypeOntologyGroup constructor.
DefaultPhenotypeOntologyGroup() - Constructor for class gov.usda.gdpc.DefaultPhenotypeOntologyGroup: DefaultPhenotypeOntologyGroup constructor.
DefaultPhenotypeOntologyGroup(List) - Constructor for class gov.usda.gdpc.DefaultPhenotypeOntologyGroup: DefaultPhenotypeOntologyGroup constructor.
DefaultPhenotypeOntologyGroup(PhenotypeOntologyGroup[]) - Constructor for class gov.usda.gdpc.DefaultPhenotypeOntologyGroup: DefaultPhenotypeOntologyGroup constructor.
DefaultTaxonGroup - class gov.usda.gdpc.DefaultTaxonGroup.: This is the default implementation of a taxon group.
DefaultTaxonGroup(Taxon[]) - Constructor for class gov.usda.gdpc.DefaultTaxonGroup: DefaultTaxonGroup constructor.
DefaultTaxonGroup() - Constructor for class gov.usda.gdpc.DefaultTaxonGroup: DefaultTaxonGroup constructor.
DefaultTaxonGroup(List) - Constructor for class gov.usda.gdpc.DefaultTaxonGroup: DefaultTaxonGroup constructor.
DefaultTaxonGroup(TaxonGroup[]) - Constructor for class gov.usda.gdpc.DefaultTaxonGroup: DefaultTaxonGroup constructor.
DeselectAction - class gov.usda.gdpc.browser.DeselectAction.
DistinctComponentAdapter - class gov.usda.gdpc.browser.DistinctComponentAdapter.
DistinctComponentAdapter(FilterValuesPanel, Browser) - Constructor for class gov.usda.gdpc.browser.DistinctComponentAdapter: DistinctComponentAdapter Constructor.
DistinctComponentAdapter(FilterValuesPanel, Property[], Browser) - Constructor for class gov.usda.gdpc.browser.DistinctComponentAdapter: DistinctComponentAdapter Constructor.
DistinctComponentAdapter(FilterValuesPanel, Property[], Browser, boolean) - Constructor for class gov.usda.gdpc.browser.DistinctComponentAdapter: DistinctComponentAdapter Constructor.
DistinctDBElementDeserializer - class gov.usda.gdpc.axis.DistinctDBElementDeserializer.
DistinctDBElementDeserializer() - Constructor for class gov.usda.gdpc.axis.DistinctDBElementDeserializer: DistinctDBElementDeserializer Constructor.
DistinctPropertyValues - class gov.usda.gdpc.DistinctPropertyValues.
DistinctPropertyValues() - Constructor for class gov.usda.gdpc.DistinctPropertyValues: DistinctPropertyValues constructor.
DistinctPropertyValues(int) - Constructor for class gov.usda.gdpc.DistinctPropertyValues: DistinctPropertyValues constructor.
DistinctValueDeserializer - class gov.usda.gdpc.axis.DistinctValueDeserializer.
DistinctValueDeserializer() - Constructor for class gov.usda.gdpc.axis.DistinctValueDeserializer: DistinctValueDeserializer Constructor.
DistinctValueDeserializerFactory - class gov.usda.gdpc.axis.DistinctValueDeserializerFactory.
DistinctValueDeserializerFactory() - Constructor for class gov.usda.gdpc.axis.DistinctValueDeserializerFactory: DistinctValueDeserializerFactory Constructor.
DistinctValueSerializer - class gov.usda.gdpc.axis.DistinctValueSerializer.
DistinctValueSerializer() - Constructor for class gov.usda.gdpc.axis.DistinctValueSerializer: DistinctValueSerializer Constructor.
DistinctValueSerializerFactory - class gov.usda.gdpc.axis.DistinctValueSerializerFactory.
DistinctValueSerializerFactory() - Constructor for class gov.usda.gdpc.axis.DistinctValueSerializerFactory: DistinctValueSerializerFactory Constructor.
DoubleArrowAction - class gov.usda.gdpc.browser.DoubleArrowAction.
DoubleArrowAction(Browser, DBElementTree, DBElementTree) - Constructor for class gov.usda.gdpc.browser.DoubleArrowAction: DoubleArrowAction Constructor.
delete(int) - Method in class gov.usda.gdpc.browser.GenericPropTableModel
delete(int) - Method in class gov.usda.gdpc.browser.PropertiesTableModel
deselect() - Method in class gov.usda.gdpc.browser.Browser
deselectAll() - Method in class gov.usda.gdpc.gui.GenericList: Deselects everything in this list.
deselectFilterLists() - Method in class gov.usda.gdpc.browser.DBElementPanel
deselectLists() - Method in class gov.usda.gdpc.browser.FilterValuesPanel: Deselects all the values in both the reference lists and distinct lists displayed by this panel.

E

ELEVATION - Static variable in class gov.usda.gdpc.LocalityProperty: Elevation of locality (data type: java.lang.Double).
EMPTY_STRING - Static variable in class gov.usda.gdpc.xml.AbstractXMLDocument
END_POSITION - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: End Position associated with genotype experiment (data type: java.lang.String).
END_POSITION - Static variable in class gov.usda.gdpc.xml.PropertyTag
ENVEXP - Static variable in class gov.usda.gdpc.panzea.PanzeaPropertyMap
ENVIRONMENT_EXPERIMENT - Static variable in class gov.usda.gdpc.PhenotypeProperty: Environment Experiment of phenotype (data type: gov.usda.gdpc.EnvironmentExperiment).
ENVIRONMENT_EXPERIMENT - Static variable in class gov.usda.gdpc.xml.GDPCTag
ENVIRONMENT_EXPERIMENTS - Variable in class gov.usda.gdpc.panzea.PanzeaCache
ENVIRONMENT_EXPERIMENT_FILTER - Static variable in class gov.usda.gdpc.xml.GDPCTag
ENVIRONMENT_EXPERIMENT_GROUP - Static variable in class gov.usda.gdpc.xml.GDPCTag
ENVIRONMENT_EXPERIMENT_PROPERTY - Static variable in class gov.usda.gdpc.xml.GDPCTag
ENVIRONMENT_EXPERIMENT_TAB - Static variable in class gov.usda.gdpc.browser.Browser
EVALUATIONSITE - Static variable in class gov.usda.gdpc.EnvironmentExperimentProperty: Evaluation Site associated with environment experiment (data type: java.lang.String).
EVALUATIONSITE - Static variable in class gov.usda.gdpc.xml.PropertyTag: ENVIRONMENT EXPERIMENT PROPERTIES
EmptyTable - class gov.usda.gdpc.util.EmptyTable.: Convenience class to create an empty table.
EmptyTable() - Constructor for class gov.usda.gdpc.util.EmptyTable: EmptyTable constructor.
EnvironmentExperiment - class gov.usda.gdpc.EnvironmentExperiment.: This is a database element representing an environment experiment.
EnvironmentExperimentFilter - class gov.usda.gdpc.EnvironmentExperimentFilter.: This is an environment experiment filter.
EnvironmentExperimentFilter() - Constructor for class gov.usda.gdpc.EnvironmentExperimentFilter: EnvironmentExperimentFilter constructor.
EnvironmentExperimentGroup - interface gov.usda.gdpc.EnvironmentExperimentGroup.: Collection of environment experiments.
EnvironmentExperimentProperty - class gov.usda.gdpc.EnvironmentExperimentProperty.: This follows the enum pattern and represents a environment experiment property.
EnvironmentExperimentProperty(String, String, String, String) - Constructor for class gov.usda.gdpc.EnvironmentExperimentProperty: EnvironmentExperimentProperty constructor.
EnvironmentExperimentProperty(String, Class, String, String) - Constructor for class gov.usda.gdpc.EnvironmentExperimentProperty: EnvironmentExperimentProperty constructor.
ExceptionUtils - class gov.usda.gdpc.util.ExceptionUtils.
ExitAction - class gov.usda.gdpc.browser.ExitAction.
Export - class gov.usda.gdpc.Export.
ExtraInfo - class gov.usda.gdpc.database.ExtraInfo.
ExtraInfo() - Constructor for class gov.usda.gdpc.database.ExtraInfo: ExtraInfo constructor.
entrySet() - Method in class gov.usda.gdpc.AbstractDBElement: Returns a read-only set view of the mappings contained in this map.
equals(Object) - Method in class gov.usda.gdpc.AbstractDBElement: This determines if two database elements are equal.
equals(Object) - Method in class gov.usda.gdpc.AbstractProperty: This method made final to prevent overriding Object.equals.
equals(Object) - Method in class gov.usda.gdpc.FilterValueType: This method made final to prevent overriding Object.equals.
equals(Object) - Method in class gov.usda.gdpc.Identifier: This determines if two identifiers are equal.
equals(Object) - Method in class gov.usda.gdpc.database.AbstractJDBCConnection: This determines if two database connections are equal.
equals(Object) - Method in class gov.usda.gdpc.database.ConstantDatabaseMapping: This determines if two database mapping are equal.
equals(Object) - Method in class gov.usda.gdpc.database.SimpleDatabaseMapping: This determines if two database mapping are equal.
equals(Object) - Method in class gov.usda.gdpc.panzea.PanzeaPositionMinutesDatabaseMapping: This determines if two database mapping are equal.
executeQuery(String) - Method in class gov.usda.gdpc.database.AbstractJDBCConnection: This executes the specified select statement.
executeQueryNoScroll(String) - Method in class gov.usda.gdpc.database.AbstractJDBCConnection
expandOneLevel() - Method in class gov.usda.gdpc.gui.DBElementTree
exportLociTabDelimitedFile(File) - Method in class gov.usda.gdpc.browser.Browser
exportPHYLIPFile(File) - Method in class gov.usda.gdpc.browser.Browser
exportPHYLIPINTERFile(File) - Method in class gov.usda.gdpc.browser.Browser
exportTabDelimitedFile(File) - Method in class gov.usda.gdpc.browser.Browser

F

FILTER - Static variable in class gov.usda.gdpc.xml.GDPCTag
FileFilter - class gov.usda.gdpc.browser.FileFilter.
FileFilter(String) - Constructor for class gov.usda.gdpc.browser.FileFilter: FileFilter Constructor.
FileFilter(String, String) - Constructor for class gov.usda.gdpc.browser.FileFilter: FileFilter Constructor.
FileFilter(String[]) - Constructor for class gov.usda.gdpc.browser.FileFilter: FileFilter Constructor.
FileFilter(String[], String) - Constructor for class gov.usda.gdpc.browser.FileFilter: FileFilter Constructor.
FileMenu - class gov.usda.gdpc.browser.FileMenu.
FileMenu(Browser) - Constructor for class gov.usda.gdpc.browser.FileMenu: FileMenu constructor comment.
Filter - interface gov.usda.gdpc.Filter.: Filter used to define search criteria when requesting data from a DBGateway.
FilterDeserializer - class gov.usda.gdpc.axis.FilterDeserializer.
FilterDeserializer() - Constructor for class gov.usda.gdpc.axis.FilterDeserializer: FilterDeserializer Constructor.
FilterDeserializerFactory - class gov.usda.gdpc.axis.FilterDeserializerFactory.
FilterDeserializerFactory() - Constructor for class gov.usda.gdpc.axis.FilterDeserializerFactory: FilterDeserializerFactory Constructor.
FilterLikeValue - class gov.usda.gdpc.FilterLikeValue.: This is a filter value which consists of a single string value which may contain the wild card(s) %, as a means of matching zero or more characters in that position.
FilterLikeValue(Property, String) - Constructor for class gov.usda.gdpc.FilterLikeValue: FilterLikeValue Constructor.
FilterRangeValue - class gov.usda.gdpc.FilterRangeValue.: This is a filter value which consists of a range of values.
FilterRangeValue(Property, Comparable, Comparable) - Constructor for class gov.usda.gdpc.FilterRangeValue: FilterRangeValue Constructor.
FilterSerializer - class gov.usda.gdpc.axis.FilterSerializer.
FilterSerializer() - Constructor for class gov.usda.gdpc.axis.FilterSerializer: FilterSerializer Constructor.
FilterSerializerFactory - class gov.usda.gdpc.axis.FilterSerializerFactory.
FilterSerializerFactory() - Constructor for class gov.usda.gdpc.axis.FilterSerializerFactory: FilterSerializerFactory Constructor.
FilterSingleValue - class gov.usda.gdpc.FilterSingleValue.: This is a filter value which consists of a single value.
FilterSingleValue(Property, Object) - Constructor for class gov.usda.gdpc.FilterSingleValue: FilterSingleValue Constructor.
FilterValue - interface gov.usda.gdpc.FilterValue.: This represents a value which is used to define the critera of a filter.
FilterValueType - class gov.usda.gdpc.FilterValueType.
FilterValueType(String) - Constructor for class gov.usda.gdpc.FilterValueType: FilterValueType constructor.
FilterValuesPanel - class gov.usda.gdpc.browser.FilterValuesPanel.
FilterValuesPanel(DBGateway, Browser) - Constructor for class gov.usda.gdpc.browser.FilterValuesPanel: FilterValuesPanel Constructor.
FilterValuesPanel(DBGateway, Property[], Browser) - Constructor for class gov.usda.gdpc.browser.FilterValuesPanel: FilterValuesPanel Constructor.
FixedTextField - class gov.usda.gdpc.gui.FixedTextField.
FixedTextField() - Constructor for class gov.usda.gdpc.gui.FixedTextField: FixedTextField constructor comment.
FixedTextField(int) - Constructor for class gov.usda.gdpc.gui.FixedTextField
FixedTextField(String) - Constructor for class gov.usda.gdpc.gui.FixedTextField
FixedTextField(String, int) - Constructor for class gov.usda.gdpc.gui.FixedTextField
FixedTextField(Document, String, int) - Constructor for class gov.usda.gdpc.gui.FixedTextField
fireTableChanged() - Method in class gov.usda.gdpc.browser.GenericPropTableModel
fireTableChanged() - Method in class gov.usda.gdpc.browser.MatrixTableModel
fireTableChanged() - Method in class gov.usda.gdpc.browser.PropertiesTableModel

G

GDPCConstants - class gov.usda.gdpc.xml.GDPCConstants.
GDPCDeserializerFactory - class gov.usda.gdpc.axis.GDPCDeserializerFactory.
GDPCDeserializerFactory() - Constructor for class gov.usda.gdpc.axis.GDPCDeserializerFactory: GDPCDeserializerFactory Constructor.
GDPCSerializer - class gov.usda.gdpc.axis.GDPCSerializer.
GDPCSerializer() - Constructor for class gov.usda.gdpc.axis.GDPCSerializer: GDPCSerializer Constructor.
GDPCSerializerFactory - class gov.usda.gdpc.axis.GDPCSerializerFactory.
GDPCSerializerFactory() - Constructor for class gov.usda.gdpc.axis.GDPCSerializerFactory: GDPCSerializerFactory Constructor.
GDPCSerializerUtil - class gov.usda.gdpc.axis.GDPCSerializerUtil.
GDPCTag - class gov.usda.gdpc.xml.GDPCTag.
GDPCTag(String, Class) - Constructor for class gov.usda.gdpc.xml.GDPCTag: GDPCTag constructor.
GDPC_NAMESPACE - Static variable in class gov.usda.gdpc.xml.GDPCConstants
GDPC_SCHEMA_LOCATION - Static variable in class gov.usda.gdpc.xml.GDPCConstants
GENELOCUS - Static variable in class gov.usda.gdpc.panzea.PanzeaPropertyMap
GENERIC_TABLE - Static variable in class gov.usda.gdpc.xml.GDPCTag
GENERIC_TABLE_ITEM - Static variable in class gov.usda.gdpc.xml.GDPCTag
GENERIC_TABLE_ITEM_ATTR - Static variable in class gov.usda.gdpc.xml.GDPCTag
GENERIC_TABLE_NUM_COLUMNS_ATTR - Static variable in class gov.usda.gdpc.xml.GDPCTag
GENERIC_TABLE_NUM_ROWS_ATTR - Static variable in class gov.usda.gdpc.xml.GDPCTag
GENERIC_TABLE_ROW - Static variable in class gov.usda.gdpc.xml.GDPCTag
GENETIC_BIN - Static variable in class gov.usda.gdpc.LocusProperty: Genetic bin of locus (data type: java.lang.String).
GENETIC_BIN - Static variable in class gov.usda.gdpc.xml.PropertyTag
GENETIC_MAP - Static variable in class gov.usda.gdpc.LocusProperty: Genetic map of locus (data type: java.lang.String).
GENETIC_MAP - Static variable in class gov.usda.gdpc.xml.PropertyTag
GENETIC_POSITION - Static variable in class gov.usda.gdpc.LocusProperty: Genetic position of locus (data type: java.lang.Double).
GENETIC_POSITION - Static variable in class gov.usda.gdpc.xml.PropertyTag
GENOTYPE - Static variable in class gov.usda.gdpc.xml.GDPCTag
GENOTYPE_EXPERIMENT - Static variable in class gov.usda.gdpc.GenotypeProperty: Genotype Experiment of genotype (data type: gov.usda.gdpc.GenotypeExperiment).
GENOTYPE_EXPERIMENT - Static variable in class gov.usda.gdpc.xml.GDPCTag
GENOTYPE_EXPERIMENTS - Variable in class gov.usda.gdpc.panzea.PanzeaCache
GENOTYPE_EXPERIMENT_FILTER - Static variable in class gov.usda.gdpc.xml.GDPCTag
GENOTYPE_EXPERIMENT_GROUP - Static variable in class gov.usda.gdpc.xml.GDPCTag
GENOTYPE_EXPERIMENT_PROPERTY - Static variable in class gov.usda.gdpc.xml.GDPCTag
GENOTYPE_EXPERIMENT_TAB - Static variable in class gov.usda.gdpc.browser.Browser
GENOTYPE_FILTER - Static variable in class gov.usda.gdpc.xml.GDPCTag
GENOTYPE_GROUP - Static variable in class gov.usda.gdpc.xml.GDPCTag
GENOTYPE_PROPERTY - Static variable in class gov.usda.gdpc.xml.GDPCTag
GENOTYPE_TAB - Static variable in class gov.usda.gdpc.browser.Browser
GENUS - Static variable in class gov.usda.gdpc.TaxonProperty: Genus of taxon (data type: java.lang.String).
GENUS - Static variable in class gov.usda.gdpc.xml.PropertyTag
GERMPLASM - Static variable in class gov.usda.gdpc.panzea.PanzeaPropertyMap
GERMPLASM_TYPE - Static variable in class gov.usda.gdpc.TaxonProperty: Germplasm type of taxon (data type: java.lang.String).
GERMPLASM_TYPE - Static variable in class gov.usda.gdpc.xml.PropertyTag
GenericList - class gov.usda.gdpc.gui.GenericList.
GenericList() - Constructor for class gov.usda.gdpc.gui.GenericList: GenericList Constructor.
GenericList(ListModel) - Constructor for class gov.usda.gdpc.gui.GenericList: GenericList Constructor.
GenericList(Object[]) - Constructor for class gov.usda.gdpc.gui.GenericList: GenericList Constructor.
GenericList(Vector) - Constructor for class gov.usda.gdpc.gui.GenericList: GenericList Constructor.
GenericPropTableData - class gov.usda.gdpc.browser.GenericPropTableData.
GenericPropTableData() - Constructor for class gov.usda.gdpc.browser.GenericPropTableData
GenericPropTableData(String, Object) - Constructor for class gov.usda.gdpc.browser.GenericPropTableData
GenericPropTableModel - class gov.usda.gdpc.browser.GenericPropTableModel.
GenericPropTableModel() - Constructor for class gov.usda.gdpc.browser.GenericPropTableModel
GenericTable - class gov.usda.gdpc.util.GenericTable.
GenericTable() - Constructor for class gov.usda.gdpc.util.GenericTable: GenericTable constructor.
GenericTable(Table) - Constructor for class gov.usda.gdpc.util.GenericTable: GenericTable constructor.
GenericTable(Object[][]) - Constructor for class gov.usda.gdpc.util.GenericTable: GenericTable constructor.
GenericTableDeserializer - class gov.usda.gdpc.axis.GenericTableDeserializer.
GenericTableDeserializer() - Constructor for class gov.usda.gdpc.axis.GenericTableDeserializer: GenericTableDeserializer Constructor.
GenericTableDeserializerFactory - class gov.usda.gdpc.axis.GenericTableDeserializerFactory.
GenericTableDeserializerFactory() - Constructor for class gov.usda.gdpc.axis.GenericTableDeserializerFactory: GenericTableDeserializerFactory Constructor.
GenericTableItemDeserializer - class gov.usda.gdpc.axis.GenericTableItemDeserializer.
GenericTableItemDeserializer() - Constructor for class gov.usda.gdpc.axis.GenericTableItemDeserializer: GenericTableItemDeserializer Constructor.
GenericTableRowDeserializer - class gov.usda.gdpc.axis.GenericTableRowDeserializer.
GenericTableRowDeserializer(int) - Constructor for class gov.usda.gdpc.axis.GenericTableRowDeserializer: GenericTableRowDeserializer Constructor.
GenericTableSerializer - class gov.usda.gdpc.axis.GenericTableSerializer.
GenericTableSerializer() - Constructor for class gov.usda.gdpc.axis.GenericTableSerializer: GenericTableSerializer Constructor.
GenericTableSerializerFactory - class gov.usda.gdpc.axis.GenericTableSerializerFactory.
GenericTableSerializerFactory() - Constructor for class gov.usda.gdpc.axis.GenericTableSerializerFactory: GenericTableSerializerFactory Constructor.
Genotype - class gov.usda.gdpc.Genotype.: This is a database element representing a genotype.
GenotypeExperiment - class gov.usda.gdpc.GenotypeExperiment.: This is a database element representing a genotype experiment.
GenotypeExperimentFilter - class gov.usda.gdpc.GenotypeExperimentFilter.: This is a genotype experiment filter.
GenotypeExperimentFilter() - Constructor for class gov.usda.gdpc.GenotypeExperimentFilter: GenotypeExperimentFilter constructor.
GenotypeExperimentGroup - interface gov.usda.gdpc.GenotypeExperimentGroup.: Collection of genotype experiments.
GenotypeExperimentProperty - class gov.usda.gdpc.GenotypeExperimentProperty.: This follows the enum pattern and represents a genotype experiment property.
GenotypeExperimentProperty(String, String, String, String) - Constructor for class gov.usda.gdpc.GenotypeExperimentProperty: GenotypeExperimentProperty constructor.
GenotypeExperimentProperty(String, Class, String, String) - Constructor for class gov.usda.gdpc.GenotypeExperimentProperty: GenotypeExperimentProperty constructor.
GenotypeFilter - class gov.usda.gdpc.GenotypeFilter.: This is a genotype filter.
GenotypeFilter() - Constructor for class gov.usda.gdpc.GenotypeFilter: GenotypeFilter constructor.
GenotypeGroup - interface gov.usda.gdpc.GenotypeGroup.: Group of genotypes.
GenotypeProperty - class gov.usda.gdpc.GenotypeProperty.: This follows the enum pattern and represents a genotype property.
GenotypeProperty(String, String, String, String) - Constructor for class gov.usda.gdpc.GenotypeProperty: GenotypeProperty constructor.
GenotypeProperty(String, Class, String, String) - Constructor for class gov.usda.gdpc.GenotypeProperty: GenotypeProperty constructor.
GenotypeTable - class gov.usda.gdpc.GenotypeTable.
GenotypeTable() - Constructor for class gov.usda.gdpc.GenotypeTable
GetStartedAction - class gov.usda.gdpc.browser.GetStartedAction.
GrameneConnection - class gov.usda.gdpc.gramene.GrameneConnection.
GrameneConnection(String, String, String, String, String, String) - Constructor for class gov.usda.gdpc.gramene.GrameneConnection: GrameneConnection Constructor.
GrameneConnection() - Constructor for class gov.usda.gdpc.gramene.GrameneConnection
Group - interface gov.usda.gdpc.Group.: List of objects.
GroupDeserializer - class gov.usda.gdpc.axis.GroupDeserializer.
GroupDeserializer() - Constructor for class gov.usda.gdpc.axis.GroupDeserializer: GroupDeserializer Constructor.
get(Object) - Method in class gov.usda.gdpc.AbstractDBElement: Returns the value to which this map maps the specified key.
get(int) - Method in class gov.usda.gdpc.AbstractGroup: Returns the element at the specified position in this list.
get(int) - Method in class gov.usda.gdpc.AlleleList: Returns the element at the specified position in this list.
get(Object, Object) - Method in class gov.usda.gdpc.util.AbstractTable: Get the data associated with specified column heading and row heading.
get(int, int) - Method in class gov.usda.gdpc.util.AbstractTable: Get the data associated with the specified indices.
get(int, int) - Method in class gov.usda.gdpc.util.GenericTable: Get the data associated with the specified indices.
get(Object, Object) - Method in class gov.usda.gdpc.util.GenericTable: Unsupported operation.
get(int) - Method in class gov.usda.gdpc.util.ReadOnlyList
get(int) - Method in class gov.usda.gdpc.util.SortedList
get(Object, Object) - Method in interface gov.usda.gdpc.util.Table: Get the data associated with specified column heading and row heading.
get(int, int) - Method in interface gov.usda.gdpc.util.Table: Get the data associated with the specified indices.
getAlignmentX() - Method in class gov.usda.gdpc.gui.FixedTextField
getAlignmentY() - Method in class gov.usda.gdpc.gui.FixedTextField
getAlleleList() - Method in class gov.usda.gdpc.Genotype: Returns the allele list of this genotype.
getAlleleList(Node) - Method in class gov.usda.gdpc.xml.AbstractXMLDocument
getAllowsChildren() - Method in class gov.usda.gdpc.gui.dbetree.HeadNode
getAllowsChildren() - Method in interface gov.usda.gdpc.gui.dbetree.Node
getAllowsChildren() - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode
getAllowsChildren() - Method in class gov.usda.gdpc.gui.dbetree.ValueNode
getBasename(String) - Static method in class gov.usda.gdpc.util.Utils
getCachedInstance(Map) - Static method in class gov.usda.gdpc.EnvironmentExperiment: This returns the environment experiment instance given specified id and source.
getCachedInstance(Map) - Static method in class gov.usda.gdpc.Genotype: This returns the genotype instance given specified id and source.
getCachedInstance(Map) - Static method in class gov.usda.gdpc.GenotypeExperiment: This returns the genotype experiment instance given specified id and source.
getCachedInstance(Map) - Static method in class gov.usda.gdpc.Locality: This returns the locality instance given specified id and source.
getCachedInstance(Map) - Static method in class gov.usda.gdpc.Locus: This returns the locus instance given specified id and source.
getCachedInstance(Map) - Static method in class gov.usda.gdpc.Phenotype: This returns the phenotype instance given specified id and source.
getCachedInstance(Map) - Static method in class gov.usda.gdpc.PhenotypeOntology: This returns the phenotype ontology instance from the cache that matches the specified id and source.
getCachedInstance(Map) - Static method in class gov.usda.gdpc.Taxon: This returns the taxon instance from the cache that matches the specified id and source.
getCentromereLocation() - Method in class gov.usda.gdpc.Chromosome: Get centromere location.
getChild(Object, int) - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: Gets the child of the given parent at the given index.
getChildAt(int) - Method in class gov.usda.gdpc.gui.dbetree.HeadNode: Returns this node's child at the given index.
getChildAt(int) - Method in interface gov.usda.gdpc.gui.dbetree.Node: Returns this node's child at the given index.
getChildAt(int) - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode: Returns this node's child at the given index.
getChildAt(int) - Method in class gov.usda.gdpc.gui.dbetree.ValueNode: Returns this node's child at the given index.
getChildCount(Object) - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: Gets the number of children for given parent.
getChildCount() - Method in class gov.usda.gdpc.gui.dbetree.HeadNode: Returns the number of children for this node.
getChildCount() - Method in interface gov.usda.gdpc.gui.dbetree.Node: Returns the number of children for this node.
getChildCount() - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode: Returns the number of children for this node.
getChildCount() - Method in class gov.usda.gdpc.gui.dbetree.ValueNode: Returns the number of children for this node.
getColumn(Object) - Method in class gov.usda.gdpc.util.AbstractTable: Get the column for the given column heading.
getColumn(int) - Method in class gov.usda.gdpc.util.AbstractTable: Get the column for the given column index.
getColumn(Object) - Method in class gov.usda.gdpc.util.GenericTable: Unsupported operation.
getColumn(int) - Method in class gov.usda.gdpc.util.GenericTable: Get the column for the given column index.
getColumn(Object) - Method in interface gov.usda.gdpc.util.Table: Get the column for the given column heading.
getColumn(int) - Method in interface gov.usda.gdpc.util.Table: Get the column for the given column index.
getColumnCount() - Method in class gov.usda.gdpc.browser.GenericPropTableModel
getColumnCount() - Method in class gov.usda.gdpc.browser.MatrixTableModel: Returns the number of columns in the model.
getColumnCount() - Method in class gov.usda.gdpc.browser.PropertiesTableModel
getColumnHeading(int) - Method in class gov.usda.gdpc.util.AbstractTable: Get the column heading at specified index.
getColumnHeading(int) - Method in class gov.usda.gdpc.util.GenericTable: Unsupported operation.
getColumnHeading(int) - Method in interface gov.usda.gdpc.util.Table: Get the column heading at specified index.
getColumnHeadings() - Method in class gov.usda.gdpc.util.AbstractTable: Get column headings for this table.
getColumnHeadings() - Method in class gov.usda.gdpc.util.GenericTable: Unsupported operation.
getColumnHeadings() - Method in interface gov.usda.gdpc.util.Table: Get column headings for this table.
getColumnName(int) - Method in class gov.usda.gdpc.browser.GenericPropTableModel
getColumnName(int) - Method in class gov.usda.gdpc.browser.MatrixTableModel: Returns the name of the column at columnIndex.
getColumnName(int) - Method in class gov.usda.gdpc.browser.PropertiesTableModel
getConnections() - Method in class gov.usda.gdpc.browser.Browser
getConstant() - Method in class gov.usda.gdpc.database.ConstantDatabaseMapping: Return the constant.
getConstants() - Method in class gov.usda.gdpc.database.SQLStatements: Returns a list of the constants.
getDBConnectionList() - Method in class gov.usda.gdpc.browser.DBConnectionsPanel
getDBConnectionListModel() - Method in class gov.usda.gdpc.browser.DBConnectionsPanel
getDBConnections() - Method in class gov.usda.gdpc.AbstractDBGateway: Returns the list of database connections that this gateway is managing.
getDBConnections() - Method in interface gov.usda.gdpc.DBGateway: Returns the list of database connections that this gateway is managing.
getDBElement(Element) - Method in class gov.usda.gdpc.xml.AbstractXMLDocument
getDBElementGroup(Filter) - Method in class gov.usda.gdpc.AbstractDBElementGroup: Gets the group of elements that match the given filter from this group.
getDBElements(String) - Method in class gov.usda.gdpc.AbstractDBElementGroup: Returns the list of elements contained in this group which originated from the given data source.
getDBElements(String) - Method in interface gov.usda.gdpc.DBElementGroup: Returns the list of elements contained in this group which originated from the given data source.
getDBElements(Element, GDPCTag) - Method in class gov.usda.gdpc.xml.AbstractXMLDocument
getDBTable() - Method in class gov.usda.gdpc.database.SimpleDatabaseMapping: Gets the database table for this mapping.
getDBTable() - Method in class gov.usda.gdpc.panzea.PanzeaPositionMinutesDatabaseMapping
getDBTables() - Method in class gov.usda.gdpc.panzea.PanzeaPositionMinutesDatabaseMapping: This returns a list of database tables associated with this database mapping.
getData() - Method in class gov.usda.gdpc.util.GenericTable
getDataSource() - Method in class gov.usda.gdpc.AbstractDBConnection: Returns the data source of this connection.
getDataSource() - Method in class gov.usda.gdpc.AbstractDBElement: Returns the data source of this element.
getDataSource() - Method in interface gov.usda.gdpc.DBConnection: Returns the data source of this connection.
getDataSource() - Method in interface gov.usda.gdpc.DBElement: Returns the data source of this element.
getDataSource() - Method in class gov.usda.gdpc.EnvironmentExperiment: Returns the data source of this environment experiment.
getDataSource() - Method in class gov.usda.gdpc.Genotype: Returns the data source of this genotype.
getDataSource() - Method in class gov.usda.gdpc.GenotypeExperiment: Returns the data source of this genotype experiment.
getDataSource() - Method in class gov.usda.gdpc.Locality: Returns the data source of this locality.
getDataSource() - Method in class gov.usda.gdpc.Locus: Returns the data source of this locus.
getDataSource() - Method in class gov.usda.gdpc.Phenotype: Returns the data source of this phenotype.
getDataSource() - Method in class gov.usda.gdpc.PhenotypeOntology: Returns the data source of this phenotype ontology.
getDataSource() - Method in class gov.usda.gdpc.Taxon: Returns the data source of this taxon.
getDataSource() - Method in class gov.usda.gdpc.axis.DBConnectionProxy: Returns the data source of this connection.
getDataType() - Method in class gov.usda.gdpc.AbstractProperty: Returns the data type of this property
getDataType() - Method in interface gov.usda.gdpc.Property: Returns the data type of this property
getDateTimeString() - Method in class gov.usda.gdpc.util.Calendar: Returns date and time of this calendar as a string.
getDefinedProperties() - Method in class gov.usda.gdpc.AbstractDBElementGroup: This returns a distinct list of properties defined by the elements in this group.
getDefinedProperties(FilterValueType) - Method in class gov.usda.gdpc.AbstractFilter: Gets all the properties that have defined criteria for the given filter value type.
getDefinedProperties() - Method in class gov.usda.gdpc.AbstractFilter: Gets all the properties that have defined criteria.
getDefinedProperties() - Method in interface gov.usda.gdpc.DBElementGroup: This returns a distinct list of properties defined by the elements in this group.
getDefinedProperties() - Method in class gov.usda.gdpc.DistinctPropertyValues: This returns a list of all properties with defined values.
getDefinedProperties() - Static method in class gov.usda.gdpc.EnvironmentExperimentProperty
getDefinedProperties(FilterValueType) - Method in interface gov.usda.gdpc.Filter: Gets all the properties that have defined criteria for the given filter value type.
getDefinedProperties() - Method in interface gov.usda.gdpc.Filter: Gets all the properties that have defined criteria.
getDefinedProperties() - Static method in class gov.usda.gdpc.GenotypeExperimentProperty
getDefinedProperties() - Static method in class gov.usda.gdpc.GenotypeProperty
getDefinedProperties() - Static method in class gov.usda.gdpc.LocalityProperty
getDefinedProperties() - Static method in class gov.usda.gdpc.LocusProperty
getDefinedProperties() - Static method in class gov.usda.gdpc.PhenotypeOntologyProperty: Returns the list of created phenotype ontology properties.
getDefinedProperties() - Static method in class gov.usda.gdpc.PhenotypeProperty
getDefinedProperties() - Static method in class gov.usda.gdpc.TaxonProperty: Returns the list of created taxon properties.
getDefinedTypes() - Method in class gov.usda.gdpc.AbstractFilter: Gets all the filter value types that have defined critera.
getDefinedTypes() - Method in interface gov.usda.gdpc.Filter: Gets all the filter value types that have defined critera.
getDescription() - Method in class gov.usda.gdpc.AbstractDBConnection: Returns a description of this connection.
getDescription() - Method in interface gov.usda.gdpc.DBConnection: Returns a description of this connection.
getDescription() - Method in class gov.usda.gdpc.axis.DBConnectionProxy: Returns a description of this connection.
getDescription() - Method in class gov.usda.gdpc.browser.FileFilter: Returns the viewed text of this filter.
getDeserializerAs(String) - Method in class gov.usda.gdpc.axis.DistinctValueDeserializerFactory: Returns a Deserializer for the specified XML processing mechanism type.
getDeserializerAs(String) - Method in class gov.usda.gdpc.axis.FilterDeserializerFactory: Returns a Deserializer for the specified XML processing mechanism type.
getDeserializerAs(String) - Method in class gov.usda.gdpc.axis.GDPCDeserializerFactory: Returns a Deserializer for the specified XML processing mechanism type.
getDeserializerAs(String) - Method in class gov.usda.gdpc.axis.GenericTableDeserializerFactory: Returns a Deserializer for the specified XML processing mechanism type.
getDeserializerAs(String) - Method in class gov.usda.gdpc.axis.PropertiesListDeserializerFactory: Returns a Deserializer for the specified XML processing mechanism type.
getDistinctProperties(List) - Method in class gov.usda.gdpc.AbstractDBConnection: This method is unsupported by this class.
getDistinctProperties(Property[]) - Method in class gov.usda.gdpc.AbstractDBElementGroup: Returns list(s) of distinct property values for the given properties.
getDistinctProperties(Property[]) - Method in class gov.usda.gdpc.AbstractDBGateway: Returns list(s) of distinct property values for the given properties.
getDistinctProperties(List) - Method in interface gov.usda.gdpc.DBConnection: Returns list(s) of distinct property values for the given properties.
getDistinctProperties(Property[]) - Method in interface gov.usda.gdpc.DBElementGroup: Returns list(s) of distinct property values for the given properties.
getDistinctProperties(Property[]) - Method in interface gov.usda.gdpc.DBGateway: Returns list(s) of distinct property values for the given properties.
getDistinctProperties(List) - Method in class gov.usda.gdpc.axis.DBConnectionProxy: Returns list(s) of distinct property values for the given properties.
getDistinctProperties(List) - Method in class gov.usda.gdpc.panzea.PanzeaDBConnection: Returns list(s) of distinct property values for the given properties.
getDistinctSQL() - Method in class gov.usda.gdpc.database.AbstractDatabaseMapping: Returns the SQL statements required to get the distinct values for the property associated with this mapping.
getDistinctSQL() - Method in class gov.usda.gdpc.database.ConstantDatabaseMapping: Returns the SQL statements required to get the distinct values for the property associated with this mapping.
getDistinctSQL() - Method in interface gov.usda.gdpc.database.DatabaseMapping: Returns the SQL statements required to get the distinct values for the property associated with this mapping.
getDistinctSQL() - Method in class gov.usda.gdpc.database.MultiDatabaseMapping: Returns the SQL statements required to get the distinct values for the property associated with this mapping.
getDistinctSQL() - Method in class gov.usda.gdpc.database.NullDatabaseMapping: Returns the SQL statements required to get the distinct values for the property associated with this mapping.
getDistinctSQL() - Method in class gov.usda.gdpc.database.SimpleDatabaseMapping: Returns the SQL statements required to get the distinct values for the property associated with this mapping.
getDistinctSQL() - Method in class gov.usda.gdpc.panzea.PanzeaPositionMinutesDatabaseMapping: Returns the SQL statements required to get the distinct values for the property associated with this mapping.
getDistinctSelectionList(Property) - Method in class gov.usda.gdpc.browser.FilterValuesPanel: Returns the distinct labeled list for the given property.
getDistinctSelectionLists() - Method in class gov.usda.gdpc.browser.FilterValuesPanel: Returns all the distinct labeled list displayed by this panel.
getDocument() - Method in class gov.usda.gdpc.xml.AbstractXMLDocument: Returns the DOM document.
getDocument() - Method in interface gov.usda.gdpc.xml.XMLDocument: Returns the DOM document.
getDoubleArrowButton() - Method in class gov.usda.gdpc.browser.DBElementPanel
getDriver() - Method in class gov.usda.gdpc.database.AbstractJDBCConnection: Returns the jdbc driver.
getElementAt(int) - Method in class gov.usda.gdpc.browser.TableRowHeaderListModel: Returns the value at the specified index.
getEndpoint() - Method in class gov.usda.gdpc.axis.DBConnectionProxy
getEnvironmentExperiment(String, Identifier) - Method in class gov.usda.gdpc.AbstractEnvironmentExperimentGroup: This returns the environment experiment instance from this group that matches the specified id and source.
getEnvironmentExperiment(String, Identifier) - Method in interface gov.usda.gdpc.EnvironmentExperimentGroup: This returns the environment experiment instance from this group that matches the specified id and source.
getEnvironmentExperiment() - Method in class gov.usda.gdpc.Phenotype: Returns the environment experiment associated with this phenotype.
getEnvironmentExperimentGroup(EnvironmentExperimentFilter) - Method in class gov.usda.gdpc.AbstractDBConnection: This method is unsupported by this class.
getEnvironmentExperimentGroup(EnvironmentExperimentFilter) - Method in class gov.usda.gdpc.AbstractDBGateway: Gets an environment experiment group based on the given environment experiment filter.
getEnvironmentExperimentGroup(EnvironmentExperimentFilter) - Method in class gov.usda.gdpc.AbstractEnvironmentExperimentGroup: Get the environment experiment group matching the given filter from this environment experiment group.
getEnvironmentExperimentGroup() - Method in class gov.usda.gdpc.AbstractPhenotypeGroup: Returns the group of environment experiments associated with this group of phenotypes.
getEnvironmentExperimentGroup(EnvironmentExperimentFilter) - Method in interface gov.usda.gdpc.DBConnection: Gets an environment experiment group based on the given environment experiment filter.
getEnvironmentExperimentGroup(EnvironmentExperimentFilter) - Method in interface gov.usda.gdpc.DBGateway: Gets an environment experiment group based on the given environment experiment filter.
getEnvironmentExperimentGroup(EnvironmentExperimentFilter) - Method in interface gov.usda.gdpc.EnvironmentExperimentGroup: Get the environment experiment group matching the given filter from this environment experiment group.
getEnvironmentExperimentGroup() - Method in interface gov.usda.gdpc.PhenotypeGroup: Returns the group of environment experiments associated with this group of phenotypes.
getEnvironmentExperimentGroup() - Method in class gov.usda.gdpc.PhenotypeTable: Get the environment experiment group for this table.
getEnvironmentExperimentGroup(EnvironmentExperimentFilter) - Method in class gov.usda.gdpc.axis.DBConnectionProxy: Gets an environment experiment group based on the given environment experiment filter.
getEnvironmentExperimentGroup(EnvironmentExperimentFilter) - Method in class gov.usda.gdpc.panzea.PanzeaDBConnection: Gets an environment experiment group based on the given environment experiment filter.
getExceptionCauses(Throwable) - Static method in class gov.usda.gdpc.util.ExceptionUtils: This gets an exception's cause history.
getExceptionCausesWithClassNames(Throwable) - Static method in class gov.usda.gdpc.util.ExceptionUtils: This gets an exception's cause history.
getExtraInfo() - Method in class gov.usda.gdpc.database.SQLStatements: This gets a list of extra information which goes with the statements.
getField() - Method in class gov.usda.gdpc.database.SimpleDatabaseMapping: Gets the field in the database table for this mapping.
getFilteredGroup() - Method in class gov.usda.gdpc.browser.DBElementPanel
getFilteredListModel() - Method in class gov.usda.gdpc.browser.DBElementPanel
getGeneticCenterPosition() - Method in class gov.usda.gdpc.Chromosome: Get numeric genetic center position of chromosome.
getGeneticPositionRange() - Method in class gov.usda.gdpc.Chromosome: Get genetic positions range shown on big image.
getGenoFlag() - Method in class gov.usda.gdpc.browser.Browser
getGenotype(String, Taxon, GenotypeExperiment) - Method in class gov.usda.gdpc.AbstractGenotypeGroup: Gets the genotype having the given taxon, genotype experiment, number, and data source.
getGenotype(String, Taxon, GenotypeExperiment) - Method in interface gov.usda.gdpc.GenotypeGroup: Gets the genotype having the given taxon, genotype experiment, number, and data source.
getGenotypeData() - Method in class gov.usda.gdpc.browser.Browser
getGenotypeExperiment(String, Identifier) - Method in class gov.usda.gdpc.AbstractGenotypeExperimentGroup: This returns the genotype experiment instance from this group that matches the specified id and source.
getGenotypeExperiment() - Method in class gov.usda.gdpc.Genotype: Returns the genotype experiment associated with this genotype.
getGenotypeExperiment(String, Identifier) - Method in interface gov.usda.gdpc.GenotypeExperimentGroup: This returns the genotype experiment instance from this group that matches the specified id and source.
getGenotypeExperimentGroup(GenotypeExperimentFilter) - Method in class gov.usda.gdpc.AbstractDBConnection: This method is unsupported by this class.
getGenotypeExperimentGroup(GenotypeExperimentFilter) - Method in class gov.usda.gdpc.AbstractDBGateway: Gets a genotype experiment group based on the given genotype experiment filter.
getGenotypeExperimentGroup(GenotypeExperimentFilter) - Method in class gov.usda.gdpc.AbstractGenotypeExperimentGroup: Get the genotype experiment group matching the given filter from this genotype experiment group.
getGenotypeExperimentGroup() - Method in class gov.usda.gdpc.AbstractGenotypeGroup: Returns the group of genotype experiments associated with this group of genotypes.
getGenotypeExperimentGroup(GenotypeExperimentFilter) - Method in interface gov.usda.gdpc.DBConnection: Gets a genotype experiment group based on the given genotype experiment filter.
getGenotypeExperimentGroup(GenotypeExperimentFilter) - Method in interface gov.usda.gdpc.DBGateway: Gets a genotype experiment group based on the given genotype experiment filter.
getGenotypeExperimentGroup(GenotypeExperimentFilter) - Method in interface gov.usda.gdpc.GenotypeExperimentGroup: Get the genotype experiment group matching the given filter from this genotype experiment group.
getGenotypeExperimentGroup() - Method in interface gov.usda.gdpc.GenotypeGroup: Returns the group of genotype experiments associated with this group of genotypes.
getGenotypeExperimentGroup() - Method in class gov.usda.gdpc.GenotypeTable: Get the genotype experiment group for this table.
getGenotypeExperimentGroup(GenotypeExperimentFilter) - Method in class gov.usda.gdpc.axis.DBConnectionProxy: Gets a genotype experiment group based on the given genotype experiment filter.
getGenotypeExperimentGroup(GenotypeExperimentFilter) - Method in class gov.usda.gdpc.panzea.PanzeaDBConnection: Gets a genotype experiment group based on the given genotype experiment filter.
getGenotypeGenericTable(GenotypeExperimentGroup, TaxonGroup) - Method in class gov.usda.gdpc.AbstractDBConnection: This method is unsupported by this class.
getGenotypeGenericTable(GenotypeExperimentGroup, TaxonGroup) - Method in interface gov.usda.gdpc.DBConnection: Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups.
getGenotypeGenericTable(GenotypeExperimentGroup, TaxonGroup) - Method in class gov.usda.gdpc.axis.DBConnectionProxy: Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups.
getGenotypeGenericTable(GenotypeExperimentGroup, TaxonGroup) - Method in class gov.usda.gdpc.panzea.PanzeaDBConnection: Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups.
getGenotypeGroup(GenotypeExperimentGroup, TaxonGroup) - Method in class gov.usda.gdpc.AbstractDBConnection: This method is unsupported by this class.
getGenotypeGroup(GenotypeExperimentGroup, TaxonGroup) - Method in class gov.usda.gdpc.AbstractDBGateway: Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups.
getGenotypeGroup(GenotypeFilter) - Method in class gov.usda.gdpc.AbstractGenotypeGroup: Get the genotype group from this group which match the critera specified by the filter.
getGenotypeGroup(GenotypeExperimentGroup, TaxonGroup) - Method in interface gov.usda.gdpc.DBConnection: Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups.
getGenotypeGroup(GenotypeExperimentGroup, TaxonGroup) - Method in interface gov.usda.gdpc.DBGateway: Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups.
getGenotypeGroup(GenotypeFilter) - Method in interface gov.usda.gdpc.GenotypeGroup: Get the genotype group from this group which match the critera specified by the filter.
getGenotypeGroup(GenotypeExperimentGroup, TaxonGroup) - Method in class gov.usda.gdpc.axis.DBConnectionProxy: Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups.
getGenotypeGroup(GenotypeExperimentGroup, TaxonGroup) - Method in class gov.usda.gdpc.panzea.PanzeaDBConnection: Gets the genotypes for all combinations of genotype experiments and taxa defined by the respective groups.
getHeadNode() - Method in class gov.usda.gdpc.gui.DBElementTree: Returns the head node of this tree.
getHint(int) - Method in class gov.usda.gdpc.Identifier: Get hint at given index.
getHints() - Method in class gov.usda.gdpc.Identifier: Get list of hints.
getID() - Method in class gov.usda.gdpc.AbstractDBElement: Returns identifier of this element.
getID() - Method in interface gov.usda.gdpc.DBElement: Returns identifier of this element.
getID() - Method in class gov.usda.gdpc.EnvironmentExperiment: Returns identifier of this environment experiment.
getID() - Method in class gov.usda.gdpc.GenotypeExperiment: Returns identifier of this genotype experiment.
getID() - Method in class gov.usda.gdpc.Locality: Returns identifier of this locality.
getID() - Method in class gov.usda.gdpc.Locus: Returns identifier of this locus.
getID() - Method in class gov.usda.gdpc.PhenotypeOntology: Returns identifier of this phenotype ontology.
getID() - Method in class gov.usda.gdpc.Taxon: Returns identifier of this taxon.
getIcon(String) - Static method in class gov.usda.gdpc.browser.Util
getIdentifier(Node) - Method in class gov.usda.gdpc.xml.AbstractXMLDocument
getInString(Object[]) - Static method in class gov.usda.gdpc.database.AbstractJDBCConnection: This returns a string generated from the specified list intended to be used in a SQL statement.
getInString(int[]) - Static method in class gov.usda.gdpc.database.AbstractJDBCConnection: This returns a string generated from the specified list intended to be used in a SQL statement.
getInStringWithQuotes(Object[]) - Static method in class gov.usda.gdpc.database.AbstractJDBCConnection: This returns a string generated from the specified list intended to be used in a SQL statement.
getIndex() - Method in class gov.usda.gdpc.database.AbstractDatabaseMappingIndex: Returns the index.
getIndex() - Method in interface gov.usda.gdpc.database.DatabaseMappingIndex: Returns the index.
getIndexOfChild(Object, Object) - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: Gets index of given child for given parent.
getIndexOfChild(Object) - Method in class gov.usda.gdpc.gui.dbetree.HeadNode: Gets index of given child.
getIndexOfChild(Object) - Method in interface gov.usda.gdpc.gui.dbetree.Node: Gets index of given child.
getIndexOfChild(Object) - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode: Gets index of given child.
getIndexOfChild(Object) - Method in class gov.usda.gdpc.gui.dbetree.ValueNode: Gets index of given child.
getInfo(DatabaseMapping) - Method in class gov.usda.gdpc.database.ExtraInfo: Get information for the specified database mapping.
getInstance() - Static method in class gov.usda.gdpc.DefaultDBGateway: This creates an instance of this class, and subsequent calls returns that same instance.
getInstance(Genotype[]) - Static method in class gov.usda.gdpc.DefaultGenotypeGroup: Factory method to create instances of DefaultGenotypeGroup.
getInstance(List) - Static method in class gov.usda.gdpc.DefaultGenotypeGroup: Factory method to create instances of DefaultGenotypeGroup.
getInstance(GenotypeGroup[]) - Static method in class gov.usda.gdpc.DefaultGenotypeGroup: Factory method to create instances of DefaultGenotypeGroup.
getInstance(GenotypeExperimentGroup, TaxonGroup, Object[][]) - Static method in class gov.usda.gdpc.DefaultGenotypeGroup: DefaultGenotypeGroup constructor.
getInstance(Map) - Static method in class gov.usda.gdpc.EnvironmentExperiment: This returns the environment experiment instance given the specified list of properties.
getInstance(String) - Static method in class gov.usda.gdpc.EnvironmentExperimentProperty
getInstance(Map) - Static method in class gov.usda.gdpc.Genotype: This returns the genotype instance given the specified list of properties.
getInstance(Map) - Static method in class gov.usda.gdpc.GenotypeExperiment: This returns the genotype experiment instance given specified list of properties.
getInstance(String) - Static method in class gov.usda.gdpc.GenotypeExperimentProperty
getInstance(String) - Static method in class gov.usda.gdpc.GenotypeProperty
getInstance(GenotypeGroup) - Static method in class gov.usda.gdpc.GenotypeTable: Factory method to create genotype tables.
getInstance(Map) - Static method in class gov.usda.gdpc.Locality: This returns the locality instance given the specified list of properties.
getInstance(String) - Static method in class gov.usda.gdpc.LocalityProperty
getInstance(Map) - Static method in class gov.usda.gdpc.Locus: This returns the Locus instance given specified list of properties.
getInstance(String) - Static method in class gov.usda.gdpc.LocusProperty
getInstance(Map) - Static method in class gov.usda.gdpc.Phenotype: This returns the phenotype instance given the specified list of properties.
getInstance(Map) - Static method in class gov.usda.gdpc.PhenotypeOntology: This returns the phenotype ontology instance given the specified list of properties.
getInstance(String) - Static method in class gov.usda.gdpc.PhenotypeOntologyProperty
getInstance(String) - Static method in class gov.usda.gdpc.PhenotypeProperty
getInstance(PhenotypeGroup, PhenotypeOntology) - Static method in class gov.usda.gdpc.PhenotypeTable: Factory method to create phenotype tables.
getInstance(Map) - Static method in class gov.usda.gdpc.Taxon: This returns the taxon instance given the specified list of properties.
getInstance(String) - Static method in class gov.usda.gdpc.TaxonProperty: Return taxon property matching given sub type.
getInstance(Browser) - Static method in class gov.usda.gdpc.browser.AboutAction
getInstance(Browser) - Static method in class gov.usda.gdpc.browser.AddDBConnectionAction
getInstance(Browser) - Static method in class gov.usda.gdpc.browser.AddSOAPConnectionAction
getInstance(Browser) - Static method in class gov.usda.gdpc.browser.DeselectAction
getInstance(Browser) - Static method in class gov.usda.gdpc.browser.ExitAction
getInstance(Browser) - Static method in class gov.usda.gdpc.browser.GetStartedAction
getInstance(Browser) - Static method in class gov.usda.gdpc.browser.HelpAction
getInstance(Browser) - Static method in class gov.usda.gdpc.browser.UpdateAction
getInstance(String) - Static method in class gov.usda.gdpc.xml.GDPCTag
getInstance(String) - Static method in class gov.usda.gdpc.xml.PropertyTag: Returns PropertyTag instance matching given tag.
getItems() - Method in class gov.usda.gdpc.gui.DBElementTree: Returns read only list of items in this tree.
getItems() - Method in class gov.usda.gdpc.gui.GenericList: Returns items in this list.
getJavaClass() - Method in class gov.usda.gdpc.xml.GDPCTag
getJavaClass() - Method in class gov.usda.gdpc.xml.PropertyTag: Returns the java class associated with this tag.
getJavaObjects(ResultSet, ExtraInfo) - Method in class gov.usda.gdpc.database.AbstractDatabaseMapping: Gets the data from the given result set as Java objects.
getJavaObjects(ResultSet, ExtraInfo) - Method in class gov.usda.gdpc.database.ConstantDatabaseMapping: This only uses the result set to determine the number of times to add the constant to the list.
getJavaObjects(ResultSet, ExtraInfo) - Method in interface gov.usda.gdpc.database.DatabaseMapping: Gets the data from the given result set as Java objects.
getJavaObjects(ResultSet, ExtraInfo) - Method in class gov.usda.gdpc.database.MultiDatabaseMapping: Gets the data from the given result set as Java objects.
getJavaObjects(ResultSet, ExtraInfo) - Method in class gov.usda.gdpc.database.NullDatabaseMapping: Gets the data from the given result set as Java objects.
getJavaObjects(ResultSet, ExtraInfo) - Method in class gov.usda.gdpc.database.SimpleDatabaseMapping: Gets the data from the given result set as Java objects.
getJavaObjects(ResultSet, ExtraInfo) - Method in class gov.usda.gdpc.panzea.PanzeaGenotypeExperimentDatabaseMapping: Gets the data from the given result set as Java objects.
getJavaObjects(ResultSet, ExtraInfo) - Method in class gov.usda.gdpc.panzea.PanzeaLocalityDatabaseMapping: Gets the data from the given result set as Java objects.
getJavaObjects(ResultSet, ExtraInfo) - Method in class gov.usda.gdpc.panzea.PanzeaLocusDatabaseMapping: Gets the data from the given result set as Java objects.
getJavaObjects(ResultSet, ExtraInfo) - Method in class gov.usda.gdpc.panzea.PanzeaLocusTypeDatabaseMapping: Gets the data from the given result set as Java objects.
getJavaObjects(ResultSet, ExtraInfo) - Method in class gov.usda.gdpc.panzea.PanzeaOntologyDatabaseMapping: Gets the data from the given result set as Java objects.
getJavaObjects(ResultSet, ExtraInfo) - Method in class gov.usda.gdpc.panzea.PanzeaPositionMinutesDatabaseMapping: Gets the data from the given result set as Java objects.
getKey() - Method in class gov.usda.gdpc.AbstractDBElement: Get the unique key for the element.
getKey() - Method in interface gov.usda.gdpc.DBElement: Get the unique key for the element.
getLabel() - Method in class gov.usda.gdpc.gui.LabeledList: Returns the label.
getLeafNodeCount() - Method in class gov.usda.gdpc.gui.dbetree.HeadNode: Returns the number of leaf nodes in this tree.
getLeafNodeCount() - Method in interface gov.usda.gdpc.gui.dbetree.Node
getLeafNodeCount() - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode
getLeafNodeCount() - Method in class gov.usda.gdpc.gui.dbetree.ValueNode
getLeafNodes() - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: Returns a list leaf nodes for this model.
getLeafNodes() - Method in class gov.usda.gdpc.gui.dbetree.HeadNode
getLeafNodes() - Method in interface gov.usda.gdpc.gui.dbetree.Node
getLeafNodes() - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode
getLeafNodes() - Method in class gov.usda.gdpc.gui.dbetree.ValueNode
getList() - Method in class gov.usda.gdpc.browser.GenericPropTableModel
getList() - Method in class gov.usda.gdpc.browser.PropertiesTableModel
getList() - Method in class gov.usda.gdpc.gui.LabeledList: Gets generic list object that's a component of this one.
getListModel() - Method in class gov.usda.gdpc.gui.DBElementTree
getLocality(String, Identifier) - Method in class gov.usda.gdpc.AbstractLocalityGroup: This returns the locality instance from this group that matches the specified id and source.
getLocality(String, Identifier) - Method in interface gov.usda.gdpc.LocalityGroup: This returns the locality instance from this group that matches the specified id and source.
getLocalityGroup(LocalityFilter) - Method in class gov.usda.gdpc.AbstractDBConnection: This method is unsupported by this class.
getLocalityGroup(LocalityFilter) - Method in class gov.usda.gdpc.AbstractDBGateway: Gets a locality group based on the given locality filter.
getLocalityGroup(LocalityFilter) - Method in class gov.usda.gdpc.AbstractLocalityGroup: Get the locality group matching the given filter from this locality group.
getLocalityGroup(LocalityFilter) - Method in interface gov.usda.gdpc.DBConnection: Gets a locality group based on the given locality filter.
getLocalityGroup(LocalityFilter) - Method in interface gov.usda.gdpc.DBGateway: Gets a locality group based on the given locality filter.
getLocalityGroup(LocalityFilter) - Method in interface gov.usda.gdpc.LocalityGroup: Get the locality group matching the given filter from this locality group.
getLocalityGroup(LocalityFilter) - Method in class gov.usda.gdpc.axis.DBConnectionProxy: Gets a locality group based on the given locality filter.
getLocalityGroup(LocalityFilter) - Method in class gov.usda.gdpc.panzea.PanzeaDBConnection: Gets a locality group based on the given locality filter.
getLocus(String, Identifier) - Method in class gov.usda.gdpc.AbstractLocusGroup: This returns the locus instance from this group that matches the specified id and source.
getLocus() - Method in class gov.usda.gdpc.GenotypeExperiment: Returns the locus associated with this genotype experiment.
getLocus(String, Identifier) - Method in interface gov.usda.gdpc.LocusGroup: This returns the locus instance from this group that matches the specified id and source.
getLocusGroup(LocusFilter) - Method in class gov.usda.gdpc.AbstractDBConnection: This method is unsupported by this class.
getLocusGroup(LocusFilter) - Method in class gov.usda.gdpc.AbstractDBGateway: Gets a locus group based on the given locus filter.
getLocusGroup(LocusFilter) - Method in class gov.usda.gdpc.AbstractLocusGroup: Get the locus group matching the given filter from this locus group.
getLocusGroup(LocusFilter) - Method in interface gov.usda.gdpc.DBConnection: Gets a locus group based on the given locus filter.
getLocusGroup(LocusFilter) - Method in interface gov.usda.gdpc.DBGateway: Gets a locus group based on the given locus filter.
getLocusGroup(LocusFilter) - Method in interface gov.usda.gdpc.LocusGroup: Get the locus group matching the given filter from this locus group.
getLocusGroup(LocusFilter) - Method in class gov.usda.gdpc.axis.DBConnectionProxy: Gets a locus group based on the given locus filter.
getLocusGroup(LocusFilter) - Method in class gov.usda.gdpc.panzea.PanzeaDBConnection: Gets a locus group based on the given locus filter.
getMapping(Property) - Method in class gov.usda.gdpc.database.AbstractPropertyMap: Gets the mapping associated with the given property.
getMapping(Property) - Method in interface gov.usda.gdpc.database.PropertyMap: Gets the mapping associated with the given property.
getMappings(Class) - Method in class gov.usda.gdpc.database.AbstractPropertyMap: Gets the database mappings from this property map that an associated property of the give type.
getMappings(Class) - Method in interface gov.usda.gdpc.database.PropertyMap: Gets the database mappings from this property map that an associated property of the give type.
getMatchingMapping(DatabaseMapping) - Method in class gov.usda.gdpc.database.AbstractPropertyMap: Gets the database mapping that matches the given database mapping.
getMatchingMapping(DatabaseMapping) - Method in interface gov.usda.gdpc.database.PropertyMap: Gets the database mapping that matches the given database mapping.
getMaxGeneticPosition() - Method in class gov.usda.gdpc.Chromosome: Get the maximum genetic position.
getMaxValue() - Method in class gov.usda.gdpc.FilterRangeValue: Gets the maximum value of this range.
getMaximumSize() - Method in class gov.usda.gdpc.gui.FixedTextField
getMechanismType() - Method in class gov.usda.gdpc.axis.DistinctValueSerializer: Gets the type of the XML processing mechanism and representation used by this Serializer.
getMechanismType() - Method in class gov.usda.gdpc.axis.FilterSerializer: Gets the type of the XML processing mechanism and representation used by this Serializer.
getMechanismType() - Method in class gov.usda.gdpc.axis.GDPCSerializer: Gets the type of the XML processing mechanism and representation used by this Serializer.
getMechanismType() - Method in class gov.usda.gdpc.axis.GenericTableSerializer: Gets the type of the XML processing mechanism and representation used by this Serializer.
getMechanismType() - Method in class gov.usda.gdpc.axis.PropertiesListSerializer: Gets the type of the XML processing mechanism and representation used by this Serializer.
getMinGeneticPosition() - Method in class gov.usda.gdpc.Chromosome: Get the minimum genetic position.
getMinValue() - Method in class gov.usda.gdpc.FilterRangeValue: Gets the minimum value of this range.
getMinutesField() - Method in class gov.usda.gdpc.panzea.PanzeaPositionMinutesDatabaseMapping
getMultiInStringWithQuotes(Object[], int) - Static method in class gov.usda.gdpc.database.AbstractJDBCConnection: This returns an array of strings generated from the specified list intended to be used in a SQL statement.
getName() - Method in class gov.usda.gdpc.AbstractDBElement: Returns the name of this database element.
getName() - Method in class gov.usda.gdpc.AbstractProperty: Returns the name of this property
getName() - Method in interface gov.usda.gdpc.DBElement: Returns the name of this database element.
getName() - Method in class gov.usda.gdpc.EnvironmentExperiment: Returns the name of this environment experiment.
getName() - Method in class gov.usda.gdpc.FilterValueType: Returns name of this instance.
getName() - Method in class gov.usda.gdpc.Genotype: Returns the name of this genotype.
getName() - Method in class gov.usda.gdpc.GenotypeExperiment: Returns the name of this genotype experiment.
getName() - Method in class gov.usda.gdpc.Locality: Returns the name of this locality.
getName() - Method in class gov.usda.gdpc.Locus: Returns the name of this locus.
getName() - Method in class gov.usda.gdpc.Phenotype: Returns the name of this phenotype.
getName() - Method in class gov.usda.gdpc.PhenotypeOntology: Returns the name of this phenotype ontology.
getName() - Method in interface gov.usda.gdpc.Property: Returns the name of this property
getName() - Method in class gov.usda.gdpc.Taxon: Returns the name of this taxon.
getNamespace() - Method in class gov.usda.gdpc.axis.DBConnectionProxy
getNumConnections() - Method in class gov.usda.gdpc.AbstractDBGateway: Returns the number of connections managed by this gateway.
getNumConnections() - Method in interface gov.usda.gdpc.DBGateway: Returns the number of connections managed by this gateway.
getNumItems() - Method in class gov.usda.gdpc.gui.DBElementTree
getNumber() - Method in class gov.usda.gdpc.Identifier: Return identifier as number.
getOntology() - Method in class gov.usda.gdpc.Phenotype: Returns the ontology of this phenotype.
getParent() - Method in class gov.usda.gdpc.gui.dbetree.HeadNode
getParent() - Method in interface gov.usda.gdpc.gui.dbetree.Node
getParent() - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode
getParent() - Method in class gov.usda.gdpc.gui.dbetree.ValueNode
getPhenoFlag() - Method in class gov.usda.gdpc.browser.Browser
getPhenotype(String, Taxon, EnvironmentExperiment, PhenotypeOntology) - Method in class gov.usda.gdpc.AbstractPhenotypeGroup: Gets the phenotype having the given taxon, environment experiment, ontology, and data source.
getPhenotype(String, Taxon, EnvironmentExperiment, PhenotypeOntology) - Method in interface gov.usda.gdpc.PhenotypeGroup: Gets the phenotype having the given taxon, environment experiment, ontology, and data source.
getPhenotypeData() - Method in class gov.usda.gdpc.browser.Browser
getPhenotypeGroup(EnvironmentExperimentGroup, TaxonGroup, PhenotypeOntologyGroup) - Method in class gov.usda.gdpc.AbstractDBConnection: This method is unsupported by this class.
getPhenotypeGroup(EnvironmentExperimentGroup, TaxonGroup, PhenotypeOntologyGroup) - Method in class gov.usda.gdpc.AbstractDBGateway: Gets the phenotypes for all combinations of environment experiments, taxa, and phenotype ontologys defined by the respective groups.
getPhenotypeGroup(PhenotypeFilter) - Method in class gov.usda.gdpc.AbstractPhenotypeGroup: Get the phenotype group from this group which match the critera specified by the filter.
getPhenotypeGroup(EnvironmentExperimentGroup, TaxonGroup, PhenotypeOntologyGroup) - Method in interface gov.usda.gdpc.DBConnection: Gets the phenotypes for all combinations of environment experiments, taxa, and phenotype ontologys defined by the respective groups.
getPhenotypeGroup(EnvironmentExperimentGroup, TaxonGroup, PhenotypeOntologyGroup) - Method in interface gov.usda.gdpc.DBGateway: Gets the phenotypes for all combinations of environment experiments, taxa, and phenotype ontologys defined by the respective groups.
getPhenotypeGroup(PhenotypeFilter) - Method in interface gov.usda.gdpc.PhenotypeGroup: Get the phenotype group from this group which match the critera specified by the filter.
getPhenotypeGroup(EnvironmentExperimentGroup, TaxonGroup, PhenotypeOntologyGroup) - Method in class gov.usda.gdpc.axis.DBConnectionProxy: Gets the phenotypes for all combinations of environment experiments, taxa, and phenotype ontologys defined by the respective groups.
getPhenotypeGroup(EnvironmentExperimentGroup, TaxonGroup, PhenotypeOntologyGroup) - Method in class gov.usda.gdpc.panzea.PanzeaDBConnection: Gets the phenotypes for all combinations of environment experiments, taxa, and phenotype ontologys defined by the respective groups.
getPhenotypeOntology(String, Identifier) - Method in class gov.usda.gdpc.AbstractPhenotypeOntologyGroup: This returns the phenotype ontology instance from this group that matches the specified id and source.
getPhenotypeOntology(String, Identifier) - Method in interface gov.usda.gdpc.PhenotypeOntologyGroup: This returns the phenotype ontology instance from this group that matches the specified id and source.
getPhenotypeOntology() - Method in class gov.usda.gdpc.PhenotypeTable: Get phenotype ontology of this table.
getPhenotypeOntologyGroup(PhenotypeOntologyFilter) - Method in class gov.usda.gdpc.AbstractDBConnection: This method is unsupported by this class.
getPhenotypeOntologyGroup(PhenotypeOntologyFilter) - Method in class gov.usda.gdpc.AbstractDBGateway: Get a phenotype ontology group based on the given pheotype ontology filter.
getPhenotypeOntologyGroup(PhenotypeOntologyFilter) - Method in class gov.usda.gdpc.AbstractPhenotypeOntologyGroup: Get the phenotype ontology group matching the given filter from this phenotype ontology group.
getPhenotypeOntologyGroup(PhenotypeOntologyFilter) - Method in interface gov.usda.gdpc.DBConnection: Get a phenotype ontology group based on the given pheotype ontology filter.
getPhenotypeOntologyGroup(PhenotypeOntologyFilter) - Method in interface gov.usda.gdpc.DBGateway: Get a phenotype ontology group based on the given pheotype ontology filter.
getPhenotypeOntologyGroup(PhenotypeOntologyFilter) - Method in interface gov.usda.gdpc.PhenotypeOntologyGroup: Get the phenotype ontology group matching the given filter from this phenotype ontology group.
getPhenotypeOntologyGroup(PhenotypeOntologyFilter) - Method in class gov.usda.gdpc.axis.DBConnectionProxy: Get a phenotype ontology group based on the given pheotype ontology filter.
getPhenotypeOntologyGroup(PhenotypeOntologyFilter) - Method in class gov.usda.gdpc.panzea.PanzeaDBConnection: Get a phenotype ontology group based on the given pheotype ontology filter.
getPhenotypeOntologyGroupFromDB(PhenotypeOntologyFilter) - Method in class gov.usda.gdpc.panzea.PanzeaDBConnection
getPositionField() - Method in class gov.usda.gdpc.panzea.PanzeaPositionMinutesDatabaseMapping
getProperties() - Method in class gov.usda.gdpc.browser.FilterValuesPanel: Returns the properties with filterable values displayed in the panel.
getProperties(Node, GDPCTag) - Method in class gov.usda.gdpc.xml.AbstractXMLDocument
getProperty(Property) - Method in class gov.usda.gdpc.AbstractDBElement: Returns the value of the specified property.
getProperty() - Method in class gov.usda.gdpc.AbstractFilterValue: Returns the property associated with this value.
getProperty(Property) - Method in interface gov.usda.gdpc.DBElement: Returns the value of the specified property.
getProperty() - Method in interface gov.usda.gdpc.FilterValue: Returns the property associated with this value.
getProperty() - Method in class gov.usda.gdpc.browser.PropertyLabeledList: Get the property associated with this list.
getProperty() - Method in class gov.usda.gdpc.database.AbstractDatabaseMapping: Gets the property associated with this database mapping.
getProperty() - Method in interface gov.usda.gdpc.database.DatabaseMapping: Gets the property associated with this database mapping.
getProperty() - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode: Returns the property associated with this node.
getProperty() - Method in class gov.usda.gdpc.gui.dbetree.ValueNode: Returns this nodes property.
getPropertyNode() - Method in class gov.usda.gdpc.gui.dbetree.HeadNode
getRefSelectionList(Property) - Method in class gov.usda.gdpc.browser.FilterValuesPanel: Returns the reference labeled list for the given property.
getRoot() - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: Gets root node of this model.
getRow(Object) - Method in class gov.usda.gdpc.util.AbstractTable: Get the row for the given row heading.
getRow(int) - Method in class gov.usda.gdpc.util.AbstractTable: Get the row for the given row index.
getRow(Object) - Method in class gov.usda.gdpc.util.GenericTable: Unsupported operation.
getRow(int) - Method in class gov.usda.gdpc.util.GenericTable: Get the row for the given row index.
getRow(Object) - Method in interface gov.usda.gdpc.util.Table: Get the row for the given row heading.
getRow(int) - Method in interface gov.usda.gdpc.util.Table: Get the row for the given row index.
getRowCount() - Method in class gov.usda.gdpc.browser.GenericPropTableModel
getRowCount() - Method in class gov.usda.gdpc.browser.MatrixTableModel: Returns the number of rows in the model.
getRowCount() - Method in class gov.usda.gdpc.browser.PropertiesTableModel
getRowHeaders() - Method in class gov.usda.gdpc.browser.MatrixTableModel
getRowHeading(int) - Method in class gov.usda.gdpc.util.AbstractTable: Get row heading at specified index.
getRowHeading(int) - Method in class gov.usda.gdpc.util.GenericTable: Unsupported operation.
getRowHeading(int) - Method in interface gov.usda.gdpc.util.Table: Get row heading at specified index.
getRowHeadings() - Method in class gov.usda.gdpc.util.AbstractTable: Get row headings for this table.
getRowHeadings() - Method in class gov.usda.gdpc.util.GenericTable: Unsupported operation.
getRowHeadings() - Method in interface gov.usda.gdpc.util.Table: Get row headings for this table.
getSQL(Filter, ExtraInfo) - Method in class gov.usda.gdpc.database.AbstractPropertyMap: Get the SQL "where" string required to retrieve the data matching the given filter for this property map.
getSQL(Filter, ExtraInfo) - Method in interface gov.usda.gdpc.database.PropertyMap: Get the SQL "where" string required to retrieve the data matching the given filter for this property map.
getSQLSubString(Filter, ExtraInfo) - Method in class gov.usda.gdpc.database.AbstractDatabaseMapping: Gets the SQL sub-string based on the given filter.
getSQLSubString(Filter, ExtraInfo) - Method in class gov.usda.gdpc.database.ConstantDatabaseMapping: Gets the SQL sub-string based on the given filter.
getSQLSubString(Filter, ExtraInfo) - Method in interface gov.usda.gdpc.database.DatabaseMapping: Gets the SQL sub-string based on the given filter.
getSQLSubString(Filter, ExtraInfo) - Method in class gov.usda.gdpc.database.DateDatabaseMapping: Gets the SQL sub-string based on the given filter.
getSQLSubString(Filter, ExtraInfo) - Method in class gov.usda.gdpc.database.MultiDatabaseMapping: Gets the SQL sub-string based on the given filter.
getSQLSubString(Filter, ExtraInfo) - Method in class gov.usda.gdpc.database.NullDatabaseMapping: Gets the SQL sub-string based on the given filter.
getSQLSubString(Filter, ExtraInfo) - Method in class gov.usda.gdpc.database.SimpleDatabaseMapping: Gets the SQL sub-string based on the given filter.
getSQLSubString(Filter, ExtraInfo) - Method in class gov.usda.gdpc.database.StringDatabaseMapping: Gets the SQL sub-string based on the given filter.
getSQLSubString(Filter, ExtraInfo) - Method in class gov.usda.gdpc.panzea.PanzeaGenotypeExperimentDatabaseMapping: Gets the SQL sub-string based on the given filter.
getSQLSubString(Filter, ExtraInfo) - Method in class gov.usda.gdpc.panzea.PanzeaLocusTypeDatabaseMapping: Gets the SQL sub-string based on the given filter.
getSQLSubString(Filter, ExtraInfo) - Method in class gov.usda.gdpc.panzea.PanzeaPositionMinutesDatabaseMapping: Gets the SQL sub-string based on the given filter.
getSelectedTab() - Method in class gov.usda.gdpc.browser.Browser
getSelectionLists() - Method in class gov.usda.gdpc.browser.FilterValuesPanel: Returns the labeled lists displayed by this panel.
getSerializerAs(String) - Method in class gov.usda.gdpc.axis.DistinctValueSerializerFactory: Returns a Serializer for the specified XML processing mechanism type.
getSerializerAs(String) - Method in class gov.usda.gdpc.axis.FilterSerializerFactory: Returns a Serializer for the specified XML processing mechanism type.
getSerializerAs(String) - Method in class gov.usda.gdpc.axis.GDPCSerializerFactory: Returns a Serializer for the specified XML processing mechanism type.
getSerializerAs(String) - Method in class gov.usda.gdpc.axis.GenericTableSerializerFactory: Returns a Serializer for the specified XML processing mechanism type.
getSerializerAs(String) - Method in class gov.usda.gdpc.axis.PropertiesListSerializerFactory: Returns a Serializer for the specified XML processing mechanism type.
getServiceName() - Method in class gov.usda.gdpc.axis.DBConnectionProxy
getSize() - Method in class gov.usda.gdpc.browser.TableRowHeaderListModel: Returns the length of the list.
getStackTrace(Exception, int) - Static method in class gov.usda.gdpc.util.ExceptionUtils: This sends an exception's stack trace to the specified logger.
getStatements() - Method in class gov.usda.gdpc.database.SQLStatements: This gets a list of statements.
getStyle() - Method in class gov.usda.gdpc.axis.DBConnectionProxy
getSubType() - Method in class gov.usda.gdpc.AbstractProperty: Get subtype of this property.
getSubType() - Method in interface gov.usda.gdpc.Property: Get subtype of this property.
getSupportedMechanismTypes() - Method in class gov.usda.gdpc.axis.DistinctValueDeserializerFactory: Returns a list of all XML processing mechanism types supported by this DeserializerFactory.
getSupportedMechanismTypes() - Method in class gov.usda.gdpc.axis.DistinctValueSerializerFactory: Returns a list of all XML processing mechanism types supported by this SerializerFactory.
getSupportedMechanismTypes() - Method in class gov.usda.gdpc.axis.FilterDeserializerFactory: Returns a list of all XML processing mechanism types supported by this DeserializerFactory.
getSupportedMechanismTypes() - Method in class gov.usda.gdpc.axis.FilterSerializerFactory: Returns a list of all XML processing mechanism types supported by this SerializerFactory.
getSupportedMechanismTypes() - Method in class gov.usda.gdpc.axis.GDPCDeserializerFactory: Returns a list of all XML processing mechanism types supported by this DeserializerFactory.
getSupportedMechanismTypes() - Method in class gov.usda.gdpc.axis.GDPCSerializerFactory: Returns a list of all XML processing mechanism types supported by this SerializerFactory.
getSupportedMechanismTypes() - Method in class gov.usda.gdpc.axis.GenericTableDeserializerFactory: Returns a list of all XML processing mechanism types supported by this DeserializerFactory.
getSupportedMechanismTypes() - Method in class gov.usda.gdpc.axis.GenericTableSerializerFactory: Returns a list of all XML processing mechanism types supported by this SerializerFactory.
getSupportedMechanismTypes() - Method in class gov.usda.gdpc.axis.PropertiesListDeserializerFactory: Returns a list of all XML processing mechanism types supported by this DeserializerFactory.
getSupportedMechanismTypes() - Method in class gov.usda.gdpc.axis.PropertiesListSerializerFactory: Returns a list of all XML processing mechanism types supported by this SerializerFactory.
getTag() - Method in class gov.usda.gdpc.xml.GDPCTag
getTag() - Method in class gov.usda.gdpc.xml.PropertyTag: Returns the XML tag.
getTaxon(String, Identifier) - Method in class gov.usda.gdpc.AbstractTaxonGroup: This returns the taxon instance from this group that matches the specified id and source.
getTaxon() - Method in class gov.usda.gdpc.Genotype: Returns the taxon associated with this genotype.
getTaxon() - Method in class gov.usda.gdpc.Phenotype: Returns the taxon associated with this phenotype.
getTaxon(String, Identifier) - Method in interface gov.usda.gdpc.TaxonGroup: This returns the taxon instance from this group that matches the specified id and source.
getTaxonGroup(TaxonFilter) - Method in class gov.usda.gdpc.AbstractDBConnection: This method is unsupported by this class.
getTaxonGroup(TaxonFilter) - Method in class gov.usda.gdpc.AbstractDBGateway: Gets a taxon group based on the given taxon filter.
getTaxonGroup() - Method in class gov.usda.gdpc.AbstractGenotypeGroup: Returns the group of taxon associated with this group of genotypes.
getTaxonGroup() - Method in class gov.usda.gdpc.AbstractPhenotypeGroup: Returns the group of taxon associated with this group of phenotypes.
getTaxonGroup(TaxonFilter) - Method in class gov.usda.gdpc.AbstractTaxonGroup: Get the taxon group matching the given filter from this taxon group.
getTaxonGroup(TaxonFilter) - Method in interface gov.usda.gdpc.DBConnection: Gets a taxon group based on the given taxon filter.
getTaxonGroup(TaxonFilter) - Method in interface gov.usda.gdpc.DBGateway: Gets a taxon group based on the given taxon filter.
getTaxonGroup() - Method in interface gov.usda.gdpc.GenotypeGroup: Returns the group of taxon associated with this group of genotypes.
getTaxonGroup() - Method in class gov.usda.gdpc.GenotypeTable: Get the taxon group for this table.
getTaxonGroup() - Method in interface gov.usda.gdpc.PhenotypeGroup: Returns the group of taxon associated with this group of phenotypes.
getTaxonGroup() - Method in class gov.usda.gdpc.PhenotypeTable: Get the taxon group for this table.
getTaxonGroup(TaxonFilter) - Method in interface gov.usda.gdpc.TaxonGroup: Get the taxon group matching the given filter from this taxon group.
getTaxonGroup(TaxonFilter) - Method in class gov.usda.gdpc.axis.DBConnectionProxy: Gets a taxon group based on the given taxon filter.
getTaxonGroup(TaxonFilter) - Method in class gov.usda.gdpc.panzea.PanzeaDBConnection: Gets a taxon group based on the given taxon filter.
getTextFromNode(Node) - Static method in class gov.usda.gdpc.xml.AbstractXMLDocument
getType() - Method in class gov.usda.gdpc.AbstractEnvironmentExperimentGroup: Get type of this group.
getType() - Method in class gov.usda.gdpc.AbstractFilter: Get type of this element.
getType() - Method in class gov.usda.gdpc.AbstractGenotypeExperimentGroup: Get type of this group.
getType() - Method in class gov.usda.gdpc.AbstractGenotypeGroup: Get type of this group.
getType() - Method in class gov.usda.gdpc.AbstractLocalityGroup: Get type of this group.
getType() - Method in class gov.usda.gdpc.AbstractLocusGroup: Get type of this group.
getType() - Method in class gov.usda.gdpc.AbstractPhenotypeGroup: Get type of this group.
getType() - Method in class gov.usda.gdpc.AbstractPhenotypeOntologyGroup: Get type of this group.
getType() - Method in class gov.usda.gdpc.AbstractProperty: Get type of this property.
getType() - Method in class gov.usda.gdpc.AbstractTaxonGroup: Get type of this group.
getType() - Method in class gov.usda.gdpc.Chromosome: Get type of this group.
getType() - Method in interface gov.usda.gdpc.DBElement: Get type of this element.
getType() - Method in interface gov.usda.gdpc.DBElementGroup: Get type of this group.
getType() - Method in class gov.usda.gdpc.EnvironmentExperiment: Get type of this element.
getType() - Method in interface gov.usda.gdpc.Filter: Get type of this filter.
getType() - Method in class gov.usda.gdpc.FilterLikeValue: Returns type of this filter value.
getType() - Method in class gov.usda.gdpc.FilterRangeValue: Returns type of this filter value.
getType() - Method in class gov.usda.gdpc.FilterSingleValue: Returns type of this filter value.
getType() - Method in interface gov.usda.gdpc.FilterValue: Returns type of this filter value.
getType() - Method in class gov.usda.gdpc.Genotype: Get type of this element.
getType() - Method in class gov.usda.gdpc.GenotypeExperiment: Get type of this element.
getType() - Method in class gov.usda.gdpc.Locality: Get type of this element.
getType() - Method in class gov.usda.gdpc.Locus: Get type of this element.
getType() - Method in class gov.usda.gdpc.Phenotype: Get type of this element.
getType() - Method in class gov.usda.gdpc.PhenotypeOntology: Get type of this element.
getType() - Method in interface gov.usda.gdpc.Property: Get type of this property.
getType() - Method in class gov.usda.gdpc.Taxon: Get type of this element.
getType() - Method in class gov.usda.gdpc.browser.DBElementPanel
getUID() - Method in class gov.usda.gdpc.database.AbstractJDBCConnection: Returns the database user on whose behalf the connection is being made.
getURL(String) - Static method in class gov.usda.gdpc.browser.Util
getURL() - Method in class gov.usda.gdpc.database.AbstractJDBCConnection: Returns the database url of the form jdbc:subprotocol:subname.
getUnique(List) - Static method in class gov.usda.gdpc.util.ArrayUtils: Returns only the objects from the given list that are unique.
getUpdateAction() - Method in class gov.usda.gdpc.browser.ViewMenu
getUse() - Method in class gov.usda.gdpc.axis.DBConnectionProxy
getValue() - Method in class gov.usda.gdpc.FilterLikeValue: Gets the like value.
getValue() - Method in class gov.usda.gdpc.FilterSingleValue: Returns the single value.
getValue() - Method in class gov.usda.gdpc.Phenotype: Returns the value of this phenotype.
getValue() - Method in class gov.usda.gdpc.gui.dbetree.ValueNode: Returns value associated with this node.
getValueAt(int, int) - Method in class gov.usda.gdpc.browser.GenericPropTableModel
getValueAt(int, int) - Method in class gov.usda.gdpc.browser.MatrixTableModel: Returns the value for the cell at columnIndex and rowIndex.
getValueAt(int, int) - Method in class gov.usda.gdpc.browser.PropertiesTableModel
getValues(Property, FilterValueType) - Method in class gov.usda.gdpc.AbstractFilter: Gets all the values set for the given property and filter value type.
getValues(FilterValueType) - Method in class gov.usda.gdpc.AbstractFilter: Gets all the values set for the given filter value type.
getValues(Property) - Method in class gov.usda.gdpc.AbstractFilter: Gets all the values set for the given property.
getValues(Property) - Method in class gov.usda.gdpc.DistinctPropertyValues: Get distinct values for specified property.
getValues(Property, FilterValueType) - Method in interface gov.usda.gdpc.Filter: Gets all the values set for the given property and filter value type.
getValues(FilterValueType) - Method in interface gov.usda.gdpc.Filter: Gets all the values set for the given filter value type.
getValues(Property) - Method in interface gov.usda.gdpc.Filter: Gets all the values set for the given property.
getWorkingGroup() - Method in class gov.usda.gdpc.browser.DBElementPanel
getWorkingListModel() - Method in class gov.usda.gdpc.browser.DBElementPanel
gov.usda.gdpc - package gov.usda.gdpc: This is the main package for The Genomic Diversity and Phenotype Connection (GDPC).
gov.usda.gdpc.axis - package gov.usda.gdpc.axis: This package provides the code to allow GDPC to work with the SOAP Engine AXIS.
gov.usda.gdpc.browser - package gov.usda.gdpc.browser: This package provides a browser which uses the GDPC gateway to retrieve Genomic and Phenotypic data.
gov.usda.gdpc.database - package gov.usda.gdpc.database: This package provides classes which support the creation of a JDBC connection to a database.
gov.usda.gdpc.gramene - package gov.usda.gdpc.gramene: This package provides a specific connection to the gramene database which is maintained by CSHL.
gov.usda.gdpc.gui - package gov.usda.gdpc.gui: This package provides generic gui class that works with GDPC.
gov.usda.gdpc.gui.dbetree - package gov.usda.gdpc.gui.dbetree: This package provides classes for working with gov.usda.gdpc.gui.DBElementTree.
gov.usda.gdpc.pal - package gov.usda.gdpc.pal: This package contains any classes which integrates the PAL library with GDPC.
gov.usda.gdpc.panzea - package gov.usda.gdpc.panzea: This package provides a specific connection to the panzea database which is maintained by NCSU.
gov.usda.gdpc.util - package gov.usda.gdpc.util: This package contains any commonly used classes or methods which are not specific to any one package.
gov.usda.gdpc.xml - package gov.usda.gdpc.xml: This package provides XML specific function.
groupValue() - Method in class gov.usda.gdpc.xml.XMLDBElementGroup: Translates this XML document to a DBElementGroup.

H

HARVEST_DATE - Static variable in class gov.usda.gdpc.EnvironmentExperimentProperty: Date crop harvested (data type: gov.usda.gdpc.util.Calendar).
HARVEST_DATE - Static variable in class gov.usda.gdpc.xml.PropertyTag
HEAD_TAG - Static variable in class gov.usda.gdpc.xml.GDPCTag
HUMAN_VALIDATION - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: Human Validation associated with genotype experiment (data type: java.lang.String).
HUMAN_VALIDATION - Static variable in class gov.usda.gdpc.xml.PropertyTag
HeadNode - class gov.usda.gdpc.gui.dbetree.HeadNode.
HeadNode(List, DBElementTreeModel) - Constructor for class gov.usda.gdpc.gui.dbetree.HeadNode: HeadNode Constructor.
HeadNode(DBElementTreeModel) - Constructor for class gov.usda.gdpc.gui.dbetree.HeadNode: HeadNode Constructor.
HelpAction - class gov.usda.gdpc.browser.HelpAction.
HelpMenu - class gov.usda.gdpc.browser.HelpMenu.
HelpMenu(Browser) - Constructor for class gov.usda.gdpc.browser.HelpMenu: HelpMenu constructor comment.
hasNext() - Method in class gov.usda.gdpc.util.ReadOnlyIterator: Returns true if the iteration has more elements.
hashCode() - Method in class gov.usda.gdpc.AbstractProperty: This method made final to prevent overriding Object.hashCode.
hashCode() - Method in class gov.usda.gdpc.FilterValueType: This method made final to prevent overriding Object.hashCode.

I

ID - Static variable in class gov.usda.gdpc.EnvironmentExperimentProperty: ID of environment experiment (data type: gov.usda.gdpc.Identifier).
ID - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: ID of genotype experiment (data type: gov.usda.gdpc.Identifier).
ID - Static variable in class gov.usda.gdpc.LocalityProperty: ID of locality (data type: gov.usda.gdpc.Identifier).
ID - Static variable in class gov.usda.gdpc.LocusProperty: ID of locus (data type: gov.usda.gdpc.Identifier).
ID - Static variable in class gov.usda.gdpc.PhenotypeOntologyProperty: Identifier of phenotype ontology (data type: gov.usda.gdpc.Identifier).
ID - Static variable in class gov.usda.gdpc.TaxonProperty: Taxon id (data type: gov.usda.gdpc.Identifier).
ID - Static variable in class gov.usda.gdpc.xml.PropertyTag: COMMON PROPERTIES
ID_HINT - Static variable in class gov.usda.gdpc.xml.PropertyTag
ID_VALUE - Static variable in class gov.usda.gdpc.xml.PropertyTag
INTEGER - Static variable in class gov.usda.gdpc.Convert
Identifier - class gov.usda.gdpc.Identifier.: This is an identifier which should uniquely identify a database element for a given database element type (e.g.
Identifier(String) - Constructor for class gov.usda.gdpc.Identifier: Identifier constructor.
Identifier(String, String[]) - Constructor for class gov.usda.gdpc.Identifier: Identifier constructor.
IdentifierDeserializer - class gov.usda.gdpc.axis.IdentifierDeserializer.
IdentifierDeserializer() - Constructor for class gov.usda.gdpc.axis.IdentifierDeserializer: IdentifierDeserializer Constructor.
index() - Method in class gov.usda.gdpc.AbstractDBElementGroup: Indexes this group of taxa based on the unique key.
index() - Method in interface gov.usda.gdpc.DBElementGroup: Indexes this group based on the unique key (getKey()).
indexOf(Object) - Method in class gov.usda.gdpc.AbstractGroup: Returns the index in this list of the first occurrence of the specified element, or -1 if this list does not contain this element.
indexOf(Object) - Method in class gov.usda.gdpc.util.ReadOnlyList
indexOf(Object) - Method in class gov.usda.gdpc.util.SortedList
insert(int) - Method in class gov.usda.gdpc.browser.GenericPropTableModel
insert(GenericPropTableData) - Method in class gov.usda.gdpc.browser.GenericPropTableModel
insert(int) - Method in class gov.usda.gdpc.browser.PropertiesTableModel
insert(PropertiesTableData) - Method in class gov.usda.gdpc.browser.PropertiesTableModel
isCellEditable(int, int) - Method in class gov.usda.gdpc.browser.GenericPropTableModel
isCellEditable(int, int) - Method in class gov.usda.gdpc.browser.MatrixTableModel: Always returns false.
isCellEditable(int, int) - Method in class gov.usda.gdpc.browser.PropertiesTableModel
isClosed() - Method in class gov.usda.gdpc.database.AbstractJDBCConnection: This returns whether database connection is closed.
isEmpty() - Method in class gov.usda.gdpc.AbstractDBElement: Returns true if this map contains no key-value mappings.
isEmpty() - Method in class gov.usda.gdpc.AbstractGroup: Returns true if this collection contains no elements.
isEmpty() - Method in class gov.usda.gdpc.gui.DBElementTree
isEmpty() - Method in class gov.usda.gdpc.util.ReadOnlyCollection
isEmpty() - Method in class gov.usda.gdpc.util.ReadOnlyList
isEmpty() - Method in class gov.usda.gdpc.util.ReadOnlySet
isEmpty() - Method in class gov.usda.gdpc.util.SortedList
isEmpty() - Method in class gov.usda.gdpc.util.TreeSetPlusNull
isLeaf(Object) - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: Returns whether given node is a leaf node.
isLeaf() - Method in class gov.usda.gdpc.gui.dbetree.HeadNode
isLeaf() - Method in interface gov.usda.gdpc.gui.dbetree.Node
isLeaf() - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode
isLeaf() - Method in class gov.usda.gdpc.gui.dbetree.ValueNode
itemStateChanged(ItemEvent) - Method in class gov.usda.gdpc.browser.PropertyCheckBox
itemStateChanged(ItemEvent) - Method in class gov.usda.gdpc.browser.PropertyCheckBoxListener
iterator() - Method in class gov.usda.gdpc.AbstractGroup: Returns an iterator over the elements in this collection.
iterator() - Method in class gov.usda.gdpc.util.ReadOnlyCollection
iterator() - Method in class gov.usda.gdpc.util.ReadOnlyList
iterator() - Method in class gov.usda.gdpc.util.ReadOnlySet
iterator() - Method in class gov.usda.gdpc.util.SortedList
iterator() - Method in class gov.usda.gdpc.util.TreeSetPlusNull

J

JAXP_SCHEMA_LANGUAGE - Static variable in class gov.usda.gdpc.xml.GDPCConstants

K

keySet() - Method in class gov.usda.gdpc.AbstractDBElement: Returns a read-only set view of the keys contained in this map.

L

LABEL - Static variable in class gov.usda.gdpc.xml.PropertyTag
LATITUDE - Static variable in class gov.usda.gdpc.LocalityProperty: Latitude of locality (data type: java.lang.Double).
LATITUDE - Static variable in class gov.usda.gdpc.xml.PropertyTag
LIKE - Static variable in class gov.usda.gdpc.xml.GDPCTag
LIKE_VALUE - Static variable in class gov.usda.gdpc.FilterValueType: Filter value which is a pattern with the wild card (%).
LOCALITIES - Variable in class gov.usda.gdpc.panzea.PanzeaCache
LOCALITY - Static variable in class gov.usda.gdpc.EnvironmentExperimentProperty: Locality associated with environment experiment (data type: gov.usda.gdpc.Locality).
LOCALITY - Static variable in class gov.usda.gdpc.TaxonProperty: Locality of Taxon (data type: gov.usda.gdpc.Locality).
LOCALITY - Static variable in class gov.usda.gdpc.xml.GDPCTag
LOCALITY_FILTER - Static variable in class gov.usda.gdpc.xml.GDPCTag
LOCALITY_GROUP - Static variable in class gov.usda.gdpc.xml.GDPCTag
LOCALITY_PROPERTY - Static variable in class gov.usda.gdpc.xml.GDPCTag
LOCALITY_TAB - Static variable in class gov.usda.gdpc.browser.Browser
LOCI - Variable in class gov.usda.gdpc.panzea.PanzeaCache
LOCUS - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: Locus associated with genotype experiment (data type: gov.usda.gdpc.Locus).
LOCUS - Static variable in class gov.usda.gdpc.xml.GDPCTag
LOCUS_FILTER - Static variable in class gov.usda.gdpc.xml.GDPCTag
LOCUS_GROUP - Static variable in class gov.usda.gdpc.xml.GDPCTag
LOCUS_PROPERTY - Static variable in class gov.usda.gdpc.xml.GDPCTag
LOCUS_TAB - Static variable in class gov.usda.gdpc.browser.Browser
LOCUS_TYPE - Static variable in class gov.usda.gdpc.LocusProperty: Type of locus (data type: java.lang.String).
LOCUS_TYPE - Static variable in class gov.usda.gdpc.xml.PropertyTag
LOCUS_TYPE_CYTOLOGICAL - Static variable in class gov.usda.gdpc.Locus: Locus type cytological.
LOCUS_TYPE_GENE - Static variable in class gov.usda.gdpc.Locus: Locus type gene.
LOCUS_TYPE_INTERGENIC - Static variable in class gov.usda.gdpc.Locus: Locus type intergenic.
LOCUS_TYPE_UNKNOWN - Static variable in class gov.usda.gdpc.Locus: Locus type unknown.
LOG_TAB - Static variable in class gov.usda.gdpc.browser.Browser
LONGITUDE - Static variable in class gov.usda.gdpc.LocalityProperty: Longitude of locality (data type: java.lang.Double).
LONGITUDE - Static variable in class gov.usda.gdpc.xml.PropertyTag
LabeledList - class gov.usda.gdpc.gui.LabeledList.
LabeledList(String) - Constructor for class gov.usda.gdpc.gui.LabeledList: LabeledList Constructor.
LabeledList(String, Vector) - Constructor for class gov.usda.gdpc.gui.LabeledList: LabeledList Constructor.
LabeledList(String, ListModel) - Constructor for class gov.usda.gdpc.gui.LabeledList: LabeledList Constructor.
LikeValueDeserializer - class gov.usda.gdpc.axis.LikeValueDeserializer.
LikeValueDeserializer(GDPCTag) - Constructor for class gov.usda.gdpc.axis.LikeValueDeserializer: LikeValueDeserializer Constructor.
ListSelectionListener - class gov.usda.gdpc.browser.ListSelectionListener.
ListSelectionListener(Properties) - Constructor for class gov.usda.gdpc.browser.ListSelectionListener: ListSelectionListener Constructor.
Locality - class gov.usda.gdpc.Locality.: This is a database element representing a locality.
LocalityFilter - class gov.usda.gdpc.LocalityFilter.: This is a locality filter.
LocalityFilter() - Constructor for class gov.usda.gdpc.LocalityFilter: LocalityFilter constructor.
LocalityGroup - interface gov.usda.gdpc.LocalityGroup.: Collection of locality.
LocalityProperty - class gov.usda.gdpc.LocalityProperty.: This follows the enum pattern and represents a locality property.
LocalityProperty(String, String, String, String) - Constructor for class gov.usda.gdpc.LocalityProperty: LocalityProperty constructor.
LocalityProperty(String, Class, String, String) - Constructor for class gov.usda.gdpc.LocalityProperty: LocalityProperty constructor.
Locus - class gov.usda.gdpc.Locus.: This is a database element representing a locus.
LocusFilter - class gov.usda.gdpc.LocusFilter.: This is a locus filter.
LocusFilter() - Constructor for class gov.usda.gdpc.LocusFilter: LocusFilter constructor.
LocusGroup - interface gov.usda.gdpc.LocusGroup.: Group of loci.
LocusProperty - class gov.usda.gdpc.LocusProperty.: This follows the enum pattern and represents a locus property.
LocusProperty(String, String, String, String) - Constructor for class gov.usda.gdpc.LocusProperty: LocusProperty constructor.
LocusProperty(String, Class, String, String) - Constructor for class gov.usda.gdpc.LocusProperty: LocusProperty constructor.
lastIndexOf(Object) - Method in class gov.usda.gdpc.AbstractGroup: Returns the index in this list of the last occurrence of the specified element, or -1 if this list does not contain this element.
lastIndexOf(Object) - Method in class gov.usda.gdpc.util.ReadOnlyList
lastIndexOf(Object) - Method in class gov.usda.gdpc.util.SortedList
listIterator() - Method in class gov.usda.gdpc.AbstractGroup: This operation is not supported.
listIterator(int) - Method in class gov.usda.gdpc.AbstractGroup: This operation is not supported.
listIterator() - Method in class gov.usda.gdpc.util.ReadOnlyList
listIterator(int) - Method in class gov.usda.gdpc.util.ReadOnlyList
listIterator() - Method in class gov.usda.gdpc.util.SortedList
listIterator(int) - Method in class gov.usda.gdpc.util.SortedList
load() - Method in class gov.usda.gdpc.browser.Browser: This method is for the load action used by TASSEL
logExceptionCauses(Throwable, Logger, Priority) - Static method in class gov.usda.gdpc.util.ExceptionUtils: This sends an exception's cause history to the specified logger.
logStackTrace(Exception, Logger) - Static method in class gov.usda.gdpc.util.ExceptionUtils: This sends an exception's stack trace to the specified logger.
logStackTrace(Exception, int, Logger, Priority) - Static method in class gov.usda.gdpc.util.ExceptionUtils: This sends an exception's stack trace to the specified logger.

M

MNEMONIC_KEY - Static variable in class gov.usda.gdpc.browser.UpdateAction
MatrixTableModel - class gov.usda.gdpc.browser.MatrixTableModel.
MatrixTableModel(Table) - Constructor for class gov.usda.gdpc.browser.MatrixTableModel
MatrixTableModel() - Constructor for class gov.usda.gdpc.browser.MatrixTableModel
MultiDatabaseMapping - class gov.usda.gdpc.database.MultiDatabaseMapping.
MultiDatabaseMapping(Property, DatabaseMapping[]) - Constructor for class gov.usda.gdpc.database.MultiDatabaseMapping: MultiDatabaseMapping Constructor.
m_columns - Static variable in class gov.usda.gdpc.browser.GenericPropTableModel
m_columns - Static variable in class gov.usda.gdpc.browser.PropertiesTableModel
m_title - Variable in class gov.usda.gdpc.browser.ColumnData
m_vector - Variable in class gov.usda.gdpc.browser.GenericPropTableModel
m_vector - Variable in class gov.usda.gdpc.browser.PropertiesTableModel
main(String[]) - Static method in class gov.usda.gdpc.PrintProperties
main(String[]) - Static method in class gov.usda.gdpc.axis.Test1Client
main(String[]) - Static method in class gov.usda.gdpc.axis.TestClient
main(String[]) - Static method in class gov.usda.gdpc.browser.Browser
main(String[]) - Static method in class gov.usda.gdpc.xml.TestValid
makeConnection() - Method in class gov.usda.gdpc.database.AbstractJDBCConnection: Make connection to database.
makeValue(String) - Method in class gov.usda.gdpc.axis.StringToObjectDeserializer
matches(Map) - Method in class gov.usda.gdpc.AbstractFilter: Returns whether the given properties match this filter.
matches(Map) - Method in interface gov.usda.gdpc.Filter: Returns whether the given properties match this filter.
matches(Map) - Method in class gov.usda.gdpc.FilterLikeValue: Returns whether the given properties match this filter value.
matches(Map) - Method in class gov.usda.gdpc.FilterRangeValue: Returns whether the given properties match this filter value.
matches(Map) - Method in class gov.usda.gdpc.FilterSingleValue: Returns whether the given properties match this filter value.
matches(Map) - Method in interface gov.usda.gdpc.FilterValue: Returns whether the given properties match this filter value.
moveDown(int) - Method in class gov.usda.gdpc.gui.GenericList: Moves down the given item one position in this list.
moveDown() - Method in class gov.usda.gdpc.gui.GenericList: Moves down selected item one position in this list.
moveUp(int) - Method in class gov.usda.gdpc.gui.GenericList: Moves up the given item one position in this list.
moveUp() - Method in class gov.usda.gdpc.gui.GenericList: Moves up selected item one position in this list.
myColumnList - Variable in class gov.usda.gdpc.xml.AbstractXMLDocument
myConnection - Variable in class gov.usda.gdpc.database.AbstractJDBCConnection: The handle to the connection
myConstant - Variable in class gov.usda.gdpc.database.ConstantDatabaseMapping
myCount - Variable in class gov.usda.gdpc.xml.AbstractXMLDocument
myDBElementsMap - Variable in class gov.usda.gdpc.xml.AbstractXMLDocument
myDBTable - Variable in class gov.usda.gdpc.database.SimpleDatabaseMapping
myDataSource - Variable in class gov.usda.gdpc.AbstractDBConnection
myDescription - Variable in class gov.usda.gdpc.AbstractDBConnection
myDocument - Variable in class gov.usda.gdpc.xml.AbstractXMLDocument
myDriver - Variable in class gov.usda.gdpc.database.AbstractJDBCConnection: The jdbc driver
myField - Variable in class gov.usda.gdpc.database.SimpleDatabaseMapping
myFont - Static variable in class gov.usda.gdpc.browser.Browser
myIDs - Variable in class gov.usda.gdpc.xml.AbstractXMLDocument
myIndex - Variable in class gov.usda.gdpc.AbstractDBElementGroup: This map indexes the elements in the group based on the value returned by DBElement.getKey()
myMappings - Variable in class gov.usda.gdpc.database.AbstractPropertyMap
myPassword - Variable in class gov.usda.gdpc.database.AbstractJDBCConnection: The user's password
myPoundString - Variable in class gov.usda.gdpc.xml.AbstractXMLDocument
myProperties - Variable in class gov.usda.gdpc.AbstractDBElement: Defined properties for this database element
myProperty - Variable in class gov.usda.gdpc.AbstractFilterValue
myProperty - Variable in class gov.usda.gdpc.browser.GenericPropTableData
myProperty - Variable in class gov.usda.gdpc.browser.PropertiesTableData
myProperty - Variable in class gov.usda.gdpc.database.AbstractDatabaseMapping: Property associated with this database mapping
myRowList - Variable in class gov.usda.gdpc.xml.AbstractXMLDocument
myUID - Variable in class gov.usda.gdpc.database.AbstractJDBCConnection: The database user on whose behalf the connection is being made
myURL - Variable in class gov.usda.gdpc.database.AbstractJDBCConnection: The database url of the form jdbc:subprotocol:subname
myValue - Variable in class gov.usda.gdpc.browser.GenericPropTableData
myValue - Variable in class gov.usda.gdpc.browser.PropertiesTableData

N

NAME - Static variable in class gov.usda.gdpc.EnvironmentExperimentProperty: Name of environment experiment (data type: java.lang.String).
NAME - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: Name of genotype experiment (data type: java.lang.String).
NAME - Static variable in class gov.usda.gdpc.LocalityProperty: Name of locality (data type: java.lang.String).
NAME - Static variable in class gov.usda.gdpc.LocusProperty: Name of locus (data type: java.lang.String).
NAME - Static variable in class gov.usda.gdpc.PhenotypeOntologyProperty: Name of phenotype ontology (data type: java.lang.String).
NAME - Static variable in class gov.usda.gdpc.TaxonProperty: Name of taxon (data type: java.lang.String).
NAME - Static variable in class gov.usda.gdpc.xml.PropertyTag
Node - interface gov.usda.gdpc.gui.dbetree.Node.
NullDatabaseMapping - class gov.usda.gdpc.database.NullDatabaseMapping.
NullDatabaseMapping(Property) - Constructor for class gov.usda.gdpc.database.NullDatabaseMapping: NullDatabaseMapping Constructor.
next() - Method in class gov.usda.gdpc.util.ReadOnlyIterator: Returns the next element in the interation.
numColumns() - Method in class gov.usda.gdpc.util.AbstractTable: Returns number of columns in this table.
numColumns() - Method in class gov.usda.gdpc.util.GenericTable: Returns number of columns in this table.
numColumns() - Method in interface gov.usda.gdpc.util.Table: Returns number of columns in this table.
numConnections() - Method in class gov.usda.gdpc.browser.Browser
numElements() - Method in class gov.usda.gdpc.gui.GenericList: Returns the number of elements in this list.
numEnvironmentExperiments() - Method in class gov.usda.gdpc.AbstractPhenotypeGroup: Return the number of phenotype experiments.
numEnvironmentExperiments() - Method in interface gov.usda.gdpc.PhenotypeGroup: Return the number of environment experiments.
numGenotypeExperiments() - Method in class gov.usda.gdpc.AbstractGenotypeGroup: Return the number of genotype experiments.
numGenotypeExperiments() - Method in interface gov.usda.gdpc.GenotypeGroup: Return the number of genotype experiments.
numHints() - Method in class gov.usda.gdpc.Identifier: Returns the number of defined hints.
numProperties() - Method in class gov.usda.gdpc.AbstractDBElement: Returns the number of properties defined for this element.
numProperties() - Method in interface gov.usda.gdpc.DBElement: Returns the number of properties defined for this element.
numRows() - Method in class gov.usda.gdpc.util.AbstractTable: Returns number of rows in this table.
numRows() - Method in class gov.usda.gdpc.util.GenericTable: Returns number of rows in this table.
numRows() - Method in interface gov.usda.gdpc.util.Table: Returns number of rows in this table.
numTaxa() - Method in class gov.usda.gdpc.AbstractGenotypeGroup: Return the number of taxa.
numTaxa() - Method in class gov.usda.gdpc.AbstractPhenotypeGroup: Return the number of taxa.
numTaxa() - Method in interface gov.usda.gdpc.GenotypeGroup: Return the number of taxa.
numTaxa() - Method in interface gov.usda.gdpc.PhenotypeGroup: Return the number of taxa.

O

ONTOLOGY - Static variable in class gov.usda.gdpc.PhenotypeProperty: Ontology of phenotype (data type: gov.usda.gdpc.PhenotypeOntology).
ONTOLOGY - Variable in class gov.usda.gdpc.panzea.PanzeaCache
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.AlleleListDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.DBElementDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.DBElementsDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.DistinctDBElementDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.DistinctValueDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.FilterDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.GenericTableDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.GenericTableItemDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.GenericTableRowDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.GroupDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.IdentifierDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.LikeValueDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.PropertiesDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.PropertiesListDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.RangeValueDeserializer
onEndElement(String, String, DeserializationContext) - Method in class gov.usda.gdpc.axis.SingleValueDeserializer
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.AlleleListDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.DBElementDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.DBElementsDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.DistinctDBElementDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.DistinctValueDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.FilterDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.GenericTableDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.GenericTableItemDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.GenericTableRowDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.GroupDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.IdentifierDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.LikeValueDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.PropertiesDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.PropertiesListDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.RangeValueDeserializer: This method is invoked when an element start tag is encountered.
onStartChild(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.SingleValueDeserializer: This method is invoked when an element start tag is encountered.
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.AlleleListDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.DBElementDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.DBElementsDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.DistinctDBElementDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.DistinctValueDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.FilterDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.GenericTableDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.GenericTableItemDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.GenericTableRowDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.GroupDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.IdentifierDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.LikeValueDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.PropertiesDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.PropertiesListDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.RangeValueDeserializer
onStartElement(String, String, String, Attributes, DeserializationContext) - Method in class gov.usda.gdpc.axis.SingleValueDeserializer
openFile(File) - Method in class gov.usda.gdpc.browser.Browser
openUpdateWorkingTree(DBElementGroup) - Method in class gov.usda.gdpc.browser.DBElementPanel

P

PALUtil - class gov.usda.gdpc.pal.PALUtil.
PASSPORT - Static variable in class gov.usda.gdpc.panzea.PanzeaPropertyMap
PHENOTYPE - Static variable in class gov.usda.gdpc.panzea.PanzeaPropertyMap
PHENOTYPE - Static variable in class gov.usda.gdpc.xml.GDPCTag
PHENOTYPE_FILTER - Static variable in class gov.usda.gdpc.xml.GDPCTag
PHENOTYPE_GROUP - Static variable in class gov.usda.gdpc.xml.GDPCTag
PHENOTYPE_ONTOLOGY - Static variable in class gov.usda.gdpc.xml.GDPCTag
PHENOTYPE_ONTOLOGY_FILTER - Static variable in class gov.usda.gdpc.xml.GDPCTag
PHENOTYPE_ONTOLOGY_GROUP - Static variable in class gov.usda.gdpc.xml.GDPCTag
PHENOTYPE_PROPERTY - Static variable in class gov.usda.gdpc.xml.GDPCTag
PHENOTYPE_TAB - Static variable in class gov.usda.gdpc.browser.Browser
PHYSICAL_POSITION - Static variable in class gov.usda.gdpc.LocusProperty: Physical position of locus (data type: java.lang.String).
PHYSICAL_POSITION - Static variable in class gov.usda.gdpc.xml.PropertyTag
PLANT - Static variable in class gov.usda.gdpc.TaxonProperty: Plant of taxon (data type: java.lang.String).
PLANT - Static variable in class gov.usda.gdpc.xml.PropertyTag
PLANT_DATE - Static variable in class gov.usda.gdpc.EnvironmentExperimentProperty: Date crop planted (data type: gov.usda.gdpc.util.Calendar).
PLANT_DATE - Static variable in class gov.usda.gdpc.xml.PropertyTag
POLYEXP - Static variable in class gov.usda.gdpc.panzea.PanzeaPropertyMap
POLYMORPHISM - Static variable in class gov.usda.gdpc.panzea.PanzeaPropertyMap
POLY_INDEX - Static variable in class gov.usda.gdpc.panzea.PanzeaGenotypeExperimentDatabaseMapping
POLY_TYPE - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: Polymorphism Type associated with genotype experiment (data type: java.lang.String).
POPULATION - Static variable in class gov.usda.gdpc.TaxonProperty: Population of taxon (data type: java.lang.String).
POPULATION - Static variable in class gov.usda.gdpc.xml.PropertyTag
POUND_SIGN - Static variable in class gov.usda.gdpc.xml.AbstractXMLDocument
PRIMER1 - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: Primer 1 associated with genotype experiment (data type: java.lang.String).
PRIMER1 - Static variable in class gov.usda.gdpc.xml.PropertyTag
PRIMER2 - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: Primer 2 associated with genotype experiment (data type: java.lang.String).
PRIMER2 - Static variable in class gov.usda.gdpc.xml.PropertyTag
PRODUCER - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: Producer's name of this genotype experiment (data type: java.lang.String)
PROPERTIES - Static variable in class gov.usda.gdpc.xml.GDPCTag
PROPERTIES_LIST - Static variable in class gov.usda.gdpc.xml.GDPCTag
PROPERTY_DESC - Static variable in class gov.usda.gdpc.xml.GDPCTag
PROPERTY_TYPE - Static variable in class gov.usda.gdpc.EnvironmentExperimentProperty: The property type.
PROPERTY_TYPE - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: The property type.
PROPERTY_TYPE - Static variable in class gov.usda.gdpc.GenotypeProperty: The property type.
PROPERTY_TYPE - Static variable in class gov.usda.gdpc.LocalityProperty: The property type.
PROPERTY_TYPE - Static variable in class gov.usda.gdpc.LocusProperty: The property type.
PROPERTY_TYPE - Static variable in class gov.usda.gdpc.PhenotypeOntologyProperty: The property type.
PROPERTY_TYPE - Static variable in class gov.usda.gdpc.PhenotypeProperty: The property type.
PROPERTY_TYPE - Static variable in class gov.usda.gdpc.TaxonProperty: The property type.
PanzeaCache - class gov.usda.gdpc.panzea.PanzeaCache.
PanzeaCache(PanzeaDBConnection) - Constructor for class gov.usda.gdpc.panzea.PanzeaCache: Creates a new instance of PanzeaCache
PanzeaDBConnection - class gov.usda.gdpc.panzea.PanzeaDBConnection.
PanzeaDBConnection(String, String, String, String, String, String) - Constructor for class gov.usda.gdpc.panzea.PanzeaDBConnection: PanzeaDBConnection Constructor.
PanzeaDBConnection(String, String, String, String, String, char[]) - Constructor for class gov.usda.gdpc.panzea.PanzeaDBConnection: PanzeaDBConnection Constructor.
PanzeaDBConnection() - Constructor for class gov.usda.gdpc.panzea.PanzeaDBConnection
PanzeaGenotypeExperimentDatabaseMapping - class gov.usda.gdpc.panzea.PanzeaGenotypeExperimentDatabaseMapping.
PanzeaGenotypeExperimentDatabaseMapping(Property, String, String) - Constructor for class gov.usda.gdpc.panzea.PanzeaGenotypeExperimentDatabaseMapping: PanzeaGenotypeExperimentDatabaseMapping Constructor.
PanzeaLocalityDatabaseMapping - class gov.usda.gdpc.panzea.PanzeaLocalityDatabaseMapping.
PanzeaLocalityDatabaseMapping(Property, String, String, PanzeaDBConnection) - Constructor for class gov.usda.gdpc.panzea.PanzeaLocalityDatabaseMapping: PanzeaLocalityDatabaseMapping Constructor.
PanzeaLocusDatabaseMapping - class gov.usda.gdpc.panzea.PanzeaLocusDatabaseMapping.
PanzeaLocusDatabaseMapping(Property, String, String, PanzeaDBConnection) - Constructor for class gov.usda.gdpc.panzea.PanzeaLocusDatabaseMapping: PanzeaLocusDatabaseMapping Constructor.
PanzeaLocusTypeDatabaseMapping - class gov.usda.gdpc.panzea.PanzeaLocusTypeDatabaseMapping.
PanzeaLocusTypeDatabaseMapping(Property, String, String) - Constructor for class gov.usda.gdpc.panzea.PanzeaLocusTypeDatabaseMapping: PanzeaLocusTypeDatabaseMapping Constructor.
PanzeaOntologyDatabaseMapping - class gov.usda.gdpc.panzea.PanzeaOntologyDatabaseMapping.
PanzeaOntologyDatabaseMapping(Property, String, String, PanzeaDBConnection) - Constructor for class gov.usda.gdpc.panzea.PanzeaOntologyDatabaseMapping: PanzeaOntologyDatabaseMapping Constructor.
PanzeaPositionMinutesDatabaseMapping - class gov.usda.gdpc.panzea.PanzeaPositionMinutesDatabaseMapping.
PanzeaPositionMinutesDatabaseMapping(Property, String, String, String) - Constructor for class gov.usda.gdpc.panzea.PanzeaPositionMinutesDatabaseMapping: PanzeaPositionMinutesDatabaseMapping Constructor.
PanzeaPropertyMap - class gov.usda.gdpc.panzea.PanzeaPropertyMap.
PanzeaPropertyMap(PanzeaDBConnection) - Constructor for class gov.usda.gdpc.panzea.PanzeaPropertyMap: PanzeaPropertyMap Constructor.
Phenotype - class gov.usda.gdpc.Phenotype.: This is a database element representing a phenotype.
PhenotypeFilter - class gov.usda.gdpc.PhenotypeFilter.: This is a phenotype filter.
PhenotypeFilter() - Constructor for class gov.usda.gdpc.PhenotypeFilter: PhenotypeFilter constructor.
PhenotypeGroup - interface gov.usda.gdpc.PhenotypeGroup.: Group of phenotypes.
PhenotypeOntology - class gov.usda.gdpc.PhenotypeOntology.: This is a database element representing a phenotype ontology.
PhenotypeOntologyFilter - class gov.usda.gdpc.PhenotypeOntologyFilter.: This is a pheontype ontology filter.
PhenotypeOntologyFilter() - Constructor for class gov.usda.gdpc.PhenotypeOntologyFilter: PhenotypeOntologyFilter constructor.
PhenotypeOntologyGroup - interface gov.usda.gdpc.PhenotypeOntologyGroup.: Collection of phenotype ontologys.
PhenotypeOntologyProperty - class gov.usda.gdpc.PhenotypeOntologyProperty.: This follows the enum pattern and represents a phenotype ontology property.
PhenotypeOntologyProperty(String, String, String, String) - Constructor for class gov.usda.gdpc.PhenotypeOntologyProperty: PhenotypeOntologyProperty constructor.
PhenotypeOntologyProperty(String, Class, String, String) - Constructor for class gov.usda.gdpc.PhenotypeOntologyProperty: PhenotypeOntologyProperty constructor.
PhenotypeProperty - class gov.usda.gdpc.PhenotypeProperty.: This follows the enum pattern and represents a phenotype property.
PhenotypeProperty(String, String, String, String) - Constructor for class gov.usda.gdpc.PhenotypeProperty: PhenotypeProperty constructor.
PhenotypeProperty(String, Class, String, String) - Constructor for class gov.usda.gdpc.PhenotypeProperty: PhenotypeProperty constructor.
PhenotypeTable - class gov.usda.gdpc.PhenotypeTable.
PrintProperties - class gov.usda.gdpc.PrintProperties.
PrintProperties() - Constructor for class gov.usda.gdpc.PrintProperties: Creates a new instance of PrintProperties
Properties - interface gov.usda.gdpc.browser.Properties.
PropertiesDeserializer - class gov.usda.gdpc.axis.PropertiesDeserializer.
PropertiesDeserializer(GDPCTag) - Constructor for class gov.usda.gdpc.axis.PropertiesDeserializer: PropertiesDeserializer Constructor.
PropertiesListDeserializer - class gov.usda.gdpc.axis.PropertiesListDeserializer.
PropertiesListDeserializer() - Constructor for class gov.usda.gdpc.axis.PropertiesListDeserializer: PropertiesListDeserializer Constructor.
PropertiesListDeserializerFactory - class gov.usda.gdpc.axis.PropertiesListDeserializerFactory.
PropertiesListDeserializerFactory() - Constructor for class gov.usda.gdpc.axis.PropertiesListDeserializerFactory: PropertiesListDeserializerFactory Constructor.
PropertiesListSerializer - class gov.usda.gdpc.axis.PropertiesListSerializer.
PropertiesListSerializer() - Constructor for class gov.usda.gdpc.axis.PropertiesListSerializer: PropertiesListSerializer Constructor.
PropertiesListSerializerFactory - class gov.usda.gdpc.axis.PropertiesListSerializerFactory.
PropertiesListSerializerFactory() - Constructor for class gov.usda.gdpc.axis.PropertiesListSerializerFactory: PropertiesListSerializerFactory Constructor.
PropertiesTableData - class gov.usda.gdpc.browser.PropertiesTableData.
PropertiesTableData() - Constructor for class gov.usda.gdpc.browser.PropertiesTableData
PropertiesTableData(Property, Object, String) - Constructor for class gov.usda.gdpc.browser.PropertiesTableData
PropertiesTableModel - class gov.usda.gdpc.browser.PropertiesTableModel.
PropertiesTableModel() - Constructor for class gov.usda.gdpc.browser.PropertiesTableModel
Property - interface gov.usda.gdpc.Property.
PropertyCheckBox - class gov.usda.gdpc.browser.PropertyCheckBox.
PropertyCheckBox(FilterValuesPanel, Property, Browser) - Constructor for class gov.usda.gdpc.browser.PropertyCheckBox: PropertyCheckBox Constructor.
PropertyCheckBox(FilterValuesPanel, String, Property, Browser) - Constructor for class gov.usda.gdpc.browser.PropertyCheckBox: PropertyCheckBox Constructor.
PropertyCheckBoxListener - class gov.usda.gdpc.browser.PropertyCheckBoxListener.
PropertyCheckBoxListener(Property, FilterValuesPanel, JComponent, Browser) - Constructor for class gov.usda.gdpc.browser.PropertyCheckBoxListener: Creates a new instance of PropertyCheckBoxListener
PropertyLabeledList - class gov.usda.gdpc.browser.PropertyLabeledList.
PropertyLabeledList(Property, Vector) - Constructor for class gov.usda.gdpc.browser.PropertyLabeledList: PropertyLabeledList Constructor.
PropertyLabeledList(String, ListModel, Property) - Constructor for class gov.usda.gdpc.browser.PropertyLabeledList: PropertyLabeledList Constructor.
PropertyMap - interface gov.usda.gdpc.database.PropertyMap.: This is a collection of database mappings for database.
PropertyNode - class gov.usda.gdpc.gui.dbetree.PropertyNode.
PropertyNode(List, Node) - Constructor for class gov.usda.gdpc.gui.dbetree.PropertyNode: PropertyNode Constructor.
PropertyNode(Node) - Constructor for class gov.usda.gdpc.gui.dbetree.PropertyNode: PropertyNode Constructor.
PropertyTag - class gov.usda.gdpc.xml.PropertyTag.
PropertyTag(String, Class) - Constructor for class gov.usda.gdpc.xml.PropertyTag: PropertyTag Constructor.
properties() - Method in class gov.usda.gdpc.AbstractDBElement: Return list of properties defined for this database element.
properties() - Method in interface gov.usda.gdpc.DBElement: Return list of properties defined for this database element.
propsEqual(Map) - Method in class gov.usda.gdpc.AbstractDBElement: Returns whether given properties exactly match properties of this instance.
propsEqual(Map) - Method in interface gov.usda.gdpc.DBElement: Returns whether given properties exactly match properties of this instance.
put(Object, Object) - Method in class gov.usda.gdpc.AbstractDBElement: This operation is not supported.
putAll(Map) - Method in class gov.usda.gdpc.AbstractDBElement: This operation is not supported.

R

RANGE - Static variable in class gov.usda.gdpc.FilterValueType: Filter value which is a range consisting of a minimum and maximum value.
RANGE - Static variable in class gov.usda.gdpc.xml.GDPCTag
REFERENCE - Static variable in class gov.usda.gdpc.TaxonProperty: Reference for taxon (data type: java.lang.String).
REFERENCE - Static variable in class gov.usda.gdpc.xml.PropertyTag
RangeValueDeserializer - class gov.usda.gdpc.axis.RangeValueDeserializer.
RangeValueDeserializer(GDPCTag) - Constructor for class gov.usda.gdpc.axis.RangeValueDeserializer: RangeValueDeserializer Constructor.
ReadOnlyCollection - class gov.usda.gdpc.util.ReadOnlyCollection.
ReadOnlyCollection(Collection) - Constructor for class gov.usda.gdpc.util.ReadOnlyCollection: ReadOnlyCollection constructor.
ReadOnlyIterator - class gov.usda.gdpc.util.ReadOnlyIterator.: ReadOnlyIterator wraps the behavior of the Iterator Class to prevent ability to modify data.
ReadOnlyIterator(Iterator) - Constructor for class gov.usda.gdpc.util.ReadOnlyIterator: ReadOnlyIterator constructor.
ReadOnlyList - class gov.usda.gdpc.util.ReadOnlyList.
ReadOnlyList(List) - Constructor for class gov.usda.gdpc.util.ReadOnlyList: Creates a new instance of ReadOnlyList
ReadOnlySet - class gov.usda.gdpc.util.ReadOnlySet.
ReadOnlySet(Set) - Constructor for class gov.usda.gdpc.util.ReadOnlySet: ReadOnlySet constructor.
RemoveAllFromTreeAction - class gov.usda.gdpc.browser.RemoveAllFromTreeAction.
RemoveAllFromTreeAction(Browser, DBElementTree) - Constructor for class gov.usda.gdpc.browser.RemoveAllFromTreeAction: RemoveAllFromTreeAction Constructor.
RemoveDBConnectionAction - class gov.usda.gdpc.browser.RemoveDBConnectionAction.
RemoveDBConnectionAction(Browser, GenericList) - Constructor for class gov.usda.gdpc.browser.RemoveDBConnectionAction
RemoveFromTreeAction - class gov.usda.gdpc.browser.RemoveFromTreeAction.
RemoveFromTreeAction(Browser, DBElementTree) - Constructor for class gov.usda.gdpc.browser.RemoveFromTreeAction
RightArrowAction - class gov.usda.gdpc.browser.RightArrowAction.
RightArrowAction(Browser, DBElementTree, DBElementTree) - Constructor for class gov.usda.gdpc.browser.RightArrowAction
reSyncItems() - Method in class gov.usda.gdpc.gui.DBElementTree: ReSynchronize the list model for this tree.
refreshDistinctPanes() - Method in class gov.usda.gdpc.browser.FilterValuesPanel: Refreshes the distinct values of the panel if needed because of data source connection changes or added distinct property panes.
refreshDistinctPanes(Property[]) - Method in class gov.usda.gdpc.browser.FilterValuesPanel: This refreshes the distinct values for the given properties regardless of whether connections have changed.
refreshDistinctPanes(Property) - Method in class gov.usda.gdpc.browser.FilterValuesPanel: This refreshes the distinct values for the given property regardless of whether connections have changed.
remove(Object) - Method in class gov.usda.gdpc.AbstractDBElement: This operation is not supported.
remove(int) - Method in class gov.usda.gdpc.AbstractGroup: This operation is not supported.
remove(Object) - Method in class gov.usda.gdpc.AbstractGroup: This operation is not supported.
remove(Object) - Method in class gov.usda.gdpc.gui.DBElementTree: Removes given object from this tree.
remove(DBElement) - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: Removes all occurances of the given element from this tree.
remove(DBElement) - Method in class gov.usda.gdpc.gui.dbetree.HeadNode: Removes given element from this node down.
remove(ValueNode) - Method in class gov.usda.gdpc.gui.dbetree.HeadNode: Removes given value node from this node down.
remove(DBElement) - Method in interface gov.usda.gdpc.gui.dbetree.Node: Removes given element from this node down.
remove(DBElement) - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode: Removes given element from this node down.
remove(ValueNode) - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode: Removes given value node from this node down.
remove(DBElement) - Method in class gov.usda.gdpc.gui.dbetree.ValueNode: Removes given element from this node down.
remove(Object) - Method in class gov.usda.gdpc.util.ReadOnlyCollection
remove() - Method in class gov.usda.gdpc.util.ReadOnlyIterator: Remove operation is not supported by this iterator.
remove(Object) - Method in class gov.usda.gdpc.util.ReadOnlyList
remove(int) - Method in class gov.usda.gdpc.util.ReadOnlyList
remove(Object) - Method in class gov.usda.gdpc.util.ReadOnlySet
remove(Object) - Method in class gov.usda.gdpc.util.SortedList
remove(int) - Method in class gov.usda.gdpc.util.SortedList
remove(Object) - Method in class gov.usda.gdpc.util.TreeSetPlusNull
removeAll(Collection) - Method in class gov.usda.gdpc.AbstractGroup: This operation is not supported.
removeAll() - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: Removes all branches of this tree leaving only the root node.
removeAll() - Method in class gov.usda.gdpc.gui.dbetree.HeadNode: Removes all DBElements from this node down.
removeAll() - Method in interface gov.usda.gdpc.gui.dbetree.Node
removeAll() - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode: Removes all value nodes from this property node.
removeAll() - Method in class gov.usda.gdpc.gui.dbetree.ValueNode
removeAll(Collection) - Method in class gov.usda.gdpc.util.ReadOnlyCollection
removeAll(Collection) - Method in class gov.usda.gdpc.util.ReadOnlyList
removeAll(Collection) - Method in class gov.usda.gdpc.util.ReadOnlySet
removeAll(Collection) - Method in class gov.usda.gdpc.util.SortedList
removeAll(Collection) - Method in class gov.usda.gdpc.util.TreeSetPlusNull
removeAllNotify() - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: This notifies this model that all nodes have been removed.
removeConnection(DBConnection) - Method in class gov.usda.gdpc.browser.Browser
removeDBConnection(DBConnection) - Method in class gov.usda.gdpc.AbstractDBGateway: Removes the specified database connection from this gateway.
removeDBConnection(DBConnection) - Method in interface gov.usda.gdpc.DBGateway: Removes the specified database connection from this gateway.
removeDistinctProperty(Property) - Method in class gov.usda.gdpc.browser.FilterValuesPanel: Removes the distinct values panel for the given property.
removeElement(Object) - Method in class gov.usda.gdpc.gui.GenericList
removeInfo(Property) - Method in class gov.usda.gdpc.database.ExtraInfo: Removes extra information for the specified property.
removeNotify(TreeModelEvent) - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: This notifies this model that nodes have been removed.
removeNotify(TreeModelEvent) - Method in class gov.usda.gdpc.gui.dbetree.HeadNode
removeNotify(TreeModelEvent) - Method in interface gov.usda.gdpc.gui.dbetree.Node
removeNotify(TreeModelEvent) - Method in class gov.usda.gdpc.gui.dbetree.PropertyNode
removeNotify(TreeModelEvent) - Method in class gov.usda.gdpc.gui.dbetree.ValueNode
removeSelectedElements() - Method in class gov.usda.gdpc.gui.GenericList
removeTreeModelListener(TreeModelListener) - Method in class gov.usda.gdpc.gui.dbetree.DBElementTreeModel: Removes give listener from this model.
resetProperty(Property) - Method in class gov.usda.gdpc.AbstractFilter: Reset the specified property to have no values for this filter.
resetProperty(Property) - Method in class gov.usda.gdpc.DistinctPropertyValues: This removes all values for the specificed property.
resetProperty(Property) - Method in interface gov.usda.gdpc.Filter: Reset the specified property to have no values for this filter.
resetTable() - Method in class gov.usda.gdpc.browser.MatrixTableModel: Resets the table backing this matrix table model to an empty table.
retainAll(Collection) - Method in class gov.usda.gdpc.AbstractGroup: This operation is not supported.
retainAll(Collection) - Method in class gov.usda.gdpc.util.ReadOnlyCollection
retainAll(Collection) - Method in class gov.usda.gdpc.util.ReadOnlyList
retainAll(Collection) - Method in class gov.usda.gdpc.util.ReadOnlySet
retainAll(Collection) - Method in class gov.usda.gdpc.util.SortedList
retainAll(Collection) - Method in class gov.usda.gdpc.util.TreeSetPlusNull
run() - Method in class gov.usda.gdpc.browser.AddDBConnectionAction
run() - Method in class gov.usda.gdpc.browser.AddSOAPConnectionAction
run() - Method in class gov.usda.gdpc.browser.Browser
run() - Method in class gov.usda.gdpc.browser.DoubleArrowAction: Method executed when this thread starts that adds all items in filtered tree to the working tree.
run() - Method in class gov.usda.gdpc.browser.FilterValuesPanel
run() - Method in class gov.usda.gdpc.browser.RemoveAllFromTreeAction: Method executed when this thread starts that removes all items from the associated tree.
run() - Method in class gov.usda.gdpc.browser.RemoveFromTreeAction
run() - Method in class gov.usda.gdpc.browser.RightArrowAction
run() - Method in class gov.usda.gdpc.panzea.PanzeaCache: When an object implementing interface Runnable is used to create a thread, starting the thread causes the object's run method to be called in that separately executing thread.

S

SCHEMA_LOCATION_DEFINITION - Static variable in class gov.usda.gdpc.xml.GDPCConstants
SCORING_TECHNOLOGY - Static variable in class gov.usda.gdpc.xml.PropertyTag
SEED_LOT - Static variable in class gov.usda.gdpc.TaxonProperty: Seed lot of taxon (data type: java.lang.String).
SEED_LOT - Static variable in class gov.usda.gdpc.xml.PropertyTag
SINGLE - Static variable in class gov.usda.gdpc.xml.GDPCTag
SINGLE_VALUE - Static variable in class gov.usda.gdpc.FilterValueType: Filter value which is a single value.
SOURCE - Static variable in class gov.usda.gdpc.TaxonProperty: Source of taxon (data type: java.lang.String).
SOURCE - Static variable in class gov.usda.gdpc.xml.PropertyTag
SPECIES - Static variable in class gov.usda.gdpc.TaxonProperty: Species of taxon (data type: java.lang.String).
SPECIES - Static variable in class gov.usda.gdpc.xml.PropertyTag
SQLStatements - class gov.usda.gdpc.database.SQLStatements.
SQLStatements() - Constructor for class gov.usda.gdpc.database.SQLStatements: SQLStatements constructor.
SRC_EXP - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: Source experiment of this genotype experiment (data type: gov.usda.gdpc.GenotypeExperiment)
START_POSITION - Static variable in class gov.usda.gdpc.GenotypeExperimentProperty: Start Position associated with genotype experiment (data type: java.lang.String).
START_POSITION - Static variable in class gov.usda.gdpc.xml.PropertyTag
STATE_PROVINCE - Static variable in class gov.usda.gdpc.LocalityProperty: State or province of locality (data type: java.lang.String).
STATE_PROVINCE - Static variable in class gov.usda.gdpc.xml.PropertyTag
STRING - Static variable in class gov.usda.gdpc.Convert
SUBSPECIES - Static variable in class gov.usda.gdpc.TaxonProperty: Subspecies of taxon (data type: java.lang.String).
SUBSPECIES - Static variable in class gov.usda.gdpc.xml.PropertyTag
SUMMARY - Static variable in class gov.usda.gdpc.EnvironmentExperimentProperty: Summary of this environment experiment (data type: java.lang.String).
SimpleDatabaseMapping - class gov.usda.gdpc.database.SimpleDatabaseMapping.
SimpleDatabaseMapping(Property, String, String) - Constructor for class gov.usda.gdpc.database.SimpleDatabaseMapping: SimpleDatabaseMapping Constructor.
SingleValueDeserializer - class gov.usda.gdpc.axis.SingleValueDeserializer.
SingleValueDeserializer(GDPCTag) - Constructor for class gov.usda.gdpc.axis.SingleValueDeserializer: SingleValueDeserializer Constructor.
SortedList - class gov.usda.gdpc.util.SortedList.
SortedList() - Constructor for class gov.usda.gdpc.util.SortedList: SortedList Constructor.
StringDatabaseMapping - class gov.usda.gdpc.database.StringDatabaseMapping.
StringDatabaseMapping(Property, String, String) - Constructor for class gov.usda.gdpc.database.StringDatabaseMapping: StringDatabaseMapping Constructor.
StringToObjectDeserializer - class gov.usda.gdpc.axis.StringToObjectDeserializer.
StringToObjectDeserializer(Class, QName) - Constructor for class gov.usda.gdpc.axis.StringToObjectDeserializer: StringToObjectDeserializer Constructor.
saveAsFile(File) - Method in class gov.usda.gdpc.browser.Browser
saveAsFile(File) - Method in class gov.usda.gdpc.browser.DBElementPanel
selectAll() - Method in class gov.usda.gdpc.gui.GenericList: Selects everything in this list.
serialize(QName, Attributes, Object, SerializationContext) - Method in class gov.usda.gdpc.axis.DistinctValueSerializer: Serialize an element named name, with the indicated attributes and value.
serialize(QName, Attributes, Object, SerializationContext) - Method in class gov.usda.gdpc.axis.FilterSerializer: Serialize an element named name, with the indicated attributes and value.
serialize(QName, Attributes, Object, SerializationContext) - Method in class gov.usda.gdpc.axis.GDPCSerializer: Serialize an element named name, with the indicated attributes and value.
serialize(QName, Attributes, Object, SerializationContext) - Method in class gov.usda.gdpc.axis.GenericTableSerializer: Serialize an element named name, with the indicated attributes and value.
serialize(QName, Attributes, Object, SerializationContext) - Method in class gov.usda.gdpc.axis.PropertiesListSerializer: Serialize an element named name, with the indicated attributes and value.
serializeDBElement(DBElement, Attributes, SerializationContext, Map) - Static method in class gov.usda.gdpc.axis.GDPCSerializerUtil
serializeProperty(Property, Object, SerializationContext, Map) - Static method in class gov.usda.gdpc.axis.GDPCSerializerUtil
set(int, Object) - Method in class gov.usda.gdpc.AbstractGroup: This operation is not supported.
set(int, Object) - Method in class gov.usda.gdpc.util.ReadOnlyList
set(int, Object) - Method in class gov.usda.gdpc.util.SortedList: Unsupported Operation.
setChildValue(Object, Object) - Method in class gov.usda.gdpc.axis.AlleleListDeserializer
setChildValue(Object, Object) - Method in class gov.usda.gdpc.axis.DistinctDBElementDeserializer
setChildValue(Object, Object) - Method in class gov.usda.gdpc.axis.DistinctValueDeserializer
setChildValue(Object, Object) - Method in class gov.usda.gdpc.axis.FilterDeserializer
setChildValue(Object, Object) - Method in class gov.usda.gdpc.axis.GenericTableDeserializer
setChildValue(Object, Object) - Method in class gov.usda.gdpc.axis.GenericTableRowDeserializer
setChildValue(Object, Object) - Method in class gov.usda.gdpc.axis.IdentifierDeserializer
setChildValue(Object, Object) - Method in class gov.usda.gdpc.axis.LikeValueDeserializer
setChildValue(Object, Object) - Method in class gov.usda.gdpc.axis.PropertiesDeserializer
setChildValue(Object, Object) - Method in class gov.usda.gdpc.axis.RangeValueDeserializer
setChildValue(Object, Object) - Method in class gov.usda.gdpc.axis.SingleValueDeserializer
setDefaultData() - Method in class gov.usda.gdpc.browser.GenericPropTableModel
setDefaultData() - Method in class gov.usda.gdpc.browser.PropertiesTableModel
setHeadNode(List) - Method in class gov.usda.gdpc.gui.DBElementTree: Sets the head node of this tree with the new list of properties.
setIndex(int) - Method in class gov.usda.gdpc.database.AbstractDatabaseMappingIndex: Sets the index.
setIndex(int) - Method in interface gov.usda.gdpc.database.DatabaseMappingIndex: Sets the index.
setLinkedWorkFilter(boolean) - Method in class gov.usda.gdpc.browser.Browser
setLinkedWorkFilter(boolean) - Method in class gov.usda.gdpc.browser.DBElementPanel
setParent(DBElementTreeModel) - Method in class gov.usda.gdpc.gui.dbetree.HeadNode
setSelectedConnection(DBConnection) - Method in class gov.usda.gdpc.browser.DBConnectionsPanel
setValue(Object) - Method in class gov.usda.gdpc.axis.DBElementDeserializer
setValue(Object) - Method in class gov.usda.gdpc.axis.GenericTableItemDeserializer
setValue(Object) - Method in class gov.usda.gdpc.axis.GroupDeserializer
setValueAt(Object, int, int) - Method in class gov.usda.gdpc.browser.GenericPropTableModel
setValueAt(Object, int, int) - Method in class gov.usda.gdpc.browser.MatrixTableModel: No operation.
setValueAt(Object, int, int) - Method in class gov.usda.gdpc.browser.PropertiesTableModel
shortenStrLineLen(String, int) - Static method in class gov.usda.gdpc.util.Utils
showHourGlass(boolean) - Method in class gov.usda.gdpc.browser.Browser
size() - Method in class gov.usda.gdpc.AbstractDBElement: Returns the number of key-value mappings in this map.
size() - Method in class gov.usda.gdpc.AbstractGroup: Returns the number of elements in this collection.
size() - Method in class gov.usda.gdpc.AlleleList: Returns the number of elements in this collection.
size() - Method in class gov.usda.gdpc.database.SQLStatements: Returns the number of statements defined in this instance.
size() - Method in class gov.usda.gdpc.util.ReadOnlyCollection
size() - Method in class gov.usda.gdpc.util.ReadOnlyList
size() - Method in class gov.usda.gdpc.util.ReadOnlySet
size() - Method in class gov.usda.gdpc.util.SortedList: Returns size of this list.
size() - Method in class gov.usda.gdpc.util.TreeSetPlusNull
subList(int, int) - Method in class gov.usda.gdpc.AbstractGroup: Returns a view of the portion of this list between the specified fromIndex, inclusive, and toIndex, exclusive.
subList(int, int) - Method in class gov.usda.gdpc.util.ReadOnlyList
subList(int, int) - Method in class gov.usda.gdpc.util.SortedList

T

TAXA - Variable in class gov.usda.gdpc.panzea.PanzeaCache
TAXON - Static variable in class gov.usda.gdpc.GenotypeProperty: Taxon of genotype (data type: gov.usda.gdpc.Taxon).
TAXON - Static variable in class gov.usda.gdpc.PhenotypeProperty: Taxon of phenotype (data type: gov.usda.gdpc.Taxon).
TAXON - Static variable in class gov.usda.gdpc.xml.GDPCTag
TAXON_FILTER - Static variable in class gov.usda.gdpc.xml.GDPCTag
TAXON_GROUP - Static variable in class gov.usda.gdpc.xml.GDPCTag
TAXON_PROPERTY - Static variable in class gov.usda.gdpc.xml.GDPCTag
TAXON_TAB - Static variable in class gov.usda.gdpc.browser.Browser
TEXT - Static variable in class gov.usda.gdpc.browser.AboutAction
TEXT - Static variable in class gov.usda.gdpc.browser.AddDBConnectionAction
TEXT - Static variable in class gov.usda.gdpc.browser.AddSOAPConnectionAction
TEXT - Static variable in class gov.usda.gdpc.browser.DeselectAction
TEXT - Static variable in class gov.usda.gdpc.browser.DoubleArrowAction
TEXT - Static variable in class gov.usda.gdpc.browser.ExitAction
TEXT - Static variable in class gov.usda.gdpc.browser.GetStartedAction
TEXT - Static variable in class gov.usda.gdpc.browser.HelpAction
TEXT - Static variable in class gov.usda.gdpc.browser.RemoveAllFromTreeAction
TEXT - Static variable in class gov.usda.gdpc.browser.RemoveFromTreeAction
TEXT - Static variable in class gov.usda.gdpc.browser.RightArrowAction
TEXT - Static variable in class gov.usda.gdpc.browser.