A B C D E F G H I J K L M N O P Q R S T U V W

A

AbstractAuditEntityHandler<T> - Class in gov.nih.nci.caarray.util.audit
 
AbstractAuditEntityHandler(CaArrayAuditLogProcessor) - Constructor for class gov.nih.nci.caarray.util.audit.AbstractAuditEntityHandler
 
AbstractCaArrayEntity - Class in gov.nih.nci.caarray.external.v1_0
AbstractCaArrayEntity is the base class for objects in the caArray external model that can be dereferenced.
AbstractCaArrayEntity() - Constructor for class gov.nih.nci.caarray.external.v1_0.AbstractCaArrayEntity
 
AbstractCaArrayServer - Class in gov.nih.nci.caarray.services
 
AbstractCaArrayServer(String, int) - Constructor for class gov.nih.nci.caarray.services.AbstractCaArrayServer
Creates a new instance configured to attach to the provided hostname and port.
AbstractCaArrayServer(String) - Constructor for class gov.nih.nci.caarray.services.AbstractCaArrayServer
Creates a new instance configured to attach to the provided JNDI url.
AbstractDataColumn - Class in gov.nih.nci.caarray.external.v1_0.data
An AbstractDataColumn represents a list of values for a particular measurement within a hybridization data set.
AbstractDataColumn() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.AbstractDataColumn
 
AbstractExperimentGraphNode - Class in gov.nih.nci.caarray.external.v1_0.sample
AbstractExperimentGraphNode represents a node within the sample-data relationship graph describing the structure of a microarray experiment.
AbstractExperimentGraphNode() - Constructor for class gov.nih.nci.caarray.external.v1_0.sample.AbstractExperimentGraphNode
 
AbstractOntologyOwlParser - Class in gov.nih.nci.caarray.util.owlparser
Base class for parsing an ontology description in OWL format.
AbstractOntologyOwlParser(String, String) - Constructor for class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
Create an ontology parser that will parse an ontology OWL file for a term source with given name and url.
AbstractValue - Class in gov.nih.nci.caarray.external.v1_0.value
Base class for values of characteristics and factor values.
AbstractValue() - Constructor for class gov.nih.nci.caarray.external.v1_0.value.AbstractValue
 
AccessProfileHandler - Class in gov.nih.nci.caarray.util.audit
 
AccessProfileHandler(CaArrayAuditLogProcessor) - Constructor for class gov.nih.nci.caarray.util.audit.AccessProfileHandler
 
addDetail(AuditLogRecord, String, String) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogProcessor
Add audit log detail entry.
addDetail(AuditLogRecord, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogProcessor
Add audit log detail entry.
addExperimentDetail(AuditLogRecord, String, Project) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogProcessor
Add audit log detail entry for an experiment header.
addProjectSecurity(AuditLogRecord, Project, Long) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogProcessor
Add project security access for an audit log record.
afterTransactionCompletion(Transaction) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
AnnotationColumn - Class in gov.nih.nci.caarray.external.v1_0.sample
An AnnotationColumn represents a column of AnnotationValueSets for a particular experiment graph node, with one AnnotationValueSet for each category in the parent AnnotationSet.
AnnotationColumn() - Constructor for class gov.nih.nci.caarray.external.v1_0.sample.AnnotationColumn
 
AnnotationCriterion - Class in gov.nih.nci.caarray.external.v1_0.query
An AnnotationCriterion specifies a criterion that matches Characteristics having the referenced category and given value.
AnnotationCriterion() - Constructor for class gov.nih.nci.caarray.external.v1_0.query.AnnotationCriterion
No-arg constructor.
AnnotationCriterion(CaArrayEntityReference, String) - Constructor for class gov.nih.nci.caarray.external.v1_0.query.AnnotationCriterion
Constructor for AnnotationCriterion with given category and value.
AnnotationSet - Class in gov.nih.nci.caarray.external.v1_0.sample
An AnnotationSet represents a table of annotation values for a particular list of characteristics across a list of experiment graph nodes.
AnnotationSet() - Constructor for class gov.nih.nci.caarray.external.v1_0.sample.AnnotationSet
 
AnnotationSetRequest - Class in gov.nih.nci.caarray.external.v1_0.query
 
AnnotationSetRequest() - Constructor for class gov.nih.nci.caarray.external.v1_0.query.AnnotationSetRequest
 
AnnotationValueSet - Class in gov.nih.nci.caarray.external.v1_0.sample
An AnnotationValueSet contains the set of values for a given category.
AnnotationValueSet() - Constructor for class gov.nih.nci.caarray.external.v1_0.sample.AnnotationValueSet
 
ApiException - Exception in gov.nih.nci.caarray.services.external.v1_0
Base class for exceptions for the External API.
ApiException - Exception in gov.nih.nci.caarray.services.external.v1_0
Base class for exceptions for the External API.
ApiException() - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.ApiException
Constructor for no message.
ApiException(String) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.ApiException
Constructor with message.
ApiException() - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.ApiException
Constructor for no message.
ApiException(String) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.ApiException
Constructor with message.
ArrayDataHandler - Class in gov.nih.nci.caarray.util.audit
 
ArrayDataHandler(CaArrayAuditLogProcessor) - Constructor for class gov.nih.nci.caarray.util.audit.ArrayDataHandler
 
ArrayDataType - Class in gov.nih.nci.caarray.external.v1_0.data
ArrayDataType represents a type of array.
ArrayDataType() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.ArrayDataType
 
ArrayDesign - Class in gov.nih.nci.caarray.external.v1_0.array
ArrayDesign describes a particular array model.
ArrayDesign() - Constructor for class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
ArrayDesignHandler - Class in gov.nih.nci.caarray.util.audit
 
ArrayDesignHandler(CaArrayAuditLogProcessor) - Constructor for class gov.nih.nci.caarray.util.audit.ArrayDesignHandler
 
ArrayProvider - Class in gov.nih.nci.caarray.external.v1_0.array
An ArrayProvider represents a provider (manufacturer) of microarrays.
ArrayProvider() - Constructor for class gov.nih.nci.caarray.external.v1_0.array.ArrayProvider
Default constructor, for use by tooling.
ArrayProvider(String) - Constructor for class gov.nih.nci.caarray.external.v1_0.array.ArrayProvider
Create a new array provider with given name.
AssayType - Class in gov.nih.nci.caarray.external.v1_0.array
AssayType represents kinds of assays (measurements) that can be run on biomaterials hybridized to microarrays.
AssayType() - Constructor for class gov.nih.nci.caarray.external.v1_0.array.AssayType
Default constructor, for tooling use.
AssayType(String) - Constructor for class gov.nih.nci.caarray.external.v1_0.array.AssayType
Create a new assay type with given name.
assemble(Serializable, Object) - Method in class gov.nih.nci.caarray.util.URIUserType
authorizeEnumerateBiomaterials(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeEnumerateBiomaterialsByKeyword(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeEnumerateByExample(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeEnumerateExperiments(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeEnumerateExperimentsByKeyword(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeEnumerateFiles(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeEnumerateHybridizations(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeGetAllCharacteristicCategories(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeGetAllPrincipalInvestigators(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeGetAnnotationSet(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeGetDataSet(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeGetFileContentsTransfer(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeGetMageTabExport(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeGetMultipleResourceProperties(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeGetResourceProperty(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeGetServiceSecurityMetadata(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeGetServiceSecurityMetadata(Subject, MessageContext, QName) - Method in class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 
authorizeGetStatusOp(Subject, MessageContext, QName) - Method in class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 
authorizeGetTermsForCategory(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizePullOp(Subject, MessageContext, QName) - Method in class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 
authorizeQueryResourceProperties(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeReleaseOp(Subject, MessageContext, QName) - Method in class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 
authorizeRenewOp(Subject, MessageContext, QName) - Method in class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 
authorizeSearchByExample(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeSearchForBiomaterials(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeSearchForBiomaterialsByKeyword(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeSearchForExperiments(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeSearchForExperimentsByKeyword(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeSearchForFiles(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeSearchForHybridizations(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
authorizeSearchForQuantitationTypes(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 

B

BaseV1_0ExternalService - Class in gov.nih.nci.caarray.services.external.v1_0.impl
Base service for v1_0 external services.
BaseV1_0ExternalService() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService
Constructor.
BaseV1_0ExternalService.EntityHandler<T extends AbstractCaArrayEntity> - Interface in gov.nih.nci.caarray.services.external.v1_0.impl
An external entity handler encapsulates the logic to perform generic operations for an external entity type.
BaseV1_0ExternalService.EntityHandlerRegistry - Class in gov.nih.nci.caarray.services.external.v1_0.impl
Class to hold a registry of entity handlers, which can be looked up by class of external entity.
BaseV1_0ExternalService.EntityHandlerRegistry() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService.EntityHandlerRegistry
 
beginTransaction() - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
Starts a transaction on the current Hibernate session.
beginTransaction() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
Starts a transaction on the current Hibernate session.
bindPropertiesAsNamed(String, Binder) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Load a properties file from given classpath resource, and create a constant binding to @Named(key) for each property using the given binder.
Biomaterial - Class in gov.nih.nci.caarray.external.v1_0.sample
Biomaterial is an experiment graph node which corresponds to a biomaterial at some stage prior to being hybridized with the array.
Biomaterial() - Constructor for class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
BIOMATERIAL_TYPE_TO_CLASS_MAP - Static variable in class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService
Map of BiomaterialType to the corresponding AbstractBiomaterial subclass in the internal model.
BiomaterialKeywordSearchCriteria - Class in gov.nih.nci.caarray.external.v1_0.query
 
BiomaterialKeywordSearchCriteria() - Constructor for class gov.nih.nci.caarray.external.v1_0.query.BiomaterialKeywordSearchCriteria
 
BiomaterialSearchCriteria - Class in gov.nih.nci.caarray.external.v1_0.query
A BiomaterialSearchCriteria specifies a set of criterions against which Biomaterials are matched.
BiomaterialSearchCriteria() - Constructor for class gov.nih.nci.caarray.external.v1_0.query.BiomaterialSearchCriteria
 
BiomaterialType - Enum in gov.nih.nci.caarray.external.v1_0.sample
BiomaterialType contains constants representing different types of Biomaterials.
BiomaterialTypeFieldHandler - Class in gov.nih.nci.caarray.services.external.v1_0.grid.common
 
BiomaterialTypeFieldHandler() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.common.BiomaterialTypeFieldHandler
 
blankStringPropsToNull(Object) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
For each String bean property on o, if o is blank or empty, converts that property to null.
BooleanColumn - Class in gov.nih.nci.caarray.external.v1_0.data
A BooleanColumn represents a data column with boolean values.
BooleanColumn() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.BooleanColumn
 
buildInClauses(List<? extends Serializable>, String, Map<String, List<? extends Serializable>>) - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
Break up a list of items into separate in clauses, to avoid limits imposed by databases or by Hibernate bug http://opensource.atlassian.com/projects/hibernate/browse/HHH-2166.
buildInClauses(List<? extends Serializable>, String, Map<String, List<? extends Serializable>>) - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperImpl
Break up a list of items into separate in clauses, to avoid limits imposed by databases or by Hibernate bug http://opensource.atlassian.com/projects/hibernate/browse/HHH-2166.
buildInClauses(List<? extends Serializable>, String, Map<String, List<? extends Serializable>>) - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
Break up a list of items into separate in clauses, to avoid limits imposed by databases or by Hibernate bug http://opensource.atlassian.com/projects/hibernate/browse/HHH-2166.

C

CaArrayAuditLogInterceptor - Class in gov.nih.nci.caarray.util
Interceptor that adds audit log records for audits.
CaArrayAuditLogInterceptor(HibernateHelper) - Constructor for class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
 
CaArrayAuditLogInterceptor() - Constructor for class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
default ctor.
CaArrayAuditLogProcessor - Class in gov.nih.nci.caarray.util
 
CaArrayEntityReference - Class in gov.nih.nci.caarray.external.v1_0
CaArrayEntityReference encapsulates an external id identifying an entity that can be retrieved via the API.
CaArrayEntityReference() - Constructor for class gov.nih.nci.caarray.external.v1_0.CaArrayEntityReference
Empty constructor, for use by tooling.
CaArrayEntityReference(String) - Constructor for class gov.nih.nci.caarray.external.v1_0.CaArrayEntityReference
Create a new CaArrayEntityReference with given id.
CaArrayFileHandler - Class in gov.nih.nci.caarray.util.audit
 
CaArrayFileHandler(CaArrayAuditLogProcessor) - Constructor for class gov.nih.nci.caarray.util.audit.CaArrayFileHandler
 
CaArrayHibernateHelper - Interface in gov.nih.nci.caarray.util
 
CaArrayHibernateHelperFactory - Class in gov.nih.nci.caarray.util
 
CaArrayHibernateHelperImpl - Class in gov.nih.nci.caarray.util
Utility class to create and retrieve Hibernate sessions.
CaArrayHibernateHelperModule - Class in gov.nih.nci.caarray.util
 
CaArrayHibernateHelperModule() - Constructor for class gov.nih.nci.caarray.util.CaArrayHibernateHelperModule
 
CaArrayHibernateHelperUnsupportedOperationImpl - Class in gov.nih.nci.caarray.util
Throws UnsupportedOperationException for all CaArrayHibernateHelper functions.
CaArrayHibernateHelperUnsupportedOperationImpl() - Constructor for class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
 
CaarrayInnoDBDialect - Class in gov.nih.nci.caarray.util
A hack: hibernate has a bug in parsing the Filter clauses with subselects where it unnecessarily prepends table qualifications to identifiers.
CaarrayInnoDBDialect() - Constructor for class gov.nih.nci.caarray.util.CaarrayInnoDBDialect
Create a new dialect.
CaArrayServer - Class in gov.nih.nci.caarray.services
Client-side representation of a caArray server, used to connect to and access a remote server.
CaArrayServer(String, int) - Constructor for class gov.nih.nci.caarray.services.CaArrayServer
Creates a new instance configured to attach to the provided hostname and port.
CaArrayServer - Class in gov.nih.nci.caarray.services.external.v1_0
Client-side representation of a caArray server, used to connect to and access a remote server.
CaArrayServer(String, int) - Constructor for class gov.nih.nci.caarray.services.external.v1_0.CaArrayServer
Creates a new instance configured to attach to the provided hostname and port.
CaArrayServer(String) - Constructor for class gov.nih.nci.caarray.services.external.v1_0.CaArrayServer
Creates a new instance configured to attach to the provided JNDI url.
CaArraySvc_v1_0Authorization - Class in gov.nih.nci.caarray.services.external.v1_0.grid.service.globus
DO NOT EDIT: This class is autogenerated! This is a PDP for use with the globus authorization callout.
CaArraySvc_v1_0Authorization() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
CaArraySvc_v1_0Client - Class in gov.nih.nci.caarray.services.external.v1_0.grid.client
This class is autogenerated, DO NOT EDIT GENERATED GRID SERVICE ACCESS METHODS.
CaArraySvc_v1_0Client(String) - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
CaArraySvc_v1_0Client(String, GlobusCredential) - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
CaArraySvc_v1_0Client(EndpointReferenceType) - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
CaArraySvc_v1_0Client(EndpointReferenceType, GlobusCredential) - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
CaArraySvc_v1_0ClientBase - Class in gov.nih.nci.caarray.services.external.v1_0.grid.client
This class is autogenerated, DO NOT EDIT GENERATED GRID SERVICE ACCESS METHODS.
CaArraySvc_v1_0ClientBase(String, GlobusCredential) - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0ClientBase
 
CaArraySvc_v1_0ClientBase(EndpointReferenceType, GlobusCredential) - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0ClientBase
 
CaArraySvc_v1_0Configuration - Class in gov.nih.nci.caarray.services.external.v1_0.grid.service
DO NOT EDIT: This class is autogenerated! This class holds all service properties which were defined for the service to have access to.
CaArraySvc_v1_0Configuration() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Configuration
 
CaArraySvc_v1_0Constants - Interface in gov.nih.nci.caarray.services.external.v1_0.grid.common
Constants class that extends the introduce managed constants.
CaArraySvc_v1_0ConstantsBase - Interface in gov.nih.nci.caarray.services.external.v1_0.grid.common
This class is autogenerated, DO NOT EDIT
CaArraySvc_v1_0I - Interface in gov.nih.nci.caarray.services.external.v1_0.grid.common
This class is autogenerated, DO NOT EDIT.
CaArraySvc_v1_0Impl - Class in gov.nih.nci.caarray.services.external.v1_0.grid.service
Implementation of the v1.0 of the CaArray grid service
CaArraySvc_v1_0Impl() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
CaArraySvc_v1_0ImplBase - Class in gov.nih.nci.caarray.services.external.v1_0.grid.service
DO NOT EDIT: This class is autogenerated! Provides some simple accessors for the Impl.
CaArraySvc_v1_0ImplBase() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0ImplBase
 
CaArraySvc_v1_0ProviderImpl - Class in gov.nih.nci.caarray.services.external.v1_0.grid.service.globus
DO NOT EDIT: This class is autogenerated! This class implements each method in the portType of the service.
CaArraySvc_v1_0ProviderImpl() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
CaArraySvc_v1_0Resource - Class in gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource
The implementation of this CaArraySvc_v1_0Resource type.
CaArraySvc_v1_0Resource() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0Resource
 
CaArraySvc_v1_0ResourceBase - Class in gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource
DO NOT EDIT: This class is autogenerated! This class is the base class of the resource type created for this service.
CaArraySvc_v1_0ResourceBase() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceBase
 
CaArraySvc_v1_0ResourceConfiguration - Class in gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource
DO NOT EDIT: This class is autogenerated! This class is used by the resource to get configuration information about the resource.
CaArraySvc_v1_0ResourceConfiguration() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceConfiguration
 
CaArraySvc_v1_0ResourceHome - Class in gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource
DO NOT EDIT: This class is autogenerated! This class implements the resource home for the resource type represented by this service.
CaArraySvc_v1_0ResourceHome() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceHome
 
CaArrayUsernameHolder - Class in gov.nih.nci.caarray.util
Holds the name of the currently-logged in user in a ThreadLocal.
CaArrayUtils - Class in gov.nih.nci.caarray.util
Utility classes for our project.
CaGridEnumerationAuthorization - Class in gov.nih.nci.cagrid.enumeration.service.globus
DO NOT EDIT: This class is autogenerated! This is a PDP for use with the globus authorization callout.
CaGridEnumerationAuthorization() - Constructor for class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 
CaGridEnumerationClient - Class in gov.nih.nci.cagrid.enumeration.client
This class is autogenerated, DO NOT EDIT GENERATED GRID SERVICE ACCESS METHODS.
CaGridEnumerationClient(String) - Constructor for class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClient
 
CaGridEnumerationClient(String, GlobusCredential) - Constructor for class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClient
 
CaGridEnumerationClient(EndpointReferenceType) - Constructor for class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClient
 
CaGridEnumerationClient(EndpointReferenceType, GlobusCredential) - Constructor for class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClient
 
CaGridEnumerationClientBase - Class in gov.nih.nci.cagrid.enumeration.client
This class is autogenerated, DO NOT EDIT GENERATED GRID SERVICE ACCESS METHODS.
CaGridEnumerationClientBase(String, GlobusCredential) - Constructor for class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClientBase
 
CaGridEnumerationClientBase(EndpointReferenceType, GlobusCredential) - Constructor for class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClientBase
 
CaGridEnumerationConstants - Interface in gov.nih.nci.cagrid.enumeration.common
Constants class that extends the introduce managed constants.
CaGridEnumerationConstantsBase - Interface in gov.nih.nci.cagrid.enumeration.common
This class is autogenerated, DO NOT EDIT
CaGridEnumerationI - Interface in gov.nih.nci.cagrid.enumeration.common
This class is autogenerated, DO NOT EDIT.
CaGridEnumerationImpl - Class in gov.nih.nci.cagrid.enumeration.service
TODO:I am the service side implementation class.
CaGridEnumerationImpl() - Constructor for class gov.nih.nci.cagrid.enumeration.service.CaGridEnumerationImpl
 
CaGridEnumerationImplBase - Class in gov.nih.nci.cagrid.enumeration.service
DO NOT EDIT: This class is autogenerated! Provides some simple accessors for the Impl.
CaGridEnumerationImplBase() - Constructor for class gov.nih.nci.cagrid.enumeration.service.CaGridEnumerationImplBase
 
CaGridEnumerationProviderImpl - Class in gov.nih.nci.cagrid.enumeration.service.globus
DO NOT EDIT: This class is autogenerated! This class implements each method in the portType of the service.
CaGridEnumerationProviderImpl() - Constructor for class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationProviderImpl
 
CASE_INSENSITIVE_ORDER - Static variable in class gov.nih.nci.caarray.util.LabelValue
Comparator that can be used for a case insensitive sort of LabelValue objects.
Category - Class in gov.nih.nci.caarray.external.v1_0.vocabulary
A Category represents a class of values in a controlled vocabulary / ontology.
Category() - Constructor for class gov.nih.nci.caarray.external.v1_0.vocabulary.Category
 
Characteristic - Class in gov.nih.nci.caarray.external.v1_0.sample
Characteristic represents a loosely typed attribute associated with a sample.
Characteristic() - Constructor for class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
 
checkFileExists(File) - Static method in class gov.nih.nci.caarray.util.io.FileUtility
Simple file argument checker to check that a file is not null and exists.
checkFileExists(FileRef) - Static method in class gov.nih.nci.caarray.util.io.FileUtility
Simple file argument checker to check that a file is not null and exists.
classToTableName(String) - Method in class gov.nih.nci.caarray.util.NamingStrategy
close() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
close() - Method in class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 
CollaboratorGroupHandler - Class in gov.nih.nci.caarray.util.audit
 
CollaboratorGroupHandler(CaArrayAuditLogProcessor) - Constructor for class gov.nih.nci.caarray.util.audit.CollaboratorGroupHandler
 
collectionTableName(String, String, String, String, String) - Method in class gov.nih.nci.caarray.util.NamingStrategy
columnName(String) - Method in class gov.nih.nci.caarray.util.NamingStrategy
compareTo(Object) - Method in class gov.nih.nci.caarray.util.LabelValue
Compare LabelValueBeans based on the label, because that's the human viewable part of the object.
configuration - Static variable in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Configuration
 
configure() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperModule
configure() - Method in class gov.nih.nci.caarray.util.UsernameHolderModule
connect() - Method in class gov.nih.nci.caarray.services.AbstractCaArrayServer
Starts a new session with this server for an anonymous (unauthenticated) user.
connect(String, String) - Method in class gov.nih.nci.caarray.services.AbstractCaArrayServer
Starts a new session with this server.
consumer - Variable in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0ClientBase
 
consumer - Variable in class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClientBase
 
consumerEPR - Variable in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0ClientBase
 
consumerEPR - Variable in class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClientBase
 
copyFileContentsToOutputStream(CaArrayEntityReference, boolean, OutputStream) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.GridDataApiUtils
copyFileContentsZipToOutputStream(Iterable<CaArrayEntityReference>, OutputStream) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.GridDataApiUtils
create() - Static method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperImpl
 
createPortType() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0ClientBase
 
createPortType() - Method in class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClientBase
 
createReflectionHelper(Class<?>) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
For given class, returns a ReflectionHelper instance with property accessors for the class.
createSingleton() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceHome
 

D

DataService - Interface in gov.nih.nci.caarray.services.external.v1_0.data
Remote service for retrieving file and parsed data.
DataSet - Class in gov.nih.nci.caarray.external.v1_0.data
A DataSet represents the collection of data across several hybridizations for a particular set of quantities (QuantitationTypes) and design elements.
DataSet() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.DataSet
 
DataSetRequest - Class in gov.nih.nci.caarray.external.v1_0.query
 
DataSetRequest() - Constructor for class gov.nih.nci.caarray.external.v1_0.query.DataSetRequest
 
DataTransferException - Exception in gov.nih.nci.caarray.services.external.v1_0.data
Exception thrown to indicate that there was an issue with transferring data over the remote connection.
DataTransferException(String) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.data.DataTransferException
Constructor for no cause.
DataType - Enum in gov.nih.nci.caarray.external.v1_0.data
DataType is an enumeration of the possible value types that a single value of a data column may have.
DataTypeFieldHandler - Class in gov.nih.nci.caarray.services.external.v1_0.grid.common
 
DataTypeFieldHandler() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.common.DataTypeFieldHandler
 
deepCopy(Object) - Method in class gov.nih.nci.caarray.util.URIUserType
dequoteString(String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Removes matched quotes (single or double) from a string.
deserialize(byte[]) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Deserializes an object from a gzipped serialized representation.
deserialize(InputStream) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Deserializes an object from a gzipped serialized representation.
DesignElement - Class in gov.nih.nci.caarray.external.v1_0.data
A DesignElement represents a single unit within an array for which measurements can be captured.
DesignElement() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.DesignElement
 
disableFilters() - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
Disable security filters on the current session.
disableFilters() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperImpl
Disable security filters on the current session.
disableFilters() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
Disable security filters on the current session.
disassemble(Object) - Method in class gov.nih.nci.caarray.util.URIUserType
DoubleColumn - Class in gov.nih.nci.caarray.external.v1_0.data
A DoubleColumn represents a data column with double values.
DoubleColumn() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.DoubleColumn
 
doUnfiltered(UnfilteredCallback) - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
Do something in an unfiltered session.
doUnfiltered(UnfilteredCallback) - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperImpl
Do something in an unfiltered session.
doUnfiltered(UnfilteredCallback) - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
Do something in an unfiltered session.
doUnfiltered(Session) - Method in interface gov.nih.nci.caarray.util.UnfilteredCallback
Do something with an unfiltered session.
downloadFileContentsToDir(Iterable<CaArrayEntityReference>, File) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.GridDataApiUtils

E

EmailUtil - Class in gov.nih.nci.caarray.util
Utility class that sends emails.
emptyCollectionOrMapFor(Class<?>) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Returns an empty collection or map of the appropriate type for a given collection class.
enumerateBiomaterials(BiomaterialSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
enumerateBiomaterials(BiomaterialSearchCriteria) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
 
enumerateBiomaterials(BiomaterialSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
enumerateBiomaterials(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.EnumerateBiomaterialsRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
enumerateBiomaterialsByKeyword(BiomaterialKeywordSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
enumerateBiomaterialsByKeyword(BiomaterialKeywordSearchCriteria) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
 
enumerateBiomaterialsByKeyword(BiomaterialKeywordSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
enumerateBiomaterialsByKeyword(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.EnumerateBiomaterialsByKeywordRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
enumerateByExample(ExampleSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
enumerateByExample(ExampleSearchCriteria) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
 
enumerateByExample(ExampleSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
enumerateByExample(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.EnumerateByExampleRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
enumerateExperiments(ExperimentSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
enumerateExperiments(ExperimentSearchCriteria) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
Begin an enumeration of experiments matching given criteria
enumerateExperiments(ExperimentSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
enumerateExperiments(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.EnumerateExperimentsRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
enumerateExperimentsByKeyword(KeywordSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
enumerateExperimentsByKeyword(KeywordSearchCriteria) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
 
enumerateExperimentsByKeyword(KeywordSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
enumerateExperimentsByKeyword(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.EnumerateExperimentsByKeywordRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
enumerateFiles(FileSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
enumerateFiles(FileSearchCriteria) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
 
enumerateFiles(FileSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
enumerateFiles(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.EnumerateFilesRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
enumerateHybridizations(HybridizationSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
enumerateHybridizations(HybridizationSearchCriteria) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
 
enumerateHybridizations(HybridizationSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
enumerateHybridizations(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.EnumerateHybridizationsRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
equals(Object) - Method in class gov.nih.nci.caarray.external.v1_0.AbstractCaArrayEntity
Id properties are used to test for euality, if they are not null; otherwise, the other properties are used.
equals(Object) - Method in class gov.nih.nci.caarray.external.v1_0.CaArrayEntityReference
equals(Object) - Method in class gov.nih.nci.caarray.external.v1_0.data.AbstractDataColumn
equals(Object) - Method in class gov.nih.nci.caarray.external.v1_0.data.FileMetadata
equals(Object) - Method in class gov.nih.nci.caarray.external.v1_0.factor.FactorValue
equals(Object) - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationColumn
equals(Object) - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationSet
equals(Object) - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationValueSet
equals(Object) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
equals(Object) - Method in class gov.nih.nci.caarray.external.v1_0.value.AbstractValue
equals(Object, Object) - Method in class gov.nih.nci.caarray.util.URIUserType
etcDirectoryPath - Variable in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Configuration
 
ExampleSearchCriteria<T extends AbstractCaArrayEntity> - Class in gov.nih.nci.caarray.external.v1_0.query
Criteria for searching by example.
ExampleSearchCriteria() - Constructor for class gov.nih.nci.caarray.external.v1_0.query.ExampleSearchCriteria
Empty constructor.
ExampleSearchCriteria(T) - Constructor for class gov.nih.nci.caarray.external.v1_0.query.ExampleSearchCriteria
 
ExampleSearchCriteria(T, MatchMode) - Constructor for class gov.nih.nci.caarray.external.v1_0.query.ExampleSearchCriteria
 
ExampleSearchCriteria(T, MatchMode, boolean) - Constructor for class gov.nih.nci.caarray.external.v1_0.query.ExampleSearchCriteria
 
ExampleSearchCriteria(T, MatchMode, boolean, boolean) - Constructor for class gov.nih.nci.caarray.external.v1_0.query.ExampleSearchCriteria
 
executeServiceForCredentialCheck() - Method in class gov.nih.nci.caarray.services.AbstractCaArrayServer
Execute some method in a remote EJB service that forces the authentication credentials to be checked.
executeServiceForCredentialCheck() - Method in class gov.nih.nci.caarray.services.CaArrayServer
Execute some method in a remote EJB service that forces the authentication credentials to be checked.
executeServiceForCredentialCheck() - Method in class gov.nih.nci.caarray.services.external.v1_0.CaArrayServer
Execute some method in a remote EJB service that forces the authentication credentials to be checked.
Experiment - Class in gov.nih.nci.caarray.external.v1_0.experiment
Experiment represents a microarray experiment.
Experiment() - Constructor for class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
ExperimentalContact - Class in gov.nih.nci.caarray.external.v1_0.experiment
ExperimentalContact represents a person who performed one or more roles in an experiment.
ExperimentalContact() - Constructor for class gov.nih.nci.caarray.external.v1_0.experiment.ExperimentalContact
 
ExperimentHandler - Class in gov.nih.nci.caarray.util.audit
 
ExperimentHandler(CaArrayAuditLogProcessor) - Constructor for class gov.nih.nci.caarray.util.audit.ExperimentHandler
 
ExperimentSearchCriteria - Class in gov.nih.nci.caarray.external.v1_0.query
 
ExperimentSearchCriteria() - Constructor for class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
exportMageTab(CaArrayEntityReference) - Method in interface gov.nih.nci.caarray.services.external.v1_0.data.DataService
Retrieves a set of files containing the MAGE-TAB IDF and SDRF for the experiment identified by the given reference.
exportMageTab(CaArrayEntityReference) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.GridDataApiUtils

F

Factor - Class in gov.nih.nci.caarray.external.v1_0.factor
Factor represents an experimental factor, e.g.
Factor() - Constructor for class gov.nih.nci.caarray.external.v1_0.factor.Factor
 
FactorValue - Class in gov.nih.nci.caarray.external.v1_0.factor
FactorValue represents the value of an experimental factor for a particular hybridization chain.
FactorValue() - Constructor for class gov.nih.nci.caarray.external.v1_0.factor.FactorValue
 
File - Class in gov.nih.nci.caarray.external.v1_0.data
File represents a file that has been uploaded to caarray.
File() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.File
 
FileCategory - Enum in gov.nih.nci.caarray.external.v1_0.data
 
FileCategoryFieldHandler - Class in gov.nih.nci.caarray.services.external.v1_0.grid.common
 
FileCategoryFieldHandler() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.common.FileCategoryFieldHandler
 
FileContents - Class in gov.nih.nci.caarray.external.v1_0.data
FileContents combines a file's metadata with its contents.
FileContents() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.FileContents
 
FileMetadata - Class in gov.nih.nci.caarray.external.v1_0.data
FileMetadata describes the metadata for a file in caarray.
FileMetadata() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.FileMetadata
 
FileSearchCriteria - Class in gov.nih.nci.caarray.external.v1_0.query
 
FileSearchCriteria() - Constructor for class gov.nih.nci.caarray.external.v1_0.query.FileSearchCriteria
 
FileStreamableContents - Class in gov.nih.nci.caarray.external.v1_0.data
FileStreamableContents combines a file's metadata with a RemoteInputStream for reading its contents.
FileStreamableContents() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.FileStreamableContents
 
FileType - Class in gov.nih.nci.caarray.external.v1_0.data
 
FileType() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.FileType
 
FileUtility - Class in gov.nih.nci.caarray.util.io
Utility methods for file handling.
FILTER_ALIAS - Static variable in class gov.nih.nci.caarray.util.CaarrayInnoDBDialect
The well known value used as the identifier in the nested subqueries for CSM filters.
find(ResourceKey) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceHome
 
find(Iterable<T>, Predicate<? super T>) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Returns the first element in iterable that satisfies the given predicate, or null if no elements do.
finishProcessing() - Method in class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
Called to indicate the end of processing the OWL doc.
finishProcessing() - Method in class gov.nih.nci.caarray.util.owlparser.SqlOntologyOwlParser
Called to indicate the end of processing the OWL doc.
FloatColumn - Class in gov.nih.nci.caarray.external.v1_0.data
A FloatColumn represents a data column with float values.
FloatColumn() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.FloatColumn
 
foreignKeyColumnName(String, String, String, String) - Method in class gov.nih.nci.caarray.util.NamingStrategy

G

get(Object) - Method in class gov.nih.nci.caarray.util.PropertyAccessor
Get the value of the property of this accessor from the given object.
getAccession() - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Category
 
getAccession() - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Term
 
getAccessors() - Method in class gov.nih.nci.caarray.util.ReflectionHelper
 
getAddressedResource() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceHome
Get the resouce that is being addressed in this current context
getAllCharacteristicCategories(CaArrayEntityReference) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
getAllCharacteristicCategories(CaArrayEntityReference) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
 
getAllCharacteristicCategories(CaArrayEntityReference) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
getAllCharacteristicCategories(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.GetAllCharacteristicCategoriesRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
getAllCharacteristicCategories(CaArrayEntityReference) - Method in interface gov.nih.nci.caarray.services.external.v1_0.search.SearchService
Retrieve the list of all categories of characteristics, either in the entire system, or for given experiment.
getAllPrincipalInvestigators() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
getAllPrincipalInvestigators() - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
return list of all persons who are principal investigators for some experiment
getAllPrincipalInvestigators() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
getAllPrincipalInvestigators(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.GetAllPrincipalInvestigatorsRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
getAllPrincipalInvestigators() - Method in interface gov.nih.nci.caarray.services.external.v1_0.search.SearchService
Retrieve list of Person entities that are Principal Investigators on at least one experiment in the system.
getAnnotationCriterions() - Method in class gov.nih.nci.caarray.external.v1_0.query.BiomaterialSearchCriteria
Returns the Set of AnnotationCriterions to match the Biomaterial against.
getAnnotationCriterions() - Method in class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
getAnnotationSet(AnnotationSetRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
getAnnotationSet(AnnotationSetRequest) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
 
getAnnotationSet(AnnotationSetRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
getAnnotationSet(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.GetAnnotationSetRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
getAnnotationSet(AnnotationSetRequest) - Method in interface gov.nih.nci.caarray.services.external.v1_0.search.SearchService
Returns an annotation set matching the given request.
getArrayDataTypes() - Method in class gov.nih.nci.caarray.external.v1_0.query.QuantitationTypeSearchCriteria
 
getArrayDesign() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Hybridization
 
getArrayDesignDetailsService() - Method in class gov.nih.nci.caarray.services.CaArrayServer
 
getArrayDesigns() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
getArrayProvider() - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
getArrayProvider() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
getArrayProvider() - Method in class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
getAssayType() - Method in class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
getAssayTypes() - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
getAssayTypes() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
getBiomaterials() - Method in class gov.nih.nci.caarray.external.v1_0.query.HybridizationSearchCriteria
 
getByExternalId(String) - Method in class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService
Retrieve the entity in the internal domain model identified by the given external id.
getByReference(CaArrayEntityReference, Class<T>) - Method in class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService
Retrieve the entity for given reference expected to have given type.
getCaArrayHibernateHelper() - Static method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperFactory
 
getCaArraySvc_v1_0ResourceHome() - Method in class gov.nih.nci.cagrid.enumeration.service.CaGridEnumerationImplBase
 
getCaGridEnumerationResourceHome() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0ImplBase
 
getCaGridWsEnumeration_iterImplType() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Configuration
 
getCallerIdentity() - Static method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
getCallerIdentity() - Static method in class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 
getCategories() - Method in class gov.nih.nci.caarray.external.v1_0.query.AnnotationSetRequest
 
getCategories() - Method in class gov.nih.nci.caarray.external.v1_0.query.FileSearchCriteria
 
getCategories() - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationSet
 
getCategory() - Method in class gov.nih.nci.caarray.external.v1_0.query.AnnotationCriterion
 
getCategory() - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationValueSet
 
getCategory() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
 
getCategory() - Method in exception gov.nih.nci.caarray.services.external.v1_0.UnsupportedCategoryException
 
getCategory() - Method in exception gov.nih.nci.caarray.services.external.v1_0.UnsupportedCategoryException
 
getCategoryCache() - Method in class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
 
getCellType() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
getCharacteristics() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
getColumns() - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationSet
 
getCommonName() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Organism
 
getCompressedSize() - Method in class gov.nih.nci.caarray.external.v1_0.data.FileMetadata
 
getConfiguration() - Static method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Configuration
 
getConfiguration() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0ImplBase
 
getConfiguration() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceBase
 
getConfiguration() - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
 
getConfiguration() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
getConfiguration() - Method in class gov.nih.nci.cagrid.enumeration.service.CaGridEnumerationImplBase
 
getConnectionTimeout() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0ClientBase
 
getConnectionTimeout() - Method in class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClientBase
 
getContacts() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
getContents() - Method in class gov.nih.nci.caarray.external.v1_0.data.FileContents
 
getContentStream() - Method in class gov.nih.nci.caarray.external.v1_0.data.FileStreamableContents
 
getCsmUser() - Static method in class gov.nih.nci.caarray.util.CaArrayUsernameHolder
 
getCurrentSession() - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
Returns the current Hibernate session.
getCurrentSession() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperImpl
Returns the current Hibernate session.
getCurrentSession() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
Returns the current Hibernate session.
getDataColumns() - Method in class gov.nih.nci.caarray.external.v1_0.data.HybridizationData
 
getDataFiles() - Method in class gov.nih.nci.caarray.external.v1_0.data.MageTabFileSet
 
getDataFiles() - Method in class gov.nih.nci.caarray.external.v1_0.query.DataSetRequest
 
getDataRetrievalService() - Method in class gov.nih.nci.caarray.services.CaArrayServer
 
getDatas() - Method in class gov.nih.nci.caarray.external.v1_0.data.DataSet
 
getDataService() - Method in class gov.nih.nci.caarray.services.external.v1_0.CaArrayServer
 
getDataSet(DataSetRequest) - Method in interface gov.nih.nci.caarray.services.external.v1_0.data.DataService
Retrieves the parsed data set identified by the given request.
getDataSet(DataSetRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
getDataSet(DataSetRequest) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
Retrieves a parsed data set
getDataSet(DataSetRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
getDataSet(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.GetDataSetRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
getDataType() - Method in class gov.nih.nci.caarray.external.v1_0.data.QuantitationType
 
getDescription() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
getDescription() - Method in class gov.nih.nci.caarray.external.v1_0.factor.Factor
 
getDescription() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
getDesignElements() - Method in class gov.nih.nci.caarray.external.v1_0.data.DataSet
 
getDiseaseState() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
getEmailAddress() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Person
 
getEntityHandlerRegistry() - Method in class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService
 
getEtcDirectoryPath() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Configuration
 
getExample() - Method in class gov.nih.nci.caarray.external.v1_0.query.ExampleSearchCriteria
 
getExperiment() - Method in class gov.nih.nci.caarray.external.v1_0.query.BiomaterialSearchCriteria
 
getExperiment() - Method in class gov.nih.nci.caarray.external.v1_0.query.FileSearchCriteria
 
getExperiment() - Method in class gov.nih.nci.caarray.external.v1_0.query.HybridizationSearchCriteria
 
getExperiment() - Method in class gov.nih.nci.caarray.external.v1_0.sample.AbstractExperimentGraphNode
 
getExperimentalDesigns() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
getExperimentGraphNodes() - Method in class gov.nih.nci.caarray.external.v1_0.query.AnnotationSetRequest
 
getExperimentGraphNodes() - Method in class gov.nih.nci.caarray.external.v1_0.query.FileSearchCriteria
 
getExtension() - Method in class gov.nih.nci.caarray.external.v1_0.query.FileSearchCriteria
 
getExternalId() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
getExternalIds() - Method in class gov.nih.nci.caarray.external.v1_0.query.BiomaterialSearchCriteria
 
getFactor() - Method in class gov.nih.nci.caarray.external.v1_0.factor.FactorValue
 
getFactors() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
getFactorValues() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Hybridization
 
getFileCategories() - Method in class gov.nih.nci.caarray.external.v1_0.query.QuantitationTypeSearchCriteria
 
getFileContentsTransfer(CaArrayEntityReference, boolean) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
getFileContentsTransfer(CaArrayEntityReference, boolean) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
Returns a grid transfer reference for retrieving the given reference
getFileContentsTransfer(CaArrayEntityReference, boolean) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
getFileContentsTransfer(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.GetFileContentsTransferRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
getFileRetrievalService() - Method in class gov.nih.nci.caarray.services.CaArrayServer
 
getFiles() - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
getFileType() - Method in class gov.nih.nci.caarray.external.v1_0.data.FileMetadata
 
getFileTypes() - Method in class gov.nih.nci.caarray.external.v1_0.query.QuantitationTypeSearchCriteria
 
getFirstName() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Person
 
getFirstResultOffset() - Method in class gov.nih.nci.caarray.external.v1_0.query.SearchResult
 
getHibernateHelper() - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
 
getHybridization() - Method in class gov.nih.nci.caarray.external.v1_0.data.HybridizationData
 
getHybridization() - Method in class gov.nih.nci.caarray.external.v1_0.query.QuantitationTypeSearchCriteria
 
getHybridizations() - Method in class gov.nih.nci.caarray.external.v1_0.query.DataSetRequest
 
getId() - Method in class gov.nih.nci.caarray.external.v1_0.AbstractCaArrayEntity
 
getId() - Method in class gov.nih.nci.caarray.external.v1_0.CaArrayEntityReference
 
getIdf() - Method in class gov.nih.nci.caarray.external.v1_0.data.MageTabFileSet
 
getJndiUrl() - Static method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
getKeyword() - Method in class gov.nih.nci.caarray.external.v1_0.query.KeywordSearchCriteria
 
getLabel() - Method in class gov.nih.nci.caarray.util.LabelValue
get label.
getLastDataModificationDate() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
getLastModifiedDataTime() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
getLastName() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Person
 
getLimit() - Method in class gov.nih.nci.caarray.external.v1_0.query.LimitOffset
 
getLsid() - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
getMageTabExport(CaArrayEntityReference) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
getMageTabExport(CaArrayEntityReference) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
Returns an export of an experiment as a set of mage-tab IDF and SDRF, along with metadata for associated data files
getMageTabExport(CaArrayEntityReference) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
getMageTabExport(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.GetMageTabExportRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
getMailSession() - Method in class gov.nih.nci.caarray.util.EmailUtil
Returns a handle on the populated mail session object.
getMapperVersionKey() - Method in class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService
getMatchMode() - Method in class gov.nih.nci.caarray.external.v1_0.query.ExampleSearchCriteria
 
getMaterialType() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
getMaxAllowedResults() - Method in class gov.nih.nci.caarray.external.v1_0.query.SearchResult
 
getMeasurement() - Method in class gov.nih.nci.caarray.external.v1_0.value.MeasurementValue
 
getMeasurementValue() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
 
getMetadata() - Method in class gov.nih.nci.caarray.external.v1_0.data.File
 
getMetadata() - Method in class gov.nih.nci.caarray.external.v1_0.data.FileContents
 
getMetadata() - Method in class gov.nih.nci.caarray.external.v1_0.data.FileStreamableContents
 
getMiddleInitials() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Person
 
getMultipleResourceProperties(GetMultipleResourceProperties_Element) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
getMultipleResourceProperties(GetMultipleResourceProperties_Element) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
 
getName() - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
getName() - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayProvider
 
getName() - Method in class gov.nih.nci.caarray.external.v1_0.array.AssayType
 
getName() - Method in class gov.nih.nci.caarray.external.v1_0.data.ArrayDataType
 
getName() - Method in enum gov.nih.nci.caarray.external.v1_0.data.DataType
 
getName() - Method in class gov.nih.nci.caarray.external.v1_0.data.DesignElement
 
getName() - Method in enum gov.nih.nci.caarray.external.v1_0.data.FileCategory
 
getName() - Method in class gov.nih.nci.caarray.external.v1_0.data.FileMetadata
 
getName() - Method in class gov.nih.nci.caarray.external.v1_0.data.FileType
 
getName() - Method in class gov.nih.nci.caarray.external.v1_0.data.QuantitationType
 
getName() - Method in class gov.nih.nci.caarray.external.v1_0.factor.Factor
 
getName() - Method in enum gov.nih.nci.caarray.external.v1_0.query.MatchMode
 
getName() - Method in class gov.nih.nci.caarray.external.v1_0.sample.AbstractExperimentGraphNode
 
getName() - Method in enum gov.nih.nci.caarray.external.v1_0.sample.BiomaterialType
 
getName() - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Category
 
getName() - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.TermSource
 
getNames() - Method in class gov.nih.nci.caarray.external.v1_0.query.BiomaterialSearchCriteria
 
getNames() - Method in class gov.nih.nci.caarray.external.v1_0.query.HybridizationSearchCriteria
 
getNewConnection() - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
 
getNewConnection() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperImpl
getNewConnection() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
getNode() - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationColumn
 
getNormalizationTypes() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
getOffset() - Method in class gov.nih.nci.caarray.external.v1_0.query.LimitOffset
 
getOrganism() - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
getOrganism() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
getOrganism() - Method in class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
getOrganism() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
getPerson() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.ExperimentalContact
 
getPolicy(Node) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
getPolicy(Node) - Method in class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 
getPolicyNames() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
getPolicyNames() - Method in class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 
getPrincipalInvestigators() - Method in class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
getProcessor() - Method in class gov.nih.nci.caarray.util.audit.AbstractAuditEntityHandler
 
getProcessor() - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
 
getPublicIdentifier() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
getPublicIdentifier() - Method in class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
getQualityControlTypes() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
getQuantitationType() - Method in class gov.nih.nci.caarray.external.v1_0.data.AbstractDataColumn
 
getQuantitationTypes() - Method in class gov.nih.nci.caarray.external.v1_0.data.ArrayDataType
 
getQuantitationTypes() - Method in class gov.nih.nci.caarray.external.v1_0.data.DataSet
 
getQuantitationTypes() - Method in class gov.nih.nci.caarray.external.v1_0.query.DataSetRequest
 
getReference() - Method in class gov.nih.nci.caarray.external.v1_0.AbstractCaArrayEntity
 
getReference() - Method in exception gov.nih.nci.caarray.services.external.v1_0.InvalidReferenceException
 
getReference() - Method in exception gov.nih.nci.caarray.services.external.v1_0.InvalidReferenceException
 
getRegistrationTemplateFile() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceConfiguration
 
getReplicateTypes() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
getRequiredByExternalId(String, Class<T>) - Method in class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService
Retrieve the entity with given external id expected to exist in the persistent store and have given type.
getResolver(Class<T>) - Method in class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService.EntityHandlerRegistry
Get the handler for given external entity class.
getResourceHome() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0ImplBase
 
getResourceHome(String) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0ImplBase
 
getResourceHome(String) - Method in class gov.nih.nci.cagrid.enumeration.service.CaGridEnumerationImplBase
 
getResourceProperty(QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
getResourceProperty(QName) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
 
getResults() - Method in class gov.nih.nci.caarray.external.v1_0.query.SearchResult
 
getRoles() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.ExperimentalContact
 
getScientificName() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Organism
 
getSdrf() - Method in class gov.nih.nci.caarray.external.v1_0.data.MageTabFileSet
 
getSearchBiomaterialsByCriteriaFunction(BiomaterialSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.GridSearchApiUtils
getSearchBiomaterialsByKeywordFunction(BiomaterialKeywordSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.GridSearchApiUtils
getSearchByExampleFunction(ExampleSearchCriteria<T>) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.GridSearchApiUtils
getSearchExperimentsByCriteriaFunction(ExperimentSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.GridSearchApiUtils
getSearchExperimentsByKeywordFunction(KeywordSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.GridSearchApiUtils
getSearchFilesFunction(FileSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.GridSearchApiUtils
getSearchHybridizationsFunction(HybridizationSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.GridSearchApiUtils
getSearchService() - Method in class gov.nih.nci.caarray.services.CaArrayServer
 
getSearchService() - Method in class gov.nih.nci.caarray.services.external.v1_0.CaArrayServer
 
getSecurityEntries() - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogProcessor
Returns a mapping of audit records with their associated security entries.
getSerializableValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.AbstractDataColumn
Get the values array of this column.
getSerializableValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.BooleanColumn
Get the values array of this column.
getSerializableValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.DoubleColumn
Get the values array of this column.
getSerializableValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.FloatColumn
Get the values array of this column.
getSerializableValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.IntegerColumn
Get the values array of this column.
getSerializableValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.LongColumn
Get the values array of this column.
getSerializableValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.ShortColumn
Get the values array of this column.
getSerializableValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.StringColumn
Get the values array of this column.
getServiceMetadata() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceBase
 
getServiceMetadataFile() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceConfiguration
 
getServiceNamespace() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
getServiceNamespace() - Method in class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 
getSessionFactory() - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
 
getSessionFactory() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
getStatusOp(GetStatus) - Method in class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClient
 
getStatusOp(GetStatus) - Method in interface gov.nih.nci.cagrid.enumeration.common.CaGridEnumerationI
 
getTechnologyType() - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
getter() - Method in class gov.nih.nci.caarray.util.PropertyAccessor
 
getTerm() - Method in class gov.nih.nci.caarray.external.v1_0.value.TermValue
 
getTermCache() - Method in class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
 
getTermsForCategory(CaArrayEntityReference, String) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
getTermsForCategory(CaArrayEntityReference, String) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
 
getTermsForCategory(CaArrayEntityReference, String) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
getTermsForCategory(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.GetTermsForCategoryRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
getTermsForCategory(CaArrayEntityReference, String) - Method in interface gov.nih.nci.caarray.services.external.v1_0.search.SearchService
Retrieve the list of all terms belonging to given category in the system.
getTermSource() - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Category
 
getTermSource() - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Term
 
getTermSource() - Method in class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
 
getTermValue() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
 
getTissueSite() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
getTitle() - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
getTitle() - Method in class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
getType() - Method in class gov.nih.nci.caarray.external.v1_0.factor.Factor
 
getType() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
getType() - Method in class gov.nih.nci.caarray.util.PropertyAccessor
 
getTypes() - Method in class gov.nih.nci.caarray.external.v1_0.query.BiomaterialKeywordSearchCriteria
 
getTypes() - Method in class gov.nih.nci.caarray.external.v1_0.query.BiomaterialSearchCriteria
 
getTypes() - Method in class gov.nih.nci.caarray.external.v1_0.query.FileSearchCriteria
 
getUncompressedSize() - Method in class gov.nih.nci.caarray.external.v1_0.data.FileMetadata
 
getUnit() - Method in class gov.nih.nci.caarray.external.v1_0.value.AbstractValue
 
getUrl() - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Category
 
getUrl() - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Term
 
getUrl() - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.TermSource
 
getUser() - Method in interface gov.nih.nci.caarray.util.UsernameHolder
 
getUser() - Method in class gov.nih.nci.caarray.util.UsernameHolderImpl
getValue() - Method in class gov.nih.nci.caarray.external.v1_0.factor.FactorValue
 
getValue() - Method in class gov.nih.nci.caarray.external.v1_0.query.AnnotationCriterion
 
getValue() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
 
getValue() - Method in class gov.nih.nci.caarray.external.v1_0.value.UserDefinedValue
 
getValue() - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Term
 
getValue() - Method in class gov.nih.nci.caarray.util.LabelValue
get value.
getValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.BooleanColumn
 
getValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.DoubleColumn
 
getValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.FloatColumn
 
getValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.IntegerColumn
 
getValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.LongColumn
 
getValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.ShortColumn
 
getValues() - Method in class gov.nih.nci.caarray.external.v1_0.data.StringColumn
 
getValues() - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationValueSet
 
getValuesAsString() - Method in class gov.nih.nci.caarray.external.v1_0.data.BooleanColumn
 
getValuesAsString() - Method in class gov.nih.nci.caarray.external.v1_0.data.DoubleColumn
 
getValuesAsString() - Method in class gov.nih.nci.caarray.external.v1_0.data.FloatColumn
 
getValuesAsString() - Method in class gov.nih.nci.caarray.external.v1_0.data.IntegerColumn
 
getValuesAsString() - Method in class gov.nih.nci.caarray.external.v1_0.data.LongColumn
 
getValuesAsString() - Method in class gov.nih.nci.caarray.external.v1_0.data.ShortColumn
 
getValuesAsString() - Method in class gov.nih.nci.caarray.external.v1_0.data.StringColumn
 
getValueSets() - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationColumn
 
getVersion() - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
getVersion() - Method in class gov.nih.nci.caarray.external.v1_0.data.ArrayDataType
 
getVersion() - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.TermSource
 
gov.nih.nci.caarray.external.v1_0 - package gov.nih.nci.caarray.external.v1_0
 
gov.nih.nci.caarray.external.v1_0.array - package gov.nih.nci.caarray.external.v1_0.array
 
gov.nih.nci.caarray.external.v1_0.data - package gov.nih.nci.caarray.external.v1_0.data
 
gov.nih.nci.caarray.external.v1_0.experiment - package gov.nih.nci.caarray.external.v1_0.experiment
 
gov.nih.nci.caarray.external.v1_0.factor - package gov.nih.nci.caarray.external.v1_0.factor
 
gov.nih.nci.caarray.external.v1_0.query - package gov.nih.nci.caarray.external.v1_0.query
 
gov.nih.nci.caarray.external.v1_0.sample - package gov.nih.nci.caarray.external.v1_0.sample
 
gov.nih.nci.caarray.external.v1_0.value - package gov.nih.nci.caarray.external.v1_0.value
 
gov.nih.nci.caarray.external.v1_0.vocabulary - package gov.nih.nci.caarray.external.v1_0.vocabulary
 
gov.nih.nci.caarray.services - package gov.nih.nci.caarray.services
 
gov.nih.nci.caarray.services.external.v1_0 - package gov.nih.nci.caarray.services.external.v1_0
 
gov.nih.nci.caarray.services.external.v1_0.grid.client - package gov.nih.nci.caarray.services.external.v1_0.grid.client
 
gov.nih.nci.caarray.services.external.v1_0.grid.common - package gov.nih.nci.caarray.services.external.v1_0.grid.common
 
gov.nih.nci.caarray.services.external.v1_0.grid.service - package gov.nih.nci.caarray.services.external.v1_0.grid.service
 
gov.nih.nci.caarray.services.external.v1_0.grid.service.globus - package gov.nih.nci.caarray.services.external.v1_0.grid.service.globus
 
gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource - package gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource
 
gov.nih.nci.caarray.util - package gov.nih.nci.caarray.util
 
gov.nih.nci.caarray.util.audit - package gov.nih.nci.caarray.util.audit
 
gov.nih.nci.caarray.util.io - package gov.nih.nci.caarray.util.io
 
gov.nih.nci.caarray.util.io.logging - package gov.nih.nci.caarray.util.io.logging
 
gov.nih.nci.caarray.util.owlparser - package gov.nih.nci.caarray.util.owlparser
 
gov.nih.nci.cagrid.enumeration.client - package gov.nih.nci.cagrid.enumeration.client
 
gov.nih.nci.cagrid.enumeration.common - package gov.nih.nci.cagrid.enumeration.common
 
gov.nih.nci.cagrid.enumeration.service - package gov.nih.nci.cagrid.enumeration.service
 
gov.nih.nci.cagrid.enumeration.service.globus - package gov.nih.nci.cagrid.enumeration.service.globus
 
GridApiUtils - Class in gov.nih.nci.caarray.services.external.v1_0.grid.client
 
GridDataApiUtils - Class in gov.nih.nci.caarray.services.external.v1_0.grid.client
DataUtils is a helper class for working with the caArray Data API.
GridDataApiUtils(CaArraySvc_v1_0Client) - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.client.GridDataApiUtils
 
GridSearchApiUtils - Class in gov.nih.nci.caarray.services.external.v1_0.grid.client
Utility class that allows for easier return of all results or iteration of results from a search service.
GridSearchApiUtils(CaArraySvc_v1_0Client) - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.client.GridSearchApiUtils
 
GroupHandler - Class in gov.nih.nci.caarray.util.audit
 
GroupHandler(CaArrayAuditLogProcessor) - Constructor for class gov.nih.nci.caarray.util.audit.GroupHandler
 
gunzip(byte[]) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
returns a byte array representing the input byte array, un-gzipped.
gzip(byte[]) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
returns a byte array representing the input byte array, gzipped.

H

hashCode() - Method in class gov.nih.nci.caarray.external.v1_0.AbstractCaArrayEntity
Hashcode, based on id when not null; otherwise, the other properties are used to comute the hash code.
hashCode() - Method in class gov.nih.nci.caarray.external.v1_0.CaArrayEntityReference
hashCode() - Method in class gov.nih.nci.caarray.external.v1_0.data.AbstractDataColumn
hashCode() - Method in class gov.nih.nci.caarray.external.v1_0.data.FileMetadata
hashCode() - Method in class gov.nih.nci.caarray.external.v1_0.factor.FactorValue
hashCode() - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationColumn
hashCode() - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationSet
hashCode() - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationValueSet
hashCode() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
hashCode() - Method in class gov.nih.nci.caarray.external.v1_0.value.AbstractValue
hashCode(Object) - Method in class gov.nih.nci.caarray.util.URIUserType
Hybridization - Class in gov.nih.nci.caarray.external.v1_0.sample
a Hybridization is an experiment graph node that represents the product of hybridizing extracted genetic material with the probes on an array.
Hybridization() - Constructor for class gov.nih.nci.caarray.external.v1_0.sample.Hybridization
 
HybridizationData - Class in gov.nih.nci.caarray.external.v1_0.data
HybridizationData represents the set of measurements captured from a single hybridization.
HybridizationData() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.HybridizationData
 
HybridizationSearchCriteria - Class in gov.nih.nci.caarray.external.v1_0.query
 
HybridizationSearchCriteria() - Constructor for class gov.nih.nci.caarray.external.v1_0.query.HybridizationSearchCriteria
 

I

InconsistentDataSetsException - Exception in gov.nih.nci.caarray.services.external.v1_0.data
Exception thrown to indicate that the data sets requested in a getDataSet call were inconsistent, e.g.
InconsistentDataSetsException(String) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.data.InconsistentDataSetsException
Constructor for no cause.
IncorrectEntityTypeException - Exception in gov.nih.nci.caarray.services.external.v1_0
Exception thrown to indicate that a passed in CaArrayEntityReference referred to an entity that was of a different type than expected by the service method.
IncorrectEntityTypeException - Exception in gov.nih.nci.caarray.services.external.v1_0
Exception thrown to indicate that a passed in CaArrayEntityReference referred to an entity that was of a different type than expected by the service method.
IncorrectEntityTypeException(CaArrayEntityReference) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.IncorrectEntityTypeException
Constructor for no cause.
IncorrectEntityTypeException(CaArrayEntityReference, String) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.IncorrectEntityTypeException
Constructor with message.
IncorrectEntityTypeException(CaArrayEntityReference) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.IncorrectEntityTypeException
Constructor for no cause.
IncorrectEntityTypeException(CaArrayEntityReference, String) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.IncorrectEntityTypeException
Constructor with message.
initialize() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0ClientBase
 
initialize(PDPConfig, String, String) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
initialize(Object, QName, Object) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceBase
 
initialize() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceHome
Initialze the singleton resource, when the home is initialized.
initialize() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperImpl
Because of circular references (for instance, SecurityUtils references this object through the static factory), we must use a two stage construction/initialization process.
initialize() - Method in class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClientBase
 
initialize(PDPConfig, String, String) - Method in class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 
IntegerColumn - Class in gov.nih.nci.caarray.external.v1_0.data
An IntegerColumn represents a data column with integer values.
IntegerColumn() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.IntegerColumn
 
InvalidInputException - Exception in gov.nih.nci.caarray.services.external.v1_0
Exception thrown to indicate that a passed in query parameter was invalid.
InvalidInputException - Exception in gov.nih.nci.caarray.services.external.v1_0
Exception thrown to indicate that a passed in query parameter was invalid.
InvalidInputException(String) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.InvalidInputException
Constructor with message.
InvalidInputException() - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.InvalidInputException
Default constructor.
InvalidInputException(String) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.InvalidInputException
Constructor with message.
InvalidInputException() - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.InvalidInputException
Default constructor.
InvalidReferenceException - Exception in gov.nih.nci.caarray.services.external.v1_0
Exception thrown to indicate that a passed in CaArrayEntityReference was invalid in some general way.
InvalidReferenceException - Exception in gov.nih.nci.caarray.services.external.v1_0
Exception thrown to indicate that a passed in CaArrayEntityReference was invalid in some general way.
InvalidReferenceException(CaArrayEntityReference) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.InvalidReferenceException
Constructor for no cause.
InvalidReferenceException(CaArrayEntityReference, String) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.InvalidReferenceException
Constructor with message.
InvalidReferenceException(CaArrayEntityReference) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.InvalidReferenceException
Constructor for no cause.
InvalidReferenceException(CaArrayEntityReference, String) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.InvalidReferenceException
Constructor with message.
isAuditableEntity(Object) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogProcessor
isCompressed() - Method in class gov.nih.nci.caarray.external.v1_0.data.FileContents
 
isCompressed() - Method in class gov.nih.nci.caarray.external.v1_0.data.FileStreamableContents
 
isExcludeNulls() - Method in class gov.nih.nci.caarray.external.v1_0.query.ExampleSearchCriteria
 
isExcludeZeroes() - Method in class gov.nih.nci.caarray.external.v1_0.query.ExampleSearchCriteria
 
isFullResult() - Method in class gov.nih.nci.caarray.external.v1_0.query.SearchResult
 
isMutable() - Method in class gov.nih.nci.caarray.util.URIUserType
isPermitted(Subject, MessageContext, QName) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
isPermitted(Subject, MessageContext, QName) - Method in class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 

J

JNDI_NAME - Static variable in interface gov.nih.nci.caarray.services.external.v1_0.data.DataService
The JNDI name to look up this Remote EJB under.
JNDI_NAME - Static variable in interface gov.nih.nci.caarray.services.external.v1_0.search.SearchService
The JNDI name to look up this Remote EJB under.
join(boolean[], String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Joins the elements of the provided array into a single String containing the provided list of elements.
join(int[], String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Joins the elements of the provided array into a single String containing the provided list of elements.
join(long[], String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Joins the elements of the provided array into a single String containing the provided list of elements.
join(short[], String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Joins the elements of the provided array into a single String containing the provided list of elements.
join(double[], String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Joins the elements of the provided array into a single String containing the provided list of elements.
join(float[], String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Joins the elements of the provided array into a single String containing the provided list of elements.
joinAsCsv(String[]) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Joins the given values as a comma-separated string.
joinKeyColumnName(String, String) - Method in class gov.nih.nci.caarray.util.NamingStrategy

K

KeywordSearchCriteria - Class in gov.nih.nci.caarray.external.v1_0.query
 
KeywordSearchCriteria() - Constructor for class gov.nih.nci.caarray.external.v1_0.query.KeywordSearchCriteria
 

L

LabelValue - Class in gov.nih.nci.caarray.util
A simple JavaBean to represent label-value pairs.
LabelValue() - Constructor for class gov.nih.nci.caarray.util.LabelValue
Default constructor.
LabelValue(String, String) - Constructor for class gov.nih.nci.caarray.util.LabelValue
Construct an instance with the supplied property values.
LimitOffset - Class in gov.nih.nci.caarray.external.v1_0.query
Bean for specifying paging and sorting constraints for a query.
LimitOffset(int, int) - Constructor for class gov.nih.nci.caarray.external.v1_0.query.LimitOffset
Constructor.
LimitOffset() - Constructor for class gov.nih.nci.caarray.external.v1_0.query.LimitOffset
Empty constructor, for serialization.
logAdd(AuditLogRecord, T, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.AbstractAuditEntityHandler
Log an addition of an entity.
logAdd(AuditLogRecord, Group, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.GroupHandler
Log an addition of an entity.
logAddOrUpdate(AuditLogRecord, T, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.AbstractAuditEntityHandler
Log an addition or an update.
logAddOrUpdate(AuditLogRecord, AccessProfile, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.AccessProfileHandler
Log an addition or an update.
logAddOrUpdate(AuditLogRecord, AbstractArrayData, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.ArrayDataHandler
Log an addition or an update.
logAddOrUpdate(AuditLogRecord, ArrayDesign, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.ArrayDesignHandler
Log an addition or an update.
logAddOrUpdate(AuditLogRecord, CaArrayFile, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.CaArrayFileHandler
Log an addition or an update.
logAddOrUpdate(AuditLogRecord, CollaboratorGroup, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.CollaboratorGroupHandler
Log an addition or an update.
logAddOrUpdate(AuditLogRecord, Experiment, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.ExperimentHandler
Log an addition or an update.
logAddOrUpdate(AuditLogRecord, Project, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.ProjectHandler
Log an addition or an update.
logAddOrUpdate(AuditLogRecord, Protocol, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.ProtocolHandler
Log an addition or an update.
logAddOrUpdate(AuditLogRecord, Term, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.TermHandler
Log an addition or an update.
logDelete(AuditLogRecord, T, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.AbstractAuditEntityHandler
Log a deletion of an entity.
logDelete(AuditLogRecord, ArrayDesign, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.ArrayDesignHandler
Log a deletion of an entity.
logDelete(AuditLogRecord, Project, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.ProjectHandler
Log a deletion of an entity.
logEntity(AuditLogRecord, T, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.AbstractAuditEntityHandler
Add an entry to the audit log record for the given object.
logicalCollectionColumnName(String, String, String) - Method in class gov.nih.nci.caarray.util.NamingStrategy
logicalCollectionTableName(String, String, String, String) - Method in class gov.nih.nci.caarray.util.NamingStrategy
logicalColumnName(String, String) - Method in class gov.nih.nci.caarray.util.NamingStrategy
logSubsystemEntry(Logger, Object...) - Static method in class gov.nih.nci.caarray.util.io.logging.LogUtil
Logs a subsystem entry tracing message (at DEBUG level), listing the method and arguments.
logSubsystemExit(Logger) - Static method in class gov.nih.nci.caarray.util.io.logging.LogUtil
Logs a subsystem exit tracing message (at DEBUG level).
logUpdate(AuditLogRecord, T, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.AbstractAuditEntityHandler
Log an update to an entity.
logUpdate(AuditLogRecord, Group, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.audit.GroupHandler
Log an update to an entity.
LogUtil - Class in gov.nih.nci.caarray.util.io.logging
Utility methods for logging functionality.
LongColumn - Class in gov.nih.nci.caarray.external.v1_0.data
A LongColumn represents a data column with long values.
LongColumn() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.LongColumn
 
lookupServices(Context) - Method in class gov.nih.nci.caarray.services.AbstractCaArrayServer
Method called after obtaining a JNDI context from the remote EJB server.
lookupServices(Context) - Method in class gov.nih.nci.caarray.services.CaArrayServer
Method called after obtaining a JNDI context from the remote EJB server.
lookupServices(Context) - Method in class gov.nih.nci.caarray.services.external.v1_0.CaArrayServer
Method called after obtaining a JNDI context from the remote EJB server.

M

MageTabFileSet - Class in gov.nih.nci.caarray.external.v1_0.data
MageTabFileSet is a container for the mage-tab representation of an experiment.
MageTabFileSet() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.MageTabFileSet
 
main(String[]) - Static method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
main(String[]) - Static method in class gov.nih.nci.caarray.util.owlparser.ParseMgedOntology
Main method.
main(String[]) - Static method in class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClient
 
makeUriQuietly(String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Utility method to create a URI from given string without throwing a checked exception.
makeUriQuietly(String, String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Utility method to create a URI from given scheme and scheme specific part without throwing a checked exception.
mapRequiredReferencesToEntities(Collection<CaArrayEntityReference>, Collection<T>, Class<T>) - Method in class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService
Convert the given list of references to the underlying internal entities pointed to by those references.
mapRequiredReferencesToEntities(Collection<CaArrayEntityReference>, Class<T>) - Method in class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService
Convert the given list of references to the underlying internal entities pointed to by those references.
matches(String, String) - Method in enum gov.nih.nci.caarray.external.v1_0.query.MatchMode
Checks whether the candidate string matches the target string, using the comparison mode for this match mode.
MatchMode - Enum in gov.nih.nci.caarray.external.v1_0.query
Enum of constants for different ways of matching an example entity.
MatchModeFieldHandler - Class in gov.nih.nci.caarray.services.external.v1_0.grid.common
 
MatchModeFieldHandler() - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.common.MatchModeFieldHandler
 
MeasurementValue - Class in gov.nih.nci.caarray.external.v1_0.value
A MeasurementValue is a numerical value.
MeasurementValue() - Constructor for class gov.nih.nci.caarray.external.v1_0.value.MeasurementValue
 
MGED_OWL_PATH - Static variable in class gov.nih.nci.caarray.util.owlparser.ParseMgedOntology
Path to the MGED owl file (as a classpath).
MGED_URL - Static variable in class gov.nih.nci.caarray.util.owlparser.ParseMgedOntology
Url for MGED ontology.

N

namesForEnums(Iterable<E>) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Return the constant names of the given enum instances.
NamingStrategy - Class in gov.nih.nci.caarray.util
CaArray Naming Strategy.
NamingStrategy() - Constructor for class gov.nih.nci.caarray.util.NamingStrategy
 
newMeasurementCharacteristic() - Static method in class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
 
newMeasurementFactorValue() - Static method in class gov.nih.nci.caarray.external.v1_0.factor.FactorValue
 
newTermCharacteristic() - Static method in class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
 
newTermFactorValue() - Static method in class gov.nih.nci.caarray.external.v1_0.factor.FactorValue
 
newUserDefinedCharacteristic() - Static method in class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
 
newUserDefinedFactorValue() - Static method in class gov.nih.nci.caarray.external.v1_0.factor.FactorValue
 
next(IterationConstraints) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.SearchEnumIterator
NoEntityMatchingReferenceException - Exception in gov.nih.nci.caarray.services.external.v1_0
Exception thrown to indicate that there was no entity matching a passed in CaArrayEntityReference.
NoEntityMatchingReferenceException - Exception in gov.nih.nci.caarray.services.external.v1_0
Exception thrown to indicate that there was no entity matching a passed in CaArrayEntityReference.
NoEntityMatchingReferenceException(CaArrayEntityReference) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.NoEntityMatchingReferenceException
Constructor for no cause.
NoEntityMatchingReferenceException(CaArrayEntityReference, String) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.NoEntityMatchingReferenceException
Constructor with message.
NoEntityMatchingReferenceException(CaArrayEntityReference) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.NoEntityMatchingReferenceException
Constructor for no cause.
NoEntityMatchingReferenceException(CaArrayEntityReference, String) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.NoEntityMatchingReferenceException
Constructor with message.
nullSafeGet(ResultSet, String[], Object) - Method in class gov.nih.nci.caarray.util.URIUserType
nullSafeSet(PreparedStatement, Object, int) - Method in class gov.nih.nci.caarray.util.URIUserType

O

onCollectionUpdate(Object, Serializable) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
onDelete(Object, Serializable, Object[], String[], Type[]) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
onFlushDirty(Object, Serializable, Object[], Object[], String[], Type[]) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
onSave(Object, Serializable, Object[], String[], Type[]) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
openAndBindSession() - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
Open a hibernate session and bind it as the current session via org.hibernate.context.ManagedSessionContext#bind(org.hibernate.classic.Session).
openAndBindSession() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperImpl
Open a hibernate session and bind it as the current session via org.hibernate.context.ManagedSessionContext#bind(org.hibernate.classic.Session).
openAndBindSession() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
Open a hibernate session and bind it as the current session via org.hibernate.context.ManagedSessionContext#bind(org.hibernate.classic.Session).
Organism - Class in gov.nih.nci.caarray.external.v1_0.experiment
An Organism is a special type of Term which represents an organism from which biomaterials for a microarray experiment can be drawn.
Organism() - Constructor for class gov.nih.nci.caarray.external.v1_0.experiment.Organism
 

P

parse(InputStream) - Method in class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
Parse an OWL document from given InputStream.
parse(Document) - Method in class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
Parse an OWL document from given Document.
ParseException - Exception in gov.nih.nci.caarray.util.owlparser
Exception thrown when there is an error parsing the owl.
ParseException() - Constructor for exception gov.nih.nci.caarray.util.owlparser.ParseException
Default.
ParseException(String) - Constructor for exception gov.nih.nci.caarray.util.owlparser.ParseException
PArse error with given message.
ParseException(Throwable) - Constructor for exception gov.nih.nci.caarray.util.owlparser.ParseException
PArse error with given cause.
ParseException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.util.owlparser.ParseException
PArse error with given message and cause.
ParseMgedOntology - Class in gov.nih.nci.caarray.util.owlparser
Executable class to parse the MGED Ontology OWL from a well-defined place in the classpath and write out a corresponding SQL file.
Person - Class in gov.nih.nci.caarray.external.v1_0.experiment
Person is a simple representation of a human.
Person() - Constructor for class gov.nih.nci.caarray.external.v1_0.experiment.Person
 
populateResourceProperties() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceBase
 
portType - Variable in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0ClientBase
 
portType - Variable in class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClientBase
 
portTypeMutex - Variable in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0ClientBase
 
portTypeMutex - Variable in class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClientBase
 
postFlush(Iterator) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
postProcessDetail(Session, Collection<AuditLogRecord>) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogProcessor
This method is called for any post processing required after the work from processDetail has been saved.
processCategory(Category) - Method in class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
Process acategory parsed from the OWL.
processCategory(Category) - Method in class gov.nih.nci.caarray.util.owlparser.SqlOntologyOwlParser
Process acategory parsed from the OWL.
processCategorySubclass(Category, Category) - Method in class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
Process a child-parent relationships between the two given categories.
processCategorySubclass(Category, Category) - Method in class gov.nih.nci.caarray.util.owlparser.SqlOntologyOwlParser
Process a child-parent relationships between the two given categories.
processDetail(AuditLogRecord, Object, Serializable, String, String, Object, Object) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogProcessor
processTerm(Term) - Method in class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
Process a term parsed from the OWL.
processTerm(Term) - Method in class gov.nih.nci.caarray.util.owlparser.SqlOntologyOwlParser
Process a term parsed from the OWL.
processTermSource(TermSource) - Method in class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
Process the term source parsed from the OWL.
processTermSource(TermSource) - Method in class gov.nih.nci.caarray.util.owlparser.SqlOntologyOwlParser
Process the term source parsed from the OWL.
ProjectHandler - Class in gov.nih.nci.caarray.util.audit
 
ProjectHandler(CaArrayAuditLogProcessor) - Constructor for class gov.nih.nci.caarray.util.audit.ProjectHandler
 
PropertyAccessor - Class in gov.nih.nci.caarray.util
Utility class representing the getter/setter pair for a property.
PropertyAccessor(Method, Method) - Constructor for class gov.nih.nci.caarray.util.PropertyAccessor
 
propertyToColumnName(String) - Method in class gov.nih.nci.caarray.util.NamingStrategy
ProtocolHandler - Class in gov.nih.nci.caarray.util.audit
 
ProtocolHandler(CaArrayAuditLogProcessor) - Constructor for class gov.nih.nci.caarray.util.audit.ProtocolHandler
 
pullOp(Pull) - Method in class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClient
 
pullOp(Pull) - Method in interface gov.nih.nci.cagrid.enumeration.common.CaGridEnumerationI
 

Q

QuantitationType - Class in gov.nih.nci.caarray.external.v1_0.data
A QuantitationType represents a quantity that can be measured by an array.
QuantitationType() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.QuantitationType
 
QuantitationTypeSearchCriteria - Class in gov.nih.nci.caarray.external.v1_0.query
 
QuantitationTypeSearchCriteria() - Constructor for class gov.nih.nci.caarray.external.v1_0.query.QuantitationTypeSearchCriteria
 
queryByExample(ExampleSearchCriteria<T>, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService.EntityHandler
return a list of entities of this handler's type, that match the given example criteria, subject to paging parameters.
queryResourceProperties(QueryResourceProperties_Element) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
queryResourceProperties(QueryResourceProperties_Element) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
 

R

readExternal(ObjectInput) - Method in class gov.nih.nci.caarray.external.v1_0.data.AbstractDataColumn
Optimizes the serialized form of this class by compressing the values array.
readFully(TransferServiceContextReference, OutputStream, boolean) - Static method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.GridDataApiUtils
Read data fully from the given Grid Transfer resource and write it to the given OutputStream.
ReflectionHelper - Class in gov.nih.nci.caarray.util
Utility class holding a set of PropertyAcessors for the properties of a class.
ReflectionHelper(PropertyAccessor[]) - Constructor for class gov.nih.nci.caarray.util.ReflectionHelper
 
ReflectionUtils - Class in gov.nih.nci.caarray.util
 
ReflectionUtils() - Constructor for class gov.nih.nci.caarray.util.ReflectionUtils
 
refreshRegistration(boolean) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceBase
This checks the configuration file, and attempts to register to the IndexService if shouldPerformRegistration==true.
release() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.SearchEnumIterator
releaseOp(Release) - Method in class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClient
 
releaseOp(Release) - Method in interface gov.nih.nci.cagrid.enumeration.common.CaGridEnumerationI
 
renewOp(Renew) - Method in class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClient
 
renewOp(Renew) - Method in interface gov.nih.nci.cagrid.enumeration.common.CaGridEnumerationI
 
replace(Object, Object, Object) - Method in class gov.nih.nci.caarray.util.URIUserType
resolve(String) - Method in interface gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService.EntityHandler
Retrieve and return the internal instance given an object id.
RESOURCE_KEY - Static variable in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0ConstantsBase
 
RESOURCE_KEY - Static variable in interface gov.nih.nci.cagrid.enumeration.common.CaGridEnumerationConstantsBase
 
RESOURCE_PROPERTY_SET - Static variable in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0ConstantsBase
 
RESOURCE_PROPERTY_SET - Static variable in interface gov.nih.nci.cagrid.enumeration.common.CaGridEnumerationConstantsBase
 
returnedClass() - Method in class gov.nih.nci.caarray.util.URIUserType
rollbackTransaction(Transaction) - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
Checks if the transaction is active and then rolls it back.
rollbackTransaction(Transaction) - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
Checks if the transaction is active and then rolls it back.

S

searchByExample(ExampleSearchCriteria, LimitOffset) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
searchByExample(ExampleSearchCriteria, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
Search using an entity as example
searchByExample(ExampleSearchCriteria, LimitOffset) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
searchByExample(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.SearchByExampleRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
searchByExample(ExampleSearchCriteria<T>, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.search.SearchService
Search for entities based on a specified example.
SearchEnumIterator<T extends AbstractCaArrayEntity> - Class in gov.nih.nci.caarray.services.external.v1_0.grid.service
 
SearchEnumIterator(Class<T>, SearchResultIterator<T>) - Constructor for class gov.nih.nci.caarray.services.external.v1_0.grid.service.SearchEnumIterator
 
searchForBiomaterials(BiomaterialSearchCriteria, LimitOffset) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
searchForBiomaterials(BiomaterialSearchCriteria, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
search for biomaterials matching criteria
searchForBiomaterials(BiomaterialSearchCriteria, LimitOffset) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
searchForBiomaterials(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.SearchForBiomaterialsRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
searchForBiomaterials(BiomaterialSearchCriteria, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.search.SearchService
Search for biomaterials satisfying the given search criteria.
searchForBiomaterialsByKeyword(BiomaterialKeywordSearchCriteria, LimitOffset) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
searchForBiomaterialsByKeyword(BiomaterialKeywordSearchCriteria, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
Search for biomaterials matching given keyword
searchForBiomaterialsByKeyword(BiomaterialKeywordSearchCriteria, LimitOffset) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
searchForBiomaterialsByKeyword(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.SearchForBiomaterialsByKeywordRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
searchForBiomaterialsByKeyword(BiomaterialKeywordSearchCriteria, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.search.SearchService
Search for biomaterials matching the given keyword criteria.
searchForExperiments(ExperimentSearchCriteria, LimitOffset) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
searchForExperiments(ExperimentSearchCriteria, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
Search for experiments matching given criteria
searchForExperiments(ExperimentSearchCriteria, LimitOffset) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
searchForExperiments(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.SearchForExperimentsRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
searchForExperiments(ExperimentSearchCriteria, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.search.SearchService
Search for experiments satisfying the given search criteria.
searchForExperimentsByKeyword(KeywordSearchCriteria, LimitOffset) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
searchForExperimentsByKeyword(KeywordSearchCriteria, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
Searches for experiments using a keyword search across fields
searchForExperimentsByKeyword(KeywordSearchCriteria, LimitOffset) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
searchForExperimentsByKeyword(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.SearchForExperimentsByKeywordRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
searchForExperimentsByKeyword(KeywordSearchCriteria, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.search.SearchService
Search for experiments matching the given keyword keyword criteria.
searchForFiles(FileSearchCriteria, LimitOffset) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
searchForFiles(FileSearchCriteria, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
Search for files matching given criteria
searchForFiles(FileSearchCriteria, LimitOffset) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
searchForFiles(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.SearchForFilesRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
searchForFiles(FileSearchCriteria, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.search.SearchService
Search for files satisfying the given search criteria.
searchForHybridizations(HybridizationSearchCriteria, LimitOffset) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
searchForHybridizations(HybridizationSearchCriteria, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
search for hybridizations matching criteria
searchForHybridizations(HybridizationSearchCriteria, LimitOffset) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
searchForHybridizations(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.SearchForHybridizationsRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
searchForHybridizations(HybridizationSearchCriteria, LimitOffset) - Method in interface gov.nih.nci.caarray.services.external.v1_0.search.SearchService
Search for hybridizations satisfying the given search criteria.
searchForQuantitationTypes(QuantitationTypeSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
searchForQuantitationTypes(QuantitationTypeSearchCriteria) - Method in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0I
Search for quantitation types matching criteria
searchForQuantitationTypes(QuantitationTypeSearchCriteria) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Impl
 
searchForQuantitationTypes(gov.nih.nci.caarray.services.external.v1_0.grid.stubs.SearchForQuantitationTypesRequest) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0ProviderImpl
 
searchForQuantitationTypes(QuantitationTypeSearchCriteria) - Method in interface gov.nih.nci.caarray.services.external.v1_0.search.SearchService
Returns a list of quantitation types satisfying the given search criteria.
SearchResult<T extends AbstractCaArrayEntity> - Class in gov.nih.nci.caarray.external.v1_0.query
SearchResult represents the result of performing a search.
SearchResult() - Constructor for class gov.nih.nci.caarray.external.v1_0.query.SearchResult
No-op constructor (for tooling).
SearchResult(List<T>, int, int) - Constructor for class gov.nih.nci.caarray.external.v1_0.query.SearchResult
Create a new SearchResult with given results and max # of results.
SearchService - Interface in gov.nih.nci.caarray.services.external.v1_0.search
Remote service for search and data enumeration.
sendMail(List<String>, String, String, String) - Static method in class gov.nih.nci.caarray.util.EmailUtil
Sends mail based upon input parameters.
sendMultipartMail(List<String>, String, String, String, String) - Static method in class gov.nih.nci.caarray.util.EmailUtil
Sends a multipart email with both HTML and plain-text bodies based upon input parameters.
SEPARATOR - Static variable in class gov.nih.nci.caarray.external.v1_0.data.AbstractDataColumn
separator to use for encoding an array of values as string, except for StringColumn.
SEQUENCE_NAME - Static variable in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
Name of the database sequence defined for audit transaction id.
serialize(Serializable) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Serializes the given object (zipped) to a byte array.
ServerConnectionException - Exception in gov.nih.nci.caarray.services
Indicates a problem connecting to a caArray server (or a dropped connection).
ServerConnectionException(String, Throwable) - Constructor for exception gov.nih.nci.caarray.services.ServerConnectionException
 
SERVICE_NAMESPACE - Static variable in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
SERVICE_NAMESPACE - Static variable in class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 
SERVICE_NS - Static variable in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0ConstantsBase
 
SERVICE_NS - Static variable in interface gov.nih.nci.cagrid.enumeration.common.CaGridEnumerationConstantsBase
 
SERVICEMETADATA - Static variable in interface gov.nih.nci.caarray.services.external.v1_0.grid.common.CaArraySvc_v1_0ConstantsBase
 
set(Object, Object) - Method in class gov.nih.nci.caarray.util.PropertyAccessor
Set the value of the property of this accessor on the given object to the given value.
setAccession(String) - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Category
 
setAccession(String) - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Term
 
setAnnotationCriterions(Set<AnnotationCriterion>) - Method in class gov.nih.nci.caarray.external.v1_0.query.BiomaterialSearchCriteria
 
setAnnotationCriterions(Set<AnnotationCriterion>) - Method in class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
setArrayDataTypes(Set<CaArrayEntityReference>) - Method in class gov.nih.nci.caarray.external.v1_0.query.QuantitationTypeSearchCriteria
 
setArrayDesign(ArrayDesign) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Hybridization
 
setArrayDesigns(Set<ArrayDesign>) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
setArrayProvider(ArrayProvider) - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
setArrayProvider(ArrayProvider) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
setArrayProvider(CaArrayEntityReference) - Method in class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
setAssayType(CaArrayEntityReference) - Method in class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
setAssayTypes(Set<AssayType>) - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
setAssayTypes(Set<AssayType>) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
setBiomaterials(Set<CaArrayEntityReference>) - Method in class gov.nih.nci.caarray.external.v1_0.query.HybridizationSearchCriteria
 
setCaGridWsEnumeration_iterImplType(String) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Configuration
 
setCategories(List<CaArrayEntityReference>) - Method in class gov.nih.nci.caarray.external.v1_0.query.AnnotationSetRequest
 
setCategories(Set<FileCategory>) - Method in class gov.nih.nci.caarray.external.v1_0.query.FileSearchCriteria
 
setCategories(List<Category>) - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationSet
 
setCategory(CaArrayEntityReference) - Method in class gov.nih.nci.caarray.external.v1_0.query.AnnotationCriterion
 
setCategory(Category) - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationValueSet
 
setCategory(Category) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
 
setCellType(TermValue) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
setCharacteristics(Set<Characteristic>) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
setColumns(List<AnnotationColumn>) - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationSet
 
setCommonName(String) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Organism
 
setCompressed(boolean) - Method in class gov.nih.nci.caarray.external.v1_0.data.FileContents
 
setCompressed(boolean) - Method in class gov.nih.nci.caarray.external.v1_0.data.FileStreamableContents
 
setCompressedSize(long) - Method in class gov.nih.nci.caarray.external.v1_0.data.FileMetadata
 
setConnectionTimeout(int) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0ClientBase
 
setConnectionTimeout(int) - Method in class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClientBase
 
setContacts(Set<ExperimentalContact>) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
setContents(byte[]) - Method in class gov.nih.nci.caarray.external.v1_0.data.FileContents
 
setContentStream(RemoteInputStream) - Method in class gov.nih.nci.caarray.external.v1_0.data.FileStreamableContents
 
setDataColumns(List<AbstractDataColumn>) - Method in class gov.nih.nci.caarray.external.v1_0.data.HybridizationData
 
setDataFiles(Set<File>) - Method in class gov.nih.nci.caarray.external.v1_0.data.MageTabFileSet
 
setDataFiles(Set<CaArrayEntityReference>) - Method in class gov.nih.nci.caarray.external.v1_0.query.DataSetRequest
 
setDatas(List<HybridizationData>) - Method in class gov.nih.nci.caarray.external.v1_0.data.DataSet
 
setDataType(DataType) - Method in class gov.nih.nci.caarray.external.v1_0.data.QuantitationType
Sets the data type for the quantity.
setDescription(String) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
setDescription(String) - Method in class gov.nih.nci.caarray.external.v1_0.factor.Factor
 
setDescription(String) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
setDesignElements(List<DesignElement>) - Method in class gov.nih.nci.caarray.external.v1_0.data.DataSet
 
setDiseaseState(TermValue) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
setEmailAddress(String) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Person
 
setEtcDirectoryPath(String) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.CaArraySvc_v1_0Configuration
 
setExample(T) - Method in class gov.nih.nci.caarray.external.v1_0.query.ExampleSearchCriteria
 
setExcludeNulls(boolean) - Method in class gov.nih.nci.caarray.external.v1_0.query.ExampleSearchCriteria
 
setExcludeZeroes(boolean) - Method in class gov.nih.nci.caarray.external.v1_0.query.ExampleSearchCriteria
 
setExperiment(CaArrayEntityReference) - Method in class gov.nih.nci.caarray.external.v1_0.query.BiomaterialSearchCriteria
 
setExperiment(CaArrayEntityReference) - Method in class gov.nih.nci.caarray.external.v1_0.query.FileSearchCriteria
 
setExperiment(CaArrayEntityReference) - Method in class gov.nih.nci.caarray.external.v1_0.query.HybridizationSearchCriteria
 
setExperiment(CaArrayEntityReference) - Method in class gov.nih.nci.caarray.external.v1_0.sample.AbstractExperimentGraphNode
 
setExperimentalDesigns(Set<Term>) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
setExperimentGraphNodes(List<CaArrayEntityReference>) - Method in class gov.nih.nci.caarray.external.v1_0.query.AnnotationSetRequest
 
setExperimentGraphNodes(Set<CaArrayEntityReference>) - Method in class gov.nih.nci.caarray.external.v1_0.query.FileSearchCriteria
 
setExtension(String) - Method in class gov.nih.nci.caarray.external.v1_0.query.FileSearchCriteria
 
setExternalId(String) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
setExternalIds(Set<String>) - Method in class gov.nih.nci.caarray.external.v1_0.query.BiomaterialSearchCriteria
 
setFactor(Factor) - Method in class gov.nih.nci.caarray.external.v1_0.factor.FactorValue
 
setFactors(Set<Factor>) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
setFactorValues(Set<FactorValue>) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Hybridization
 
setFileCategories(Set<FileCategory>) - Method in class gov.nih.nci.caarray.external.v1_0.query.QuantitationTypeSearchCriteria
 
setFiles(Set<File>) - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
setFileType(FileType) - Method in class gov.nih.nci.caarray.external.v1_0.data.FileMetadata
 
setFileTypeRegistry(FileTypeRegistry) - Method in class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService
 
setFileTypes(Set<CaArrayEntityReference>) - Method in class gov.nih.nci.caarray.external.v1_0.query.QuantitationTypeSearchCriteria
 
setFiltersEnabled(boolean) - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
Set whether security filters should be enabled for the next session returned from getCurrentSession().
setFiltersEnabled(boolean) - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperImpl
Set whether security filters should be enabled for the next session returned from getCurrentSession().
setFiltersEnabled(boolean) - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
Set whether security filters should be enabled for the next session returned from getCurrentSession().
setFirstName(String) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Person
 
setFirstResultOffset(int) - Method in class gov.nih.nci.caarray.external.v1_0.query.SearchResult
 
setHibernateHelper(HibernateHelper) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
 
setHybridization(Hybridization) - Method in class gov.nih.nci.caarray.external.v1_0.data.HybridizationData
 
setHybridization(CaArrayEntityReference) - Method in class gov.nih.nci.caarray.external.v1_0.query.QuantitationTypeSearchCriteria
 
setHybridizations(Set<CaArrayEntityReference>) - Method in class gov.nih.nci.caarray.external.v1_0.query.DataSetRequest
 
setId(String) - Method in class gov.nih.nci.caarray.external.v1_0.AbstractCaArrayEntity
 
setId(String) - Method in class gov.nih.nci.caarray.external.v1_0.CaArrayEntityReference
 
setIdf(FileContents) - Method in class gov.nih.nci.caarray.external.v1_0.data.MageTabFileSet
 
setKeyword(String) - Method in class gov.nih.nci.caarray.external.v1_0.query.KeywordSearchCriteria
 
setLabel(String) - Method in class gov.nih.nci.caarray.util.LabelValue
set label.
setLastDataModificationDate(Date) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
setLastModifiedDataTime(Date) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
setLastName(String) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Person
 
setLimit(int) - Method in class gov.nih.nci.caarray.external.v1_0.query.LimitOffset
 
setLsid(String) - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
setMapperVersionKey(String) - Method in class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService
Set a new mapper version key.
setMatchMode(MatchMode) - Method in class gov.nih.nci.caarray.external.v1_0.query.ExampleSearchCriteria
 
setMaterialType(TermValue) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
setMaxAllowedResults(int) - Method in class gov.nih.nci.caarray.external.v1_0.query.SearchResult
 
setMeasurement(Float) - Method in class gov.nih.nci.caarray.external.v1_0.value.MeasurementValue
 
setMeasurementValue(Float) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
Set the value of this charactestic to be a MeasurementValue with given measurement.
setMetadata(FileMetadata) - Method in class gov.nih.nci.caarray.external.v1_0.data.File
 
setMetadata(FileMetadata) - Method in class gov.nih.nci.caarray.external.v1_0.data.FileContents
 
setMetadata(FileMetadata) - Method in class gov.nih.nci.caarray.external.v1_0.data.FileStreamableContents
 
setMiddleInitials(String) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Person
 
setName(String) - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
setName(String) - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayProvider
 
setName(String) - Method in class gov.nih.nci.caarray.external.v1_0.array.AssayType
 
setName(String) - Method in class gov.nih.nci.caarray.external.v1_0.data.ArrayDataType
 
setName(String) - Method in class gov.nih.nci.caarray.external.v1_0.data.DesignElement
 
setName(String) - Method in class gov.nih.nci.caarray.external.v1_0.data.FileMetadata
 
setName(String) - Method in class gov.nih.nci.caarray.external.v1_0.data.FileType
 
setName(String) - Method in class gov.nih.nci.caarray.external.v1_0.data.QuantitationType
Sets the name for this quanity.
setName(String) - Method in class gov.nih.nci.caarray.external.v1_0.factor.Factor
 
setName(String) - Method in class gov.nih.nci.caarray.external.v1_0.sample.AbstractExperimentGraphNode
 
setName(String) - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Category
 
setName(String) - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.TermSource
 
setNames(Set<String>) - Method in class gov.nih.nci.caarray.external.v1_0.query.BiomaterialSearchCriteria
 
setNames(Set<String>) - Method in class gov.nih.nci.caarray.external.v1_0.query.HybridizationSearchCriteria
 
setNode(AbstractExperimentGraphNode) - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationColumn
 
setNormalizationTypes(Set<Term>) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
setOffset(int) - Method in class gov.nih.nci.caarray.external.v1_0.query.LimitOffset
 
setOrganism(Organism) - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
setOrganism(Organism) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
setOrganism(CaArrayEntityReference) - Method in class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
setOrganism(Organism) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
setPerformRegistration(boolean) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceConfiguration
 
setPerson(Person) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.ExperimentalContact
 
setPolicy(Node) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.CaArraySvc_v1_0Authorization
 
setPolicy(Node) - Method in class gov.nih.nci.cagrid.enumeration.service.globus.CaGridEnumerationAuthorization
 
setPrincipalInvestigators(Set<CaArrayEntityReference>) - Method in class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
setProcessor(DefaultProcessor) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
 
setPublicIdentifier(String) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
setPublicIdentifier(String) - Method in class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
setQualityControlTypes(Set<Term>) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
setQuantitationType(QuantitationType) - Method in class gov.nih.nci.caarray.external.v1_0.data.AbstractDataColumn
 
setQuantitationTypes(Set<QuantitationType>) - Method in class gov.nih.nci.caarray.external.v1_0.data.ArrayDataType
 
setQuantitationTypes(List<QuantitationType>) - Method in class gov.nih.nci.caarray.external.v1_0.data.DataSet
 
setQuantitationTypes(Set<CaArrayEntityReference>) - Method in class gov.nih.nci.caarray.external.v1_0.query.DataSetRequest
 
setQueryParams(Map<String, Object>, Query) - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
Sets the named parameters in the given query from the given map.
setQueryParams(Map<String, Object>, Query) - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperImpl
Sets the named parameters in the given query from the given map.
setQueryParams(Map<String, Object>, Query) - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
Sets the named parameters in the given query from the given map.
setRegistrationTemplateFile(String) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceConfiguration
 
setReplicateTypes(Set<Term>) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
setRoles(Set<Term>) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.ExperimentalContact
 
setScientificName(String) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Organism
 
setSdrf(FileContents) - Method in class gov.nih.nci.caarray.external.v1_0.data.MageTabFileSet
 
setSerializableValues(Serializable) - Method in class gov.nih.nci.caarray.external.v1_0.data.AbstractDataColumn
Set the values array of this column.
setSerializableValues(Serializable) - Method in class gov.nih.nci.caarray.external.v1_0.data.BooleanColumn
Set the values array of this column.
setSerializableValues(Serializable) - Method in class gov.nih.nci.caarray.external.v1_0.data.DoubleColumn
Set the values array of this column.
setSerializableValues(Serializable) - Method in class gov.nih.nci.caarray.external.v1_0.data.FloatColumn
Set the values array of this column.
setSerializableValues(Serializable) - Method in class gov.nih.nci.caarray.external.v1_0.data.IntegerColumn
Set the values array of this column.
setSerializableValues(Serializable) - Method in class gov.nih.nci.caarray.external.v1_0.data.LongColumn
Set the values array of this column.
setSerializableValues(Serializable) - Method in class gov.nih.nci.caarray.external.v1_0.data.ShortColumn
Set the values array of this column.
setSerializableValues(Serializable) - Method in class gov.nih.nci.caarray.external.v1_0.data.StringColumn
Set the values array of this column.
setServiceMetadata(gov.nih.nci.cagrid.metadata.ServiceMetadata) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceBase
 
setServiceMetadataFile(String) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceConfiguration
 
setTechnologyType(Term) - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
setter() - Method in class gov.nih.nci.caarray.util.PropertyAccessor
 
setTerm(Term) - Method in class gov.nih.nci.caarray.external.v1_0.value.TermValue
 
setTermSource(TermSource) - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Category
 
setTermSource(TermSource) - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Term
 
setTermValue(Term) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
Set the value of this charactestic to be a TermValue with given term.
setTissueSite(TermValue) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
setTitle(String) - Method in class gov.nih.nci.caarray.external.v1_0.experiment.Experiment
 
setTitle(String) - Method in class gov.nih.nci.caarray.external.v1_0.query.ExperimentSearchCriteria
 
setType(Term) - Method in class gov.nih.nci.caarray.external.v1_0.factor.Factor
 
setType(BiomaterialType) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Biomaterial
 
setTypes(Set<BiomaterialType>) - Method in class gov.nih.nci.caarray.external.v1_0.query.BiomaterialKeywordSearchCriteria
 
setTypes(Set<BiomaterialType>) - Method in class gov.nih.nci.caarray.external.v1_0.query.BiomaterialSearchCriteria
 
setTypes(Set<CaArrayEntityReference>) - Method in class gov.nih.nci.caarray.external.v1_0.query.FileSearchCriteria
 
setUncompressedSize(long) - Method in class gov.nih.nci.caarray.external.v1_0.data.FileMetadata
 
setUnit(Term) - Method in class gov.nih.nci.caarray.external.v1_0.value.AbstractValue
 
setUrl(String) - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Category
 
setUrl(String) - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Term
 
setUrl(String) - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.TermSource
 
setUser(String) - Method in interface gov.nih.nci.caarray.util.UsernameHolder
 
setUser(String) - Method in class gov.nih.nci.caarray.util.UsernameHolderImpl
setValue(AbstractValue) - Method in class gov.nih.nci.caarray.external.v1_0.factor.FactorValue
 
setValue(String) - Method in class gov.nih.nci.caarray.external.v1_0.query.AnnotationCriterion
 
setValue(AbstractValue) - Method in class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
 
setValue(String) - Method in class gov.nih.nci.caarray.external.v1_0.value.UserDefinedValue
 
setValue(String) - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.Term
 
setValue(String) - Method in class gov.nih.nci.caarray.util.LabelValue
set value.
setValues(boolean[]) - Method in class gov.nih.nci.caarray.external.v1_0.data.BooleanColumn
 
setValues(double[]) - Method in class gov.nih.nci.caarray.external.v1_0.data.DoubleColumn
 
setValues(float[]) - Method in class gov.nih.nci.caarray.external.v1_0.data.FloatColumn
 
setValues(int[]) - Method in class gov.nih.nci.caarray.external.v1_0.data.IntegerColumn
 
setValues(long[]) - Method in class gov.nih.nci.caarray.external.v1_0.data.LongColumn
 
setValues(short[]) - Method in class gov.nih.nci.caarray.external.v1_0.data.ShortColumn
 
setValues(String[]) - Method in class gov.nih.nci.caarray.external.v1_0.data.StringColumn
 
setValues(Set<AbstractValue>) - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationValueSet
 
setValuesAsString(String) - Method in class gov.nih.nci.caarray.external.v1_0.data.BooleanColumn
Set values from a String representation.
setValuesAsString(String) - Method in class gov.nih.nci.caarray.external.v1_0.data.DoubleColumn
Set values from a String representation.
setValuesAsString(String) - Method in class gov.nih.nci.caarray.external.v1_0.data.FloatColumn
Set values from a String representation.
setValuesAsString(String) - Method in class gov.nih.nci.caarray.external.v1_0.data.IntegerColumn
Set values from a String representation.
setValuesAsString(String) - Method in class gov.nih.nci.caarray.external.v1_0.data.LongColumn
Set values from a String representation.
setValuesAsString(String) - Method in class gov.nih.nci.caarray.external.v1_0.data.ShortColumn
Set values from a String representation.
setValuesAsString(String) - Method in class gov.nih.nci.caarray.external.v1_0.data.StringColumn
Sets the values of this column from a string, which must contain a comma-separated list of strings.
setValueSets(List<AnnotationValueSet>) - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationColumn
 
setVersion(String) - Method in class gov.nih.nci.caarray.external.v1_0.array.ArrayDesign
 
setVersion(String) - Method in class gov.nih.nci.caarray.external.v1_0.data.ArrayDataType
 
setVersion(String) - Method in class gov.nih.nci.caarray.external.v1_0.vocabulary.TermSource
 
ShortColumn - Class in gov.nih.nci.caarray.external.v1_0.data
A ShortColumn represents a data column with short values.
ShortColumn() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.ShortColumn
 
shouldPerformRegistration() - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.globus.resource.CaArraySvc_v1_0ResourceConfiguration
 
splitFromCsv(String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Splits the provided CSV String into an array of parsed values.
splitIntoBooleans(String, String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Splits the provided text into an array of parsed boolean values, using specified separator.
splitIntoDoubles(String, String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Splits the provided text into an array of parsed double values, using specified separator.
splitIntoFloats(String, String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Splits the provided text into an array of parsed float values, using specified separator.
splitIntoInts(String, String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Splits the provided text into an array of parsed int values, using specified separator.
splitIntoLongs(String, String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Splits the provided text into an array of parsed long values, using specified separator.
splitIntoShorts(String, String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Splits the provided text into an array of parsed short values, using specified separator.
SQL_FILE_NAME - Static variable in class gov.nih.nci.caarray.util.owlparser.ParseMgedOntology
Name of sql file to write out (filename only, directory to be passed in as command line argument).
SqlOntologyOwlParser - Class in gov.nih.nci.caarray.util.owlparser
OWL Parser that writes out sql statements createing the term source, categories and terms from the OWL data.
SqlOntologyOwlParser(String, String, File) - Constructor for class gov.nih.nci.caarray.util.owlparser.SqlOntologyOwlParser
Create a new parser that will write out to the given file.
sqlTypes() - Method in class gov.nih.nci.caarray.util.URIUserType
startProcessing() - Method in class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
Called to indicate the start of processing the OWL doc.
startProcessing() - Method in class gov.nih.nci.caarray.util.owlparser.SqlOntologyOwlParser
Called to indicate the start of processing the OWL doc.
streamFileContents(CaArrayEntityReference, boolean) - Method in interface gov.nih.nci.caarray.services.external.v1_0.data.DataService
Returns a RemoteInputStream through which the client can retrieve the data for the file identified by the given reference.
StringColumn - Class in gov.nih.nci.caarray.external.v1_0.data
A StringColumn represents a data column with string values.
StringColumn() - Constructor for class gov.nih.nci.caarray.external.v1_0.data.StringColumn
 

T

tableName(String) - Method in class gov.nih.nci.caarray.util.NamingStrategy
Term - Class in gov.nih.nci.caarray.external.v1_0.vocabulary
A Term represents a value from a controlled vocabulary / ontology.
Term() - Constructor for class gov.nih.nci.caarray.external.v1_0.vocabulary.Term
 
TermHandler - Class in gov.nih.nci.caarray.util.audit
 
TermHandler(CaArrayAuditLogProcessor) - Constructor for class gov.nih.nci.caarray.util.audit.TermHandler
 
TermSource - Class in gov.nih.nci.caarray.external.v1_0.vocabulary
A TermSource represents a controlled vocabulary / ontology.
TermSource() - Constructor for class gov.nih.nci.caarray.external.v1_0.vocabulary.TermSource
 
TermValue - Class in gov.nih.nci.caarray.external.v1_0.value
A TermValue is a value defined by a term within a controlled vocabulary.
TermValue() - Constructor for class gov.nih.nci.caarray.external.v1_0.value.TermValue
 
toInternalParams(LimitOffset, SortCriterion<T>, boolean) - Method in class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService
convert given external paging params instance into internal paging params.
toInternalParams(LimitOffset, String, boolean) - Method in class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService
convert given external paging params instance into internal paging params.
toInternalParams(LimitOffset, String, boolean, Class<T>) - Method in class gov.nih.nci.caarray.services.external.v1_0.impl.BaseV1_0ExternalService
convert given external paging params instance into internal ones.
toString() - Method in class gov.nih.nci.caarray.external.v1_0.AbstractCaArrayEntity
toString() - Method in class gov.nih.nci.caarray.external.v1_0.CaArrayEntityReference
toString() - Method in class gov.nih.nci.caarray.external.v1_0.data.DesignElement
toString() - Method in class gov.nih.nci.caarray.external.v1_0.data.FileMetadata
toString() - Method in class gov.nih.nci.caarray.external.v1_0.data.FileType
toString() - Method in class gov.nih.nci.caarray.external.v1_0.factor.FactorValue
toString() - Method in class gov.nih.nci.caarray.external.v1_0.query.KeywordSearchCriteria
toString() - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationColumn
toString() - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationSet
toString() - Method in class gov.nih.nci.caarray.external.v1_0.sample.AnnotationValueSet
toString() - Method in class gov.nih.nci.caarray.external.v1_0.sample.Characteristic
toString() - Method in class gov.nih.nci.caarray.external.v1_0.value.AbstractValue
toString() - Method in class gov.nih.nci.caarray.util.LabelValue
Return a string representation of this object.

U

unbindAndCleanupSession() - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
Close the current session and unbind it via ManagedSessionContext#unbind(SessionFactory).
unbindAndCleanupSession() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
Close the current session and unbind it via ManagedSessionContext#unbind(SessionFactory).
UnfilteredCallback - Interface in gov.nih.nci.caarray.util
 
uniqueResult(Collection<T>) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Method to take a get a unique result from a set and return it or null.
UnsupportedCategoryException - Exception in gov.nih.nci.caarray.services.external.v1_0
Exception thrown to indicate that a category used in an AnnotationCriterion is not currently supported.
UnsupportedCategoryException - Exception in gov.nih.nci.caarray.services.external.v1_0
Exception thrown to indicate that a category used in an AnnotationCriterion is not currently supported.
UnsupportedCategoryException(CaArrayEntityReference) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.UnsupportedCategoryException
Constructor for no cause.
UnsupportedCategoryException(CaArrayEntityReference, String) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.UnsupportedCategoryException
Constructor for no cause.
UnsupportedCategoryException(CaArrayEntityReference) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.UnsupportedCategoryException
Constructor for no cause.
UnsupportedCategoryException(CaArrayEntityReference, String) - Constructor for exception gov.nih.nci.caarray.services.external.v1_0.UnsupportedCategoryException
Constructor for no cause.
unwrapProxy(Object) - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
If entity is a hibernate proxy, return the actual object it proxies, otherwise return the entity itself.
unwrapProxy(Object) - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperImpl
If entity is a hibernate proxy, return the actual object it proxies, otherwise return the entity itself.
unwrapProxy(Object) - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
If entity is a hibernate proxy, return the actual object it proxies, otherwise return the entity itself.
URIUserType - Class in gov.nih.nci.caarray.util
Custom Hibernate Type for URIs.
URIUserType() - Constructor for class gov.nih.nci.caarray.util.URIUserType
 
usage() - Static method in class gov.nih.nci.caarray.services.external.v1_0.grid.client.CaArraySvc_v1_0Client
 
usage() - Static method in class gov.nih.nci.cagrid.enumeration.client.CaGridEnumerationClient
 
UserDefinedValue - Class in gov.nih.nci.caarray.external.v1_0.value
A UserDefinedValue is a free text value.
UserDefinedValue() - Constructor for class gov.nih.nci.caarray.external.v1_0.value.UserDefinedValue
 
UsernameHolder - Interface in gov.nih.nci.caarray.util
Holds the name of the currently-logged in user.
UsernameHolderImpl - Class in gov.nih.nci.caarray.util
Delegates to the static UsernameHolder class.
UsernameHolderImpl() - Constructor for class gov.nih.nci.caarray.util.UsernameHolderImpl
 
UsernameHolderModule - Class in gov.nih.nci.caarray.util
 
UsernameHolderModule() - Constructor for class gov.nih.nci.caarray.util.UsernameHolderModule
 

V

valueOf(String) - Static method in enum gov.nih.nci.caarray.external.v1_0.data.DataType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.external.v1_0.data.FileCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.external.v1_0.query.MatchMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.external.v1_0.sample.BiomaterialType
Returns the enum constant of this type with the specified name.
values() - Static method in enum gov.nih.nci.caarray.external.v1_0.data.DataType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum gov.nih.nci.caarray.external.v1_0.data.FileCategory
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum gov.nih.nci.caarray.external.v1_0.query.MatchMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum gov.nih.nci.caarray.external.v1_0.sample.BiomaterialType
Returns an array containing the constants of this enum type, in the order they are declared.

W

wrapUpElements(List<SOAPElement>, boolean) - Method in class gov.nih.nci.caarray.services.external.v1_0.grid.service.SearchEnumIterator
 
writeExternal(ObjectOutput) - Method in class gov.nih.nci.caarray.external.v1_0.data.AbstractDataColumn
Optimizes the serialized form of this class by compressing the values array.

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