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

A

AbstractArrayData - Class in gov.nih.nci.caarray.domain.data
 
AbstractArrayData() - Constructor for class gov.nih.nci.caarray.domain.data.AbstractArrayData
 
AbstractBioMaterial - Class in gov.nih.nci.caarray.domain.sample
AbstractBiomaterial represents a biomaterial at some stage prior to being hybridized to an array.
AbstractBioMaterial() - Constructor for class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
AbstractBioMaterialSortCriterion - Enum in gov.nih.nci.caarray.domain.search
 
AbstractCaArrayEntity - Class in gov.nih.nci.caarray.domain
Base class for all caArray domain entities.
AbstractCaArrayEntity() - Constructor for class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
Default constructor.
AbstractCaArrayEntity(String, String, String) - Constructor for class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
Constructor with LSID information.
AbstractCaArrayObject - Class in gov.nih.nci.caarray.domain
Base class for all persistent caArray domain objects.
AbstractCaArrayObject() - Constructor for class gov.nih.nci.caarray.domain.AbstractCaArrayObject
 
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.
AbstractCharacteristic - Class in gov.nih.nci.caarray.domain.sample
 
AbstractCharacteristic() - Constructor for class gov.nih.nci.caarray.domain.sample.AbstractCharacteristic
Hibernate-only constructor.
AbstractCharacteristic(Category) - Constructor for class gov.nih.nci.caarray.domain.sample.AbstractCharacteristic
Creates a new AbstractCharacteristic with given category.
AbstractCharacteristic(Category, Term) - Constructor for class gov.nih.nci.caarray.domain.sample.AbstractCharacteristic
Creates a new AbstractCharacteristic with given category and unit.
AbstractContact - Class in gov.nih.nci.caarray.domain.contact
 
AbstractContact() - Constructor for class gov.nih.nci.caarray.domain.contact.AbstractContact
 
AbstractDataColumn - Class in gov.nih.nci.caarray.domain.data
Subclasses of AbstractDataColumn contain the actual array data corresponding to a single QuantitationType.
AbstractDataColumn() - Constructor for class gov.nih.nci.caarray.domain.data.AbstractDataColumn
 
AbstractDesignElement - Class in gov.nih.nci.caarray.domain.array
Base class for all array design elements.
AbstractDesignElement() - Constructor for class gov.nih.nci.caarray.domain.array.AbstractDesignElement
Element constructor.
AbstractExperimentDesignNode - Class in gov.nih.nci.caarray.domain.project
Common interface for the nodes in the experiment design graph.
AbstractExperimentDesignNode() - Constructor for class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
 
AbstractFactorValue - Class in gov.nih.nci.caarray.domain.project
 
AbstractFactorValue() - Constructor for class gov.nih.nci.caarray.domain.project.AbstractFactorValue
Hibernate-only constructor.
AbstractFactorValue(Term) - Constructor for class gov.nih.nci.caarray.domain.project.AbstractFactorValue
Create a new factor value with given unit.
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.
AbstractParameterValue - Class in gov.nih.nci.caarray.domain.protocol
A value for a parameter of a Protocol for a specific ProtocolApplication of that Protocol.
AbstractParameterValue() - Constructor for class gov.nih.nci.caarray.domain.protocol.AbstractParameterValue
Default constructor.
AbstractParameterValue(AbstractParameterValue) - Constructor for class gov.nih.nci.caarray.domain.protocol.AbstractParameterValue
Constructs a new ParameterValue based on an existing one.
AbstractParameterValue(Term) - Constructor for class gov.nih.nci.caarray.domain.protocol.AbstractParameterValue
Constructs a new ParameterValue with given unit.
AbstractProbe - Class in gov.nih.nci.caarray.domain.array
Reports on the presence or intensity of a given target probe.
AbstractProbe() - Constructor for class gov.nih.nci.caarray.domain.array.AbstractProbe
Constructor.
AbstractProbeAnnotation - Class in gov.nih.nci.caarray.domain.array
Base class for caArray probe annotations.
AbstractProbeAnnotation() - Constructor for class gov.nih.nci.caarray.domain.array.AbstractProbeAnnotation
 
AbstractUnitableValue - Class in gov.nih.nci.caarray.domain
Base class for UnitableValue implementations.
AbstractUnitableValue() - Constructor for class gov.nih.nci.caarray.domain.AbstractUnitableValue
 
Accession - Class in gov.nih.nci.caarray.domain.array
Uniquely identifies a gene relative to a public sequence database.
Accession() - Constructor for class gov.nih.nci.caarray.domain.array.Accession
Deprecated. public for castor and hibernate only.
Accession(String, String) - Constructor for class gov.nih.nci.caarray.domain.array.Accession
 
AccessProfile - Class in gov.nih.nci.caarray.domain.permissions
Container class that models the read and write permissions to samples.
AccessProfile() - Constructor for class gov.nih.nci.caarray.domain.permissions.AccessProfile
Hibernate-only constructor.
AccessProfile(SecurityLevel) - Constructor for class gov.nih.nci.caarray.domain.permissions.AccessProfile
Creates a new profile with given initial security level.
add(CaArrayFile) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFileSet
Adds a file to the set.
addAccessionNumber(String, String) - Method in class gov.nih.nci.caarray.domain.array.Gene
Add an accession to this gene.
addAccessionNumber(String, String) - Method in class gov.nih.nci.caarray.domain.array.MiRNAProbeAnnotation
Add an accession to this gene.
addAll(Collection<CaArrayFile>) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFileSet
Adds a collection of files to this set.
addArrayData(AbstractArrayData) - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Add a new array data to this hybridization.
addBlob(Blob) - Method in class gov.nih.nci.caarray.domain.MultiPartBlob
Add a blob part.
addChild(CaArrayFile) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
Adds a new child CaArrayFile.
addDesignElement(AbstractDesignElement) - Method in class gov.nih.nci.caarray.domain.data.DataRetrievalRequest
Include data related to this design element.
addDesignFile(CaArrayFile) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Add a new design file to this design.
addDirectPredecessor(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
Add a new node as a direct predecessor of this node.
addDirectSuccessor(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
Add a new node as a direct successor of this node.
addFeature(Feature) - Method in class gov.nih.nci.caarray.domain.array.PhysicalProbe
Add a feature to this physical probe.
addGroupProfile(CollaboratorGroup) - Method in class gov.nih.nci.caarray.domain.project.Project
Add a new AccessProfile for a collaborator group unless the project already has a profile for this group.
addHybridization(Hybridization) - Method in class gov.nih.nci.caarray.domain.data.AbstractArrayData
Add a new hybridization to the collection of associated hybridizations.
addHybridization(Hybridization) - Method in class gov.nih.nci.caarray.domain.data.DataRetrievalRequest
Include data related to this hybridization.
addHybridizationData(Hybridization) - Method in class gov.nih.nci.caarray.domain.data.DataSet
Creates a new HybridizationData for this DataSet.
AdditionalOrganismName - Class in edu.georgetown.pir
Other common or scientific names by which the organism known.
AdditionalOrganismName() - Constructor for class edu.georgetown.pir.AdditionalOrganismName
 
addProbe(PhysicalProbe) - Method in class gov.nih.nci.caarray.domain.array.LogicalProbe
Add a physical probe to this logical probe.
addProtocolApplication(ProtocolApplication) - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Add the given protocol application to the protocol applications of this.
addProtocolApplication(ProtocolApplication) - Method in interface gov.nih.nci.caarray.domain.protocol.ProtocolApplicable
Add the given protocol application to the protocol applications of this.
addProtocolApplication(ProtocolApplication) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Add the given protocol application to the protocol applications of this.
addQuantitationType(QuantitationType) - Method in class gov.nih.nci.caarray.domain.data.DataRetrievalRequest
Return data for this quantitation type.
addQuantitationType(QuantitationType) - Method in class gov.nih.nci.caarray.domain.data.DataSet
Adds a new type to this DataSet, creating the appropriate columns for all HybridizationDatas.
addQuantitationTypes(List<QuantitationType>) - Method in class gov.nih.nci.caarray.domain.data.DataSet
Adds a list of new types to this DataSet, creating the appropriate columns for all HybridizationDatas.
Address - Class in gov.nih.nci.caarray.domain.contact
 
Address() - Constructor for class gov.nih.nci.caarray.domain.contact.Address
 
AdHocSortCriterion<T> - Class in gov.nih.nci.caarray.domain.search
Class for creating an ad-hoc sort criterion, ie when there is no enumeration of sort fields for an entity.
AdHocSortCriterion(String) - Constructor for class gov.nih.nci.caarray.domain.search.AdHocSortCriterion
Create a new criterion using given sort field.
afterTransactionCompletion(Transaction) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
AnnotationCriterion - Class in gov.nih.nci.caarray.domain.search
An AnnotationCriterion specifies a criterion that matches Characteristics having the given category and value.
AnnotationCriterion() - Constructor for class gov.nih.nci.caarray.domain.search.AnnotationCriterion
Empty constructor.
AnnotationCriterion(Category, String) - Constructor for class gov.nih.nci.caarray.domain.search.AnnotationCriterion
Constructor for AnnotationCriterion with given category and value.
areColumnsLoaded(Collection<QuantitationType>) - Method in class gov.nih.nci.caarray.domain.data.HybridizationData
Determine whether all columns for the given quantitation types in this HybridizationData have been loaded with data values.
Array - Class in gov.nih.nci.caarray.domain.array
Represents a single, physical microarray used in an experiment.
Array() - Constructor for class gov.nih.nci.caarray.domain.array.Array
 
ArrayDataType - Class in gov.nih.nci.caarray.domain.data
Indicates the source of array data and the complete list of QuantitationTypes that may be associated with the particular type and version.
ArrayDataType() - Constructor for class gov.nih.nci.caarray.domain.data.ArrayDataType
 
ArrayDataTypeDescriptor - Interface in gov.nih.nci.caarray.domain.data
Interface that enums of specific supported array data types must implement in order to register potentially new ArrayDataTypes with caArray.
ArrayDesign - Class in gov.nih.nci.caarray.domain.array
The design details for a type of microarray.
ArrayDesign() - Constructor for class gov.nih.nci.caarray.domain.array.ArrayDesign
Default constructor.
ArrayDesign(ArrayDesign) - Constructor for class gov.nih.nci.caarray.domain.array.ArrayDesign
Copy constructor.
ArrayDesignDetails - Class in gov.nih.nci.caarray.domain.array
Contains the low-level array design details (Features, PhysicalProbes, and LogicalProbes) for a microarray design.
ArrayDesignDetails() - Constructor for class gov.nih.nci.caarray.domain.array.ArrayDesignDetails
 
ArrayDesignDetailsService - Interface in gov.nih.nci.caarray.services.arraydesign
Remote API interface used to retrieve low-level microarray design details.
ArrayGroup - Class in gov.nih.nci.caarray.domain.array
Groupping mechanism for Arrays.
ArrayGroup() - Constructor for class gov.nih.nci.caarray.domain.array.ArrayGroup
 
ArrayReporter - Class in gov.nih.nci.cabio.domain
 
ArrayReporter() - Constructor for class gov.nih.nci.cabio.domain.ArrayReporter
 
AssayType - Class in gov.nih.nci.caarray.domain.project
Represents a single assay type associated with an Experiment or Array Design.
AssayType() - Constructor for class gov.nih.nci.caarray.domain.project.AssayType
Deprecated. hibernate & castor only
AssayType(String) - Constructor for class gov.nih.nci.caarray.domain.project.AssayType
 
assemble(Serializable, Object) - Method in class gov.nih.nci.caarray.util.URIUserType
AuditLogSearchCriteria - Class in gov.nih.nci.caarray.domain.search
 
AuditLogSearchCriteria() - Constructor for class gov.nih.nci.caarray.domain.search.AuditLogSearchCriteria
 
AuditLogSecurity - Class in gov.nih.nci.caarray.domain.audit
This object maps access to an audit log record based on project permissions.
AuditLogSecurity() - Constructor for class gov.nih.nci.caarray.domain.audit.AuditLogSecurity
For UI / Hibernate Usage only.
AuditLogSecurity(String, Long, Long, AuditLogRecord) - Constructor for class gov.nih.nci.caarray.domain.audit.AuditLogSecurity
Constructor.
AuditLogSortCriterion - Enum in gov.nih.nci.caarray.domain.search
 
authorizeCreateFileTransfer() - Static method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
authorizeGetDataSet() - Static method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
authorizeGetDesignDetails() - Static method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
authorizeGetMultipleResourceProperties() - Static method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
authorizeGetResourceProperty() - Static method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
authorizeGetServiceSecurityMetadata() - Static method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
authorizeQuery() - Static method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
authorizeQueryResourceProperties() - Static method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
authorizeReadFile() - Static method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 

B

BaseJob - Interface in gov.nih.nci.caarray.domain.project
 
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_FILTER_NAME - Static variable in class gov.nih.nci.caarray.domain.project.Experiment
Biomaterial Filter name.
BiomaterialSearchCategory - Interface in gov.nih.nci.caarray.domain.search
 
BiomaterialSearchCriteria - Class in gov.nih.nci.caarray.domain.search
Simple bean to hold search criteria for biomaterials.
BiomaterialSearchCriteria() - Constructor for class gov.nih.nci.caarray.domain.search.BiomaterialSearchCriteria
 
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.
BlobHolder - Class in gov.nih.nci.caarray.domain
 
BlobHolder() - Constructor for class gov.nih.nci.caarray.domain.BlobHolder
 
BooleanColumn - Class in gov.nih.nci.caarray.domain.data
Contains a column of boolean values.
BooleanColumn() - Constructor for class gov.nih.nci.caarray.domain.data.BooleanColumn
 
BrowseCategory - Enum in gov.nih.nci.caarray.domain.search
 
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

CaArray2xGrid - Class in gov.nih.nci.cagrid.caarray.client
 
CaArray2xGrid() - Constructor for class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
CaArray2xGrid(String) - Constructor for class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
CAARRAY_LSID_AUTHORITY - Static variable in class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
LSID Authority for CAARRAY.
CAARRAY_LSID_NAMESPACE - Static variable in class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
LSID Namespace for CAARRAY.
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
 
CaArrayCQLQueryProcessor - Class in gov.nih.nci.cagrid.caarray.stubs.cql
The actual CaArray CQL processing implementation.
CaArrayCQLQueryProcessor() - Constructor for class gov.nih.nci.cagrid.caarray.stubs.cql.CaArrayCQLQueryProcessor
 
CaArrayDeserializer - Class in gov.nih.nci.cagrid.caarray.util
This is identical to the SDK Serializer but turns off validation.
CaArrayDeserializer(Class, QName) - Constructor for class gov.nih.nci.cagrid.caarray.util.CaArrayDeserializer
 
CaArrayFile - Class in gov.nih.nci.caarray.domain.file
This class represents metadata about a file managed by caArray.
CaArrayFile() - Constructor for class gov.nih.nci.caarray.domain.file.CaArrayFile
Default blank constructor.
CaArrayFile(CaArrayFile) - Constructor for class gov.nih.nci.caarray.domain.file.CaArrayFile
Creates a CaArrayFile with a parent.
CaArrayFileSet - Class in gov.nih.nci.caarray.domain.file
Provides functionality to handle multiple CaArrayFiles as a single set.
CaArrayFileSet(Project) - Constructor for class gov.nih.nci.caarray.domain.file.CaArrayFileSet
 
CaArrayFileSet(Long) - Constructor for class gov.nih.nci.caarray.domain.file.CaArrayFileSet
 
CaArrayFileSet(CaArrayFileSet) - Constructor for class gov.nih.nci.caarray.domain.file.CaArrayFileSet
Construct a new file set, with the same files and associated project.
CaArrayFileSet() - Constructor for class gov.nih.nci.caarray.domain.file.CaArrayFileSet
File set.
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.
CaArraySearchService - Interface in gov.nih.nci.caarray.services.search
Search API for caArray, based on various types of criteria.
CaArraySerializer - Class in gov.nih.nci.cagrid.caarray.util
This is identical to the SDK Serializer but turns off validation.
CaArraySerializer() - Constructor for class gov.nih.nci.cagrid.caarray.util.CaArraySerializer
 
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.
CaArraySvcAuthorization - Class in gov.nih.nci.cagrid.caarray.service.globus
DO NOT EDIT: This class is autogenerated! This is a PDP for use with the globus authorization callout.
CaArraySvcAuthorization() - Constructor for class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
CaArraySvcClient - Class in gov.nih.nci.cagrid.caarray.client
This class is autogenerated, DO NOT EDIT GENERATED GRID SERVICE ACCESS METHODS.
CaArraySvcClient(String) - Constructor for class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
CaArraySvcClient(String, GlobusCredential) - Constructor for class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
CaArraySvcClient(EndpointReferenceType) - Constructor for class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
CaArraySvcClient(EndpointReferenceType, GlobusCredential) - Constructor for class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
CaArraySvcClientBase - Class in gov.nih.nci.cagrid.caarray.client
This class is autogenerated, DO NOT EDIT GENERATED GRID SERVICE ACCESS METHODS.
CaArraySvcClientBase(String, GlobusCredential) - Constructor for class gov.nih.nci.cagrid.caarray.client.CaArraySvcClientBase
 
CaArraySvcClientBase(EndpointReferenceType, GlobusCredential) - Constructor for class gov.nih.nci.cagrid.caarray.client.CaArraySvcClientBase
 
CaArraySvcConfiguration - Class in gov.nih.nci.cagrid.caarray.service
DO NOT EDIT: This class is autogenerated! This class holds all service properties which were defined for the service to have access to.
CaArraySvcConfiguration() - Constructor for class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
CaArraySvcConstants - Interface in gov.nih.nci.cagrid.caarray.common
Constants class that extends the introduce managed constants.
CaArraySvcConstantsBase - Interface in gov.nih.nci.cagrid.caarray.common
This class is autogenerated, DO NOT EDIT
CaArraySvcI - Interface in gov.nih.nci.cagrid.caarray.common
This class is autogenerated, DO NOT EDIT.
CaArraySvcImpl - Class in gov.nih.nci.cagrid.caarray.service
Primary service side implementation of the remote caArray API.
CaArraySvcImpl() - Constructor for class gov.nih.nci.cagrid.caarray.service.CaArraySvcImpl
Constructs the service implementation.
CaArraySvcImplBase - Class in gov.nih.nci.cagrid.caarray.service
DO NOT EDIT: This class is autogenerated! Provides some simple accessors for the Impl.
CaArraySvcImplBase() - Constructor for class gov.nih.nci.cagrid.caarray.service.CaArraySvcImplBase
 
CaArraySvcProviderImpl - Class in gov.nih.nci.cagrid.caarray.service.globus
DO NOT EDIT: This class is autogenerated! This class implements each method in the portType of the service.
CaArraySvcProviderImpl() - Constructor for class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcProviderImpl
 
CaArraySvcResource - Class in gov.nih.nci.cagrid.caarray.service.globus.resource
The implementation of this CaArraySvcResource type.
CaArraySvcResource() - Constructor for class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResource
 
CaArraySvcResourceBase - Class in gov.nih.nci.cagrid.caarray.service.globus.resource
DO NOT EDIT: This class is autogenerated! This class is the base class of the resource type created for this service.
CaArraySvcResourceBase() - Constructor for class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceBase
 
CaArraySvcResourceConfiguration - Class in gov.nih.nci.cagrid.caarray.service.globus.resource
DO NOT EDIT: This class is autogenerated! This class is used by the resource to get configuration information about the resource.
CaArraySvcResourceConfiguration() - Constructor for class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceConfiguration
 
CaArraySvcResourceHome - Class in gov.nih.nci.cagrid.caarray.service.globus.resource
DO NOT EDIT: This class is autogenerated! This class implements the resource home for the resource type represented by this service.
CaArraySvcResourceHome() - Constructor for class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceHome
 
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.
canModifyPermissions(User) - Method in class gov.nih.nci.caarray.domain.project.Project
Returns whether the given user has permission to modify permissions for this project.
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.domain.vocabulary
 
Category() - Constructor for class gov.nih.nci.caarray.domain.vocabulary.Category
Empty constructor (for tools).
Category(String, TermSource) - Constructor for class gov.nih.nci.caarray.domain.vocabulary.Category
Create Category with given name and source.
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.
checkType(String) - Static method in enum gov.nih.nci.caarray.domain.data.DesignElementType
Checks to see that the value given is a legal DesignElementType value.
classToTableName(String) - Method in class gov.nih.nci.caarray.util.NamingStrategy
clearProtocolApplications() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Remove all protocol applications of this.
clearProtocolApplications() - Method in interface gov.nih.nci.caarray.domain.protocol.ProtocolApplicable
Remove all protocol applications of this.
clearProtocolApplications() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Remove all protocol applications of this.
close() - Method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
CollaboratorGroup - Class in gov.nih.nci.caarray.domain.permissions
CollaboratorGroups bridge CSM groups with owners.
CollaboratorGroup(Group, User) - Constructor for class gov.nih.nci.caarray.domain.permissions.CollaboratorGroup
 
CollaboratorGroup() - Constructor for class gov.nih.nci.caarray.domain.permissions.CollaboratorGroup
For UI / Hibernate Usage only.
collaboratorGroupLevels() - Static method in enum gov.nih.nci.caarray.domain.permissions.SecurityLevel
 
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
compare(Sample, Sample) - Method in class gov.nih.nci.caarray.domain.sample.Sample.ByNameComparator
Compares samples by name.
compareTo(Country) - Method in class gov.nih.nci.caarray.domain.country.Country
Compares countries by name, putting a preferred country ahead of all others.
compareTo(CaArrayFile) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
compareTo(FileType) - Method in class gov.nih.nci.caarray.domain.file.FileType
compareTo(AccessProfile) - Method in class gov.nih.nci.caarray.domain.permissions.AccessProfile
Compares Access Profiles by group name, putting "The Public" after Collaboration groups.
compareTo(AssayType) - Method in class gov.nih.nci.caarray.domain.project.AssayType
Compares assayTypes by name.
compareTo(Project) - Method in class gov.nih.nci.caarray.domain.project.Project
compareTo(Term) - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
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.
ConfigParamEnum - Enum in gov.nih.nci.caarray.domain
Various configuration parameters.
configuration - Static variable in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
configuration - Static variable in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
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.cagrid.caarray.client.CaArraySvcClientBase
 
consumerEPR - Variable in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClientBase
 
Country - Class in gov.nih.nci.caarray.domain.country
 
Country() - Constructor for class gov.nih.nci.caarray.domain.country.Country
 
create() - Static method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperImpl
 
create(Class<?>, QName) - Static method in class gov.nih.nci.cagrid.caarray.util.DeserializationFactory
 
create(Class<?>, QName) - Static method in class gov.nih.nci.cagrid.caarray.util.SerializationFactory
 
createFileTransfer(CaArrayFile) - Method in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
createFileTransfer(CaArrayFile) - Method in interface gov.nih.nci.cagrid.caarray.common.CaArraySvcI
Requests a Grid Transfer handle for the given file
createFileTransfer(CaArrayFile) - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcImpl
 
createFileTransfer(gov.nih.nci.cagrid.caarray.stubs.CreateFileTransferRequest) - Method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcProviderImpl
 
createPortType() - Method in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClientBase
 
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.cagrid.caarray.service.globus.resource.CaArraySvcResourceHome
 

D

DataRetrievalRequest - Class in gov.nih.nci.caarray.domain.data
Allows for the specification of precisely which array data are to be returned from caArray.
DataRetrievalRequest() - Constructor for class gov.nih.nci.caarray.domain.data.DataRetrievalRequest
Creates a new, empty request instance.
DataRetrievalService - Interface in gov.nih.nci.caarray.services.data
Returns requested array data from caArray.
DataSet - Class in gov.nih.nci.caarray.domain.data
Contains hybridization data represented by an AbstractArrayData or as requested by a client.
DataSet() - Constructor for class gov.nih.nci.caarray.domain.data.DataSet
 
datasLoaded(List<QuantitationType>) - Method in class gov.nih.nci.caarray.domain.data.DataSet
Determine whether all columns for the given quantitation types in each HybridizationData in this DataSet have been loaded with data values.
DataType - Enum in gov.nih.nci.caarray.domain.data
Enumerates the data types allowed for quantitation types.
deepCopy(Object) - Method in class gov.nih.nci.caarray.util.URIUserType
DEFAULT_BATCH_SIZE - Static variable in class gov.nih.nci.caarray.domain.AbstractCaArrayObject
Default hibernate batch size.
DEFAULT_STRING_COLUMN_SIZE - Static variable in class gov.nih.nci.caarray.domain.AbstractCaArrayObject
The default column size for string columns in the db.
DefaultJobMessageSenderImpl - Class in gov.nih.nci.caarray.domain.project
 
DefaultJobMessageSenderImpl() - Constructor for class gov.nih.nci.caarray.domain.project.DefaultJobMessageSenderImpl
 
DELETABLE_FILE_STATUSES - Static variable in enum gov.nih.nci.caarray.domain.file.FileStatus
The set of FileStatuses in which a file can be deleted.
dequoteString(String) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Removes matched quotes (single or double) from a string.
DerivedArrayData - Class in gov.nih.nci.caarray.domain.data
 
DerivedArrayData() - Constructor for class gov.nih.nci.caarray.domain.data.DerivedArrayData
 
DeserializationFactory - Class in gov.nih.nci.cagrid.caarray.util
Pass through to the grid deserialization factory, but with the correct API to actually work.
DeserializationFactory(Class, QName) - Constructor for class gov.nih.nci.cagrid.caarray.util.DeserializationFactory
 
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.
DesignElementList - Class in gov.nih.nci.caarray.domain.data
Contains an ordered list of the microarray design elements (features or probes) for which data values are provided.
DesignElementList() - Constructor for class gov.nih.nci.caarray.domain.data.DesignElementList
 
DesignElementReference - Class in gov.nih.nci.caarray.domain.data
 
DesignElementReference() - Constructor for class gov.nih.nci.caarray.domain.data.DesignElementReference
 
DesignElementType - Enum in gov.nih.nci.caarray.domain.data
Specifies whether a microarray element refers to a location (feature), probe, or probeset.
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
DISCRIMINATOR - Static variable in class gov.nih.nci.caarray.domain.data.DerivedArrayData
the Hibernate discriminator for this ArrayData subclass.
DISCRIMINATOR - Static variable in class gov.nih.nci.caarray.domain.data.RawArrayData
the Hibernate discriminator for this ArrayData subclass.
DISCRIMINATOR - Static variable in class gov.nih.nci.caarray.domain.sample.Extract
the Hibernate discriminator for this biomaterial subclass.
DISCRIMINATOR - Static variable in class gov.nih.nci.caarray.domain.sample.LabeledExtract
the Hibernate discriminator for this biomaterial subclass.
DISCRIMINATOR - Static variable in class gov.nih.nci.caarray.domain.sample.Sample
the Hibernate discriminator for this biomaterial subclass.
DISCRIMINATOR - Static variable in class gov.nih.nci.caarray.domain.sample.Source
the Hibernate discriminator for this biomaterial subclass.
doAddDirectPredecessor(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Actually add the new node as a direct predecessor of this node.
doAddDirectPredecessor(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
Actually add the new node as a direct predecessor of this node.
doAddDirectPredecessor(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.sample.Extract
Actually add the new node as a direct predecessor of this node.
doAddDirectPredecessor(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.sample.LabeledExtract
Actually add the new node as a direct predecessor of this node.
doAddDirectPredecessor(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.sample.Sample
Actually add the new node as a direct predecessor of this node.
doAddDirectPredecessor(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.sample.Source
Actually add the new node as a direct predecessor of this node.
doAddDirectSuccessor(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Actually add the new node as a direct successor of this node.
doAddDirectSuccessor(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
Actually add the new node as a direct successor of this node.
doAddDirectSuccessor(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.sample.Extract
Actually add the new node as a direct successor of this node.
doAddDirectSuccessor(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.sample.LabeledExtract
Actually add the new node as a direct successor of this node.
doAddDirectSuccessor(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.sample.Sample
Actually add the new node as a direct successor of this node.
doAddDirectSuccessor(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.sample.Source
Actually add the new node as a direct successor of this node.
DOMAINMODEL - Static variable in interface gov.nih.nci.cagrid.caarray.common.CaArraySvcConstantsBase
 
DOMAINMODEL_Value_RP - Static variable in interface gov.nih.nci.cagrid.caarray.service.globus.resource.ResourceConstants
 
DoubleColumn - Class in gov.nih.nci.caarray.domain.data
Contains a column of double values.
DoubleColumn() - Constructor for class gov.nih.nci.caarray.domain.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.

E

edu.georgetown.pir - package edu.georgetown.pir
 
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.
ENSEMBLE - Static variable in class gov.nih.nci.caarray.domain.array.Gene
Name of the Ensemble database.
ENTREZ_GENE - Static variable in class gov.nih.nci.caarray.domain.array.Gene
Name of the Entrez Gene database.
equals(Object) - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayObject
The default comparison uses the id.
equals(Object) - Method in class gov.nih.nci.caarray.domain.array.Accession
equals(Object) - Method in class gov.nih.nci.caarray.domain.contact.AbstractContact
The default comparison uses the id.
equals(Object) - Method in class gov.nih.nci.caarray.domain.contact.Address
The default comparison uses the id.
equals(Object) - Method in class gov.nih.nci.caarray.domain.contact.Organization
The default comparison uses the id.
equals(Object) - Method in class gov.nih.nci.caarray.domain.contact.Person
The default comparison uses the id.
equals(Object) - Method in class gov.nih.nci.caarray.domain.file.FileType
equals(Object) - Method in class gov.nih.nci.caarray.domain.protocol.Parameter
The default comparison uses the id.
equals(Object) - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
The default comparison uses the id.
equals(Object) - Method in class gov.nih.nci.caarray.domain.publication.Publication
The default comparison uses the id.
equals(Object) - Method in class gov.nih.nci.caarray.domain.vocabulary.Category
The default comparison uses the id.
equals(Object) - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
The default comparison uses the id.
equals(Object) - Method in class gov.nih.nci.caarray.domain.vocabulary.TermSource
The default comparison uses the id.
equals(Object, Object) - Method in class gov.nih.nci.caarray.util.URIUserType
equalsBaseContact(ExperimentContact) - Method in class gov.nih.nci.caarray.domain.project.ExperimentContact
Returns true if the underlying contact information is the same, ignoring the roles and Experiment.
ERROR_NOT_INITIALIZED - Static variable in class gov.nih.nci.caarray.domain.data.AbstractDataColumn
Error message for incorrect usage of uninitialized values array.
ExampleSearchCriteria<T extends com.fiveamsolutions.nci.commons.data.persistent.PersistentObject> - Class in gov.nih.nci.caarray.domain.search
Simple bean to hold example search criteria.
ExampleSearchCriteria(T) - Constructor for class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
Create a new example search criteria with given example, using exact matching, excluding null properties.
ExampleSearchCriteria(T, MatchMode) - Constructor for class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
Create a new example search criteria with given example, using the given match mode, excluding null properties.
ExampleSearchCriteria(T, MatchMode, boolean) - Constructor for class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
Create a new example search criteria with given example, using the given match mode and given null property handling.
ExampleSearchCriteria(T, MatchMode, boolean, Collection<String>) - Constructor for class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
Create a new example search criteria with given example, using the given match mode and given null property handling.
excludeNulls() - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
Set this criteria to exclude null properties from comparison.
excludeProperties(String...) - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
Set this criteria to exclude given properties from comparison.
excludeZeroes() - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
Set this criteria to exclude zero-valued properties from comparison.
ExecutableJob - Interface in gov.nih.nci.caarray.domain.project
Adds functionality to Job for execution purposes.
execute() - Method in interface gov.nih.nci.caarray.domain.project.ExecutableJob
Perform the job.
executeCQLQuery(CQLQuery) - Static method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
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.
ExonArrayReporter - Class in gov.nih.nci.cabio.domain
 
ExonArrayReporter() - Constructor for class gov.nih.nci.cabio.domain.ExonArrayReporter
 
ExonProbeAnnotation - Class in gov.nih.nci.caarray.domain.array
 
ExonProbeAnnotation() - Constructor for class gov.nih.nci.caarray.domain.array.ExonProbeAnnotation
 
Experiment - Class in gov.nih.nci.caarray.domain.project
 
Experiment() - Constructor for class gov.nih.nci.caarray.domain.project.Experiment
 
ExperimentContact - Class in gov.nih.nci.caarray.domain.project
 
ExperimentContact() - Constructor for class gov.nih.nci.caarray.domain.project.ExperimentContact
Default constructor, mostly for hibernate.
ExperimentContact(Experiment, Person, Collection<Term>) - Constructor for class gov.nih.nci.caarray.domain.project.ExperimentContact
Create a new ExperimentContact for given experiment, contacts, and roles.
ExperimentContact(Experiment, Person, Term) - Constructor for class gov.nih.nci.caarray.domain.project.ExperimentContact
Create a new ExperimentContact for given experiment, contacts, and role.
ExperimentDesignNodeType - Enum in gov.nih.nci.caarray.domain.project
An enumeration of different type of nodes in the experiment design graph.
ExperimentOntology - Enum in gov.nih.nci.caarray.domain.project
Enum of Ontologies for various concepts used by Experiment.
ExperimentOntologyCategory - Enum in gov.nih.nci.caarray.domain.project
Enum of Ontology categories for various concepts used in caarray The majority of these categories come from the MGED ontology.
ExperimentSearchCriteria - Class in gov.nih.nci.caarray.domain.search
Simple bean to hold search criteria for an experiment.
ExperimentSearchCriteria() - Constructor for class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
ExpressionArrayReporter - Class in gov.nih.nci.cabio.domain
 
ExpressionArrayReporter() - Constructor for class gov.nih.nci.cabio.domain.ExpressionArrayReporter
 
ExpressionProbeAnnotation - Class in gov.nih.nci.caarray.domain.array
 
ExpressionProbeAnnotation() - Constructor for class gov.nih.nci.caarray.domain.array.ExpressionProbeAnnotation
 
ExternalBiomaterialSearchCategory - Enum in gov.nih.nci.caarray.domain.search
Search criteria for the external API search for biomaterials by keyword.
Extract - Class in gov.nih.nci.caarray.domain.sample
 
Extract() - Constructor for class gov.nih.nci.caarray.domain.sample.Extract
 
EXTRACTS_FILTER - Static variable in class gov.nih.nci.caarray.domain.project.Experiment
 
ExtractSortCriterion - Enum in gov.nih.nci.caarray.domain.search
Enum of possible sort criterions for extracts.

F

Factor - Class in gov.nih.nci.caarray.domain.project
 
Factor() - Constructor for class gov.nih.nci.caarray.domain.project.Factor
 
FactorSortCriterion - Enum in gov.nih.nci.caarray.domain.search
Enum of possible sort criterions for factors.
Feature - Class in gov.nih.nci.caarray.domain.array
Represents a physical location on a microarray.
Feature(ArrayDesignDetails) - Constructor for class gov.nih.nci.caarray.domain.array.Feature
Creates a new Feature.
Feature() - Constructor for class gov.nih.nci.caarray.domain.array.Feature
Deprecated. hibernate & castor only
FileCategory - Enum in gov.nih.nci.caarray.domain.file
FileCategory classifies files according to the kind of data they contain.
FileRetrievalService - Interface in gov.nih.nci.caarray.services.file
Allows remote API access to download files stored in caArray.
FileSearchCriteria - Class in gov.nih.nci.caarray.domain.search
Simple bean to hold search criteria for files.
FileSearchCriteria() - Constructor for class gov.nih.nci.caarray.domain.search.FileSearchCriteria
 
FileStatus - Enum in gov.nih.nci.caarray.domain.file
Status of a CaArrayFile.
FileType - Class in gov.nih.nci.caarray.domain.file
Describes a type of file that can be uploaded to caArray.
FileType() - Constructor for class gov.nih.nci.caarray.domain.file.FileType
create an uninitialized file type.
FileType(String, FileCategory, boolean, String...) - Constructor for class gov.nih.nci.caarray.domain.file.FileType
Constructs a file type with given properties.
FileType(String, FileCategory, boolean, boolean, String...) - Constructor for class gov.nih.nci.caarray.domain.file.FileType
Constructs a file type with given properties.
FileTypeRegistry - Interface in gov.nih.nci.caarray.domain.file
A registry of file types.
FileTypeRegistryImpl - Class in gov.nih.nci.caarray.domain.file
Default implementation of FileTypeRegistry.
FileTypeRegistryImpl(Set<DataFileHandler>, Set<DesignFileHandler>) - Constructor for class gov.nih.nci.caarray.domain.file.FileTypeRegistryImpl
Create a FileTypeRegistryImpl with the set of types provided by the given array data and array design file handlers.
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(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.
find(ResourceKey) - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceHome
 
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.domain.data
Contains a column of float values.
FloatColumn() - Constructor for class gov.nih.nci.caarray.domain.data.FloatColumn
 
foreignKeyColumnName(String, String, String, String) - Method in class gov.nih.nci.caarray.util.NamingStrategy
forEntity(T) - Static method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
Create a new example search criteria with given example, using exact matching, excluding null properties.
fromTypeClass(Class<?>) - Static method in enum gov.nih.nci.caarray.domain.data.DataType
Returns the DataType enumeration value corresponding to the given type class.

G

GENBANK - Static variable in class gov.nih.nci.caarray.domain.array.Gene
Name of the GenBank database.
Gene - Class in gov.nih.nci.caarray.domain.array
A hereditary unit consisting of a sequence of DNA that occupies a specific location on a chromosome and determines a particular characteristic in an organism.
Gene() - Constructor for class gov.nih.nci.caarray.domain.array.Gene
 
get(Object) - Method in class gov.nih.nci.caarray.util.PropertyAccessor
Get the value of the property of this accessor from the given object.
get(CaArraySvcClient, String, String, String) - Static method in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
getAccession() - Method in class gov.nih.nci.caarray.domain.vocabulary.Category
 
getAccession() - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
Gets the accession, which is a unique identifier for this term within its term source.
getAccessionNumber() - Method in class gov.nih.nci.caarray.domain.array.Accession
Deprecated. 
getAccessionNumbers(String) - Method in class gov.nih.nci.caarray.domain.array.Gene
Get all the accessions associated with this gene in the given public database.
getAccessionNumbers(String) - Method in class gov.nih.nci.caarray.domain.array.MiRNAProbeAnnotation
Get all the accessions associated with this gene in the given public database.
getAccessors() - Method in class gov.nih.nci.caarray.util.ReflectionHelper
 
getAccessProfiles() - Method in class gov.nih.nci.caarray.domain.permissions.CollaboratorGroup
 
getAdditionalOrganismNameCollection() - Method in class edu.georgetown.pir.Organism
 
getAddress() - Method in class gov.nih.nci.caarray.domain.contact.AbstractContact
Gets the address.
getAddress1() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getAddress2() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getAddressedResource() - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceHome
Get the resouce that is being addressed in this current context
getAffiliations() - Method in class gov.nih.nci.caarray.domain.contact.Person
Gets the affiliations.
getAllAccessProfiles() - Method in class gov.nih.nci.caarray.domain.project.Project
 
getAllDataFiles() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
getAllDataFiles() - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
 
getAllDataFiles() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
The data files related to this biomaterial is the set of files that is related to at least one hybridization that is related to this biomaterial (@see getRelatedHybs()).
getAlleleA() - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
getAlleleB() - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
getAllTypes() - Method in interface gov.nih.nci.caarray.domain.file.FileTypeRegistry
 
getAllTypes() - Method in class gov.nih.nci.caarray.domain.file.FileTypeRegistryImpl
getAmountOfMaterial() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
 
getAmountOfMaterialUnit() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
 
getAnnotation() - Method in class gov.nih.nci.caarray.domain.array.AbstractProbe
 
getAnnotationCriterions() - Method in class gov.nih.nci.caarray.domain.search.BiomaterialSearchCriteria
 
getAnnotationCriterions() - Method in class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
getAnnotationFile() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
 
getArray() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Gets the array.
getArrayData() - Method in class gov.nih.nci.caarray.domain.data.DataSet
 
getArrayDataFiles() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFileSet
Get a subset of CaArrayFile objects that are array data file types.
getArrayDataTypes() - Method in class gov.nih.nci.caarray.domain.data.QuantitationType
 
getArrayDataTypes() - Method in class gov.nih.nci.caarray.domain.search.QuantitationTypeSearchCriteria
 
getArrayDesignDetails() - Method in class gov.nih.nci.caarray.domain.array.Feature
 
getArrayDesignDetails() - Method in class gov.nih.nci.caarray.domain.array.LogicalProbe
 
getArrayDesignDetails() - Method in class gov.nih.nci.caarray.domain.array.PhysicalProbe
 
getArrayDesignDetails() - Method in class gov.nih.nci.caarray.domain.array.ProbeGroup
 
getArrayDesignDetailsService() - Method in class gov.nih.nci.caarray.services.CaArrayServer
 
getArrayDesignJob() - Method in enum gov.nih.nci.caarray.domain.project.JobType
Determine if the job is related to an experiment or not.
getArrayDesigns() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the arrayDesigns.
getArrayDesignsFromHybs() - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
getArrayDesignTypes() - Method in interface gov.nih.nci.caarray.domain.file.FileTypeRegistry
 
getArrayDesignTypes() - Method in class gov.nih.nci.caarray.domain.file.FileTypeRegistryImpl
getArrayGroup() - Method in class gov.nih.nci.caarray.domain.array.Array
 
getArrayProvider() - Method in class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
getArrays() - Method in class gov.nih.nci.caarray.domain.array.ArrayGroup
 
getArrays() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the arrays.
getAssayType() - Method in class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
getAssayTypes() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Gets the assay type for this Experiment.
getAssayTypes() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the assay type for this Experiment.
getAuthority() - Method in class gov.nih.nci.caarray.domain.LSID
 
getAuthors() - Method in class gov.nih.nci.caarray.domain.publication.Publication
Gets the authors.
getBatch() - Method in class gov.nih.nci.caarray.domain.array.Array
Gets the batch.
getBigid() - Method in class gov.nih.nci.cabio.domain.ArrayReporter
 
getBioMaterial() - Method in class gov.nih.nci.caarray.domain.sample.AbstractCharacteristic
 
getBiomaterialClasses() - Method in class gov.nih.nci.caarray.domain.search.BiomaterialSearchCriteria
 
getBiomaterials() - Method in class gov.nih.nci.caarray.domain.search.HybridizationSearchCriteria
 
getBlobParts() - Method in class gov.nih.nci.caarray.domain.MultiPartBlob
The blobParts as stored by hibernate.
getBlockColumn() - Method in class gov.nih.nci.caarray.domain.array.Feature
 
getBlockRow() - Method in class gov.nih.nci.caarray.domain.array.Feature
 
getByValue(String) - Static method in enum gov.nih.nci.caarray.domain.data.DesignElementType
Returns the DesignElementType corresponding to the given value.
getCaArrayHibernateHelper() - Static method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperFactory
 
getCaBigId() - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayObject
 
getCallerIdentity() - Static method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
getCategories() - Method in class gov.nih.nci.caarray.domain.search.FileSearchCriteria
 
getCategories() - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
 
getCategory() - Method in class gov.nih.nci.caarray.domain.file.FileType
 
getCategory() - Method in class gov.nih.nci.caarray.domain.sample.AbstractCharacteristic
 
getCategory() - Method in class gov.nih.nci.caarray.domain.search.AnnotationCriterion
 
getCategoryCache() - Method in class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
 
getCategoryName() - Method in enum gov.nih.nci.caarray.domain.project.ExperimentOntologyCategory
 
getCellType() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
getCharacteristic(String) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Return the characteristic with given category name in this biomaterial.
getCharacteristics(Category) - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
Return the characteristics with given category that are directly present on this ExperimentDesignNode.
getCharacteristics() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Gets the characteristics.
getCharacteristics(Category) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Return the characteristics with given category in this biomaterial.
getCharacteristicsRecursively(Category) - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
Return the characteristics with given category that are present in the chain terminating at this node.
getChildren() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
getChildren() - Method in interface gov.nih.nci.caarray.domain.project.BaseJob
Return an empty list if there are no children.
getChildren() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
Return an empty list if there are no children.
getChildren() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
Return an empty list if there are no children.
getChildren() - Method in class gov.nih.nci.caarray.domain.vocabulary.Category
Gets the children.
getChromosome() - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
getChromosomeEndPosition() - Method in class gov.nih.nci.caarray.domain.array.ExpressionProbeAnnotation
 
getChromosomeName() - Method in class gov.nih.nci.caarray.domain.array.ExpressionProbeAnnotation
 
getChromosomeStartPosition() - Method in class gov.nih.nci.caarray.domain.array.ExpressionProbeAnnotation
 
getCity() - Method in class gov.nih.nci.caarray.domain.contact.Address
Gets the city.
getCity() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getClassToQnameMappings() - Method in class gov.nih.nci.cagrid.caarray.stubs.cql.CaArrayCQLQueryProcessor
Get xml mappings.
getCode() - Method in class gov.nih.nci.caarray.domain.country.Country
 
getCode() - Method in class gov.nih.nci.caarray.domain.state.State
 
getColumn() - Method in class gov.nih.nci.caarray.domain.array.Feature
 
getColumn(QuantitationType) - Method in class gov.nih.nci.caarray.domain.data.HybridizationData
Returns the column matching the provided type, if one exists.
getColumn(QuantitationTypeDescriptor) - Method in class gov.nih.nci.caarray.domain.data.HybridizationData
Returns the column matching the provided type, if one exists.
getColumns() - Method in class gov.nih.nci.caarray.domain.data.HybridizationData
 
getComment() - Method in class edu.georgetown.pir.AdditionalOrganismName
 
getCommonName() - Method in class edu.georgetown.pir.Organism
 
getCompressedSize() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
getCompressedSize() - Method in class gov.nih.nci.caarray.domain.MultiPartBlob
 
getConfiguration() - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
 
getConfiguration() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
getConfiguration() - Static method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
getConfiguration() - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcImplBase
 
getConfiguration() - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceBase
 
getConfiguration() - Static method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
getContact() - Method in class gov.nih.nci.caarray.domain.project.ExperimentContact
Gets the contact.
getContact() - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Gets the contact.
getContents() - Method in class gov.nih.nci.caarray.domain.BlobHolder
 
getControlType() - Method in class gov.nih.nci.caarray.domain.array.PhysicalProbe
 
getCoordinateUnits() - Method in class gov.nih.nci.caarray.domain.array.Feature
 
getCountry() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getCreationTimestamp() - Method in class gov.nih.nci.caarray.domain.MultiPartBlob
 
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.
getDatabaseName() - Method in class gov.nih.nci.caarray.domain.array.Accession
Deprecated. should only be used by castor and hibernate.
getDataFile() - Method in class gov.nih.nci.caarray.domain.data.AbstractArrayData
Gets the dataFile.
getDataHandle() - Method in class gov.nih.nci.caarray.domain.data.AbstractDataColumn
 
getDataHandle() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
getDataRetrievalService() - Method in class gov.nih.nci.caarray.services.CaArrayServer
 
getDataService() - Method in class gov.nih.nci.caarray.services.external.v1_0.CaArrayServer
 
getDataService_auditorsConfigFile() - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
getDataService_auditorsConfigFile() - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
getDataService_classMappingsFilename() - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
getDataService_classMappingsFilename() - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
getDataService_cqlValidatorClass() - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
getDataService_cqlValidatorClass() - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
getDataService_domainModelValidatorClass() - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
getDataService_domainModelValidatorClass() - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
getDataService_validateCqlFlag() - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
getDataService_validateCqlFlag() - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
getDataService_validateDomainModelFlag() - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
getDataService_validateDomainModelFlag() - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
getDataSet() - Method in class gov.nih.nci.caarray.domain.data.AbstractArrayData
 
getDataSet() - Method in class gov.nih.nci.caarray.domain.data.HybridizationData
 
getDataSet(DataRetrievalRequest) - Method in interface gov.nih.nci.caarray.services.data.DataRetrievalService
Returns the requested data as configured within the request object.
getDataSet(DataRetrievalRequest) - Method in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
getDataSet(DataRetrievalRequest) - Method in interface gov.nih.nci.cagrid.caarray.common.CaArraySvcI
 
getDataSet(DataRetrievalRequest) - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcImpl
 
getDataSet(gov.nih.nci.cagrid.caarray.stubs.GetDataSetRequest) - Method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcProviderImpl
 
getDataType() - Method in class gov.nih.nci.caarray.domain.data.QuantitationType
 
getDataType() - Method in interface gov.nih.nci.caarray.domain.data.QuantitationTypeDescriptor
Returns the data type of values of this quantitation type.
getDate() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the date of this Experiment.
getDbSNPId() - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
getDbSNPVersion() - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
getDefaultValue() - Method in class gov.nih.nci.caarray.domain.protocol.Parameter
Gets the defaultValue.
getDerivedArrayDataTypes() - Method in interface gov.nih.nci.caarray.domain.file.FileTypeRegistry
 
getDerivedArrayDataTypes() - Method in class gov.nih.nci.caarray.domain.file.FileTypeRegistryImpl
getDerivedDataCollection() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Gets the derivedDatas.
getDerivedFromArrayDataCollection() - Method in class gov.nih.nci.caarray.domain.data.DerivedArrayData
 
getDescription() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
 
getDescription() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
 
getDescription() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the description.
getDescription() - Method in class gov.nih.nci.caarray.domain.project.Factor
 
getDescription() - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Gets the description.
getDescription() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Gets the description.
getDescription() - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
Gets the description.
getDesign() - Method in class gov.nih.nci.caarray.domain.array.Array
Gets the design.
getDesignDescription() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Get the description of the experiment design.
getDesignDetails() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
 
getDesignDetails(ArrayDesign) - Method in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDetailsService
Returns complete details of all design elements and relationships for the requested design.
getDesignDetails(ArrayDesign) - Method in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
getDesignDetails(ArrayDesign) - Method in interface gov.nih.nci.cagrid.caarray.common.CaArraySvcI
 
getDesignDetails(ArrayDesign) - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcImpl
Returns complete details of all design elements and relationships for the requested design.
getDesignDetails(gov.nih.nci.cagrid.caarray.stubs.GetDesignDetailsRequest) - Method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcProviderImpl
 
getDesignElement() - Method in class gov.nih.nci.caarray.domain.data.DesignElementReference
 
getDesignElementList() - Method in class gov.nih.nci.caarray.domain.data.DataSet
 
getDesignElementList() - Method in class gov.nih.nci.caarray.domain.data.DesignElementReference
 
getDesignElementReferences() - Method in class gov.nih.nci.caarray.domain.data.DesignElementList
 
getDesignElements() - Method in class gov.nih.nci.caarray.domain.data.DataRetrievalRequest
 
getDesignElements() - Method in class gov.nih.nci.caarray.domain.data.DesignElementList
 
getDesignElementType() - Method in class gov.nih.nci.caarray.domain.data.DesignElementList
 
getDesignElementTypeEnum() - Method in class gov.nih.nci.caarray.domain.data.DesignElementList
 
getDesignFiles() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
 
getDesignFileSet() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
 
getDirectPredecessors() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
getDirectPredecessors() - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
 
getDirectPredecessors() - Method in class gov.nih.nci.caarray.domain.sample.Extract
getDirectPredecessors() - Method in class gov.nih.nci.caarray.domain.sample.LabeledExtract
getDirectPredecessors() - Method in class gov.nih.nci.caarray.domain.sample.Sample
getDirectPredecessors() - Method in class gov.nih.nci.caarray.domain.sample.Source
getDirectSuccessors() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
getDirectSuccessors() - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
 
getDirectSuccessors() - Method in class gov.nih.nci.caarray.domain.sample.Extract
getDirectSuccessors() - Method in class gov.nih.nci.caarray.domain.sample.LabeledExtract
getDirectSuccessors() - Method in class gov.nih.nci.caarray.domain.sample.Sample
getDirectSuccessors() - Method in class gov.nih.nci.caarray.domain.sample.Source
getDiseaseState() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
getDisplayValue() - Method in class gov.nih.nci.caarray.domain.AbstractUnitableValue
getDisplayValue() - Method in enum gov.nih.nci.caarray.domain.file.FileStatus
 
getDisplayValue() - Method in enum gov.nih.nci.caarray.domain.project.JobStatus
 
getDisplayValue() - Method in enum gov.nih.nci.caarray.domain.project.JobType
 
getDisplayValue() - Method in interface gov.nih.nci.caarray.domain.UnitableValue
 
getDisplayValueWithoutUnit() - Method in class gov.nih.nci.caarray.domain.project.MeasurementFactorValue
getDisplayValueWithoutUnit() - Method in class gov.nih.nci.caarray.domain.project.TermBasedFactorValue
getDisplayValueWithoutUnit() - Method in class gov.nih.nci.caarray.domain.project.UserDefinedFactorValue
getDisplayValueWithoutUnit() - Method in class gov.nih.nci.caarray.domain.protocol.MeasurementParameterValue
getDisplayValueWithoutUnit() - Method in class gov.nih.nci.caarray.domain.protocol.TermBasedParameterValue
getDisplayValueWithoutUnit() - Method in class gov.nih.nci.caarray.domain.protocol.UserDefinedParameterValue
getDisplayValueWithoutUnit() - Method in class gov.nih.nci.caarray.domain.sample.MeasurementCharacteristic
getDisplayValueWithoutUnit() - Method in class gov.nih.nci.caarray.domain.sample.TermBasedCharacteristic
getDisplayValueWithoutUnit() - Method in class gov.nih.nci.caarray.domain.sample.UserDefinedCharacteristic
getDisplayValueWithoutUnit() - Method in interface gov.nih.nci.caarray.domain.UnitableValue
 
getDoi() - Method in class gov.nih.nci.caarray.domain.publication.Publication
Gets the doi.
getDomainModel() - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceBase
 
getDomainModelFile() - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceConfiguration
 
getDomainModelFile() - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.ResourceConfiguration
 
getEditor() - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
getEmail() - Method in class gov.nih.nci.caarray.domain.contact.AbstractContact
Gets the email.
getEmail() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getEnsemblgeneID() - Method in class gov.nih.nci.caarray.domain.array.Gene
 
getEntityId() - Method in class gov.nih.nci.caarray.domain.audit.AuditLogSecurity
 
getEntityName() - Method in class gov.nih.nci.caarray.domain.audit.AuditLogSecurity
 
getEntrezgeneID() - Method in class gov.nih.nci.caarray.domain.array.Gene
 
getEtcDirectoryPath() - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
getEthnicityStrain() - Method in class edu.georgetown.pir.Organism
 
getExample() - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
 
getExcludeProperties() - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
 
getExonArrayReporter() - Method in class gov.nih.nci.caarray.domain.array.ExonProbeAnnotation
 
getExperiment() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Get the experiment to which this node belongs.
getExperiment() - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
Get the experiment to which this node belongs.
getExperiment() - Method in class gov.nih.nci.caarray.domain.project.ExperimentContact
 
getExperiment() - Method in class gov.nih.nci.caarray.domain.project.Factor
 
getExperiment() - Method in class gov.nih.nci.caarray.domain.project.Project
Gets the experiment.
getExperiment() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Get the experiment to which this node belongs.
getExperiment() - Method in class gov.nih.nci.caarray.domain.search.BiomaterialSearchCriteria
 
getExperiment() - Method in class gov.nih.nci.caarray.domain.search.FileSearchCriteria
 
getExperiment() - Method in class gov.nih.nci.caarray.domain.search.HybridizationSearchCriteria
 
getExperimentContacts() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the experimentContacts.
getExperimentDesignTypes() - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
getExperimentNodes() - Method in class gov.nih.nci.caarray.domain.search.FileSearchCriteria
 
getExpressionArrayReporter() - Method in class gov.nih.nci.caarray.domain.array.ExpressionProbeAnnotation
 
getExtension() - Method in class gov.nih.nci.caarray.domain.search.FileSearchCriteria
 
getExtensions() - Method in class gov.nih.nci.caarray.domain.file.FileType
 
getExternalId() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
getExternalIds() - Method in class gov.nih.nci.caarray.domain.search.BiomaterialSearchCriteria
 
getExtractByName(String) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Return the extract with given name in this experiment.
getExtracts() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the extracts.
getExtracts() - Method in class gov.nih.nci.caarray.domain.sample.LabeledExtract
Gets the extracts.
getExtracts() - Method in class gov.nih.nci.caarray.domain.sample.Sample
Gets the extracts.
getFactor() - Method in class gov.nih.nci.caarray.domain.project.AbstractFactorValue
Gets the factor.
getFactors() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the factors.
getFactorValue(String) - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Return the factor value for the factor with given name in this hybridization.
getFactorValues() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Gets the factorValues.
getFactorValues() - Method in class gov.nih.nci.caarray.domain.project.Factor
Gets the factorValues.
getFax() - Method in class gov.nih.nci.caarray.domain.contact.AbstractContact
Gets the fax.
getFax() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getFeatureNumber() - Method in class gov.nih.nci.caarray.domain.array.Feature
 
getFeatures() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesignDetails
 
getFeatures() - Method in class gov.nih.nci.caarray.domain.array.PhysicalProbe
 
getField() - Method in enum gov.nih.nci.caarray.domain.search.BrowseCategory
 
getFile(File) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFileSet
Returns the CaArrayFile in the set corresponding to the given file object or null if no match.
getFile(String) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFileSet
Returns the CaArrayFile in the set with the given name or null if no match.
getFileCategories() - Method in class gov.nih.nci.caarray.domain.search.QuantitationTypeSearchCriteria
 
getFilename() - Method in enum gov.nih.nci.caarray.domain.file.UnsupportedAffymetrixCdfFiles
 
getFileNames() - Method in class gov.nih.nci.caarray.domain.project.Project
 
getFileRetrievalService() - Method in class gov.nih.nci.caarray.services.CaArrayServer
 
getFiles() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFileSet
Returns the contained files.
getFiles() - Method in class gov.nih.nci.caarray.domain.project.Project
Gets all the files.
getFilesByType(FileType) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFileSet
Get a subset of CaArrayFile objects with file type specified.
getFileSet() - Method in interface gov.nih.nci.caarray.domain.project.ExecutableJob
 
getFileSet() - Method in class gov.nih.nci.caarray.domain.project.Project
 
getFileStatus() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
getFileType() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
getFileTypes() - Method in class gov.nih.nci.caarray.domain.search.QuantitationTypeSearchCriteria
 
getFirstDesignFile() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Gets the first (or only) design file.
getFirstName() - Method in class gov.nih.nci.caarray.domain.contact.Person
Gets the firstName.
getFirstName() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getFlank() - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
getFullName() - Method in class gov.nih.nci.caarray.domain.array.Gene
 
getGenbankAccession() - Method in class gov.nih.nci.caarray.domain.array.Gene
 
getGenbankAccessionVersion() - Method in class gov.nih.nci.caarray.domain.array.Gene
 
getGene() - Method in class gov.nih.nci.caarray.domain.array.ExonProbeAnnotation
 
getGene() - Method in class gov.nih.nci.caarray.domain.array.ExpressionProbeAnnotation
 
getGeoAccession() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
GEO accession.
getGroup() - Method in class gov.nih.nci.caarray.domain.permissions.AccessProfile
 
getGroup() - Method in class gov.nih.nci.caarray.domain.permissions.CollaboratorGroup
 
getGroupProfiles() - Method in class gov.nih.nci.caarray.domain.project.Project
 
getHardware() - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Gets the hardware.
getHibernateHelper() - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
 
getHybridization() - Method in class gov.nih.nci.caarray.domain.data.HybridizationData
 
getHybridization() - Method in class gov.nih.nci.caarray.domain.data.Image
 
getHybridization() - Method in class gov.nih.nci.caarray.domain.project.AbstractFactorValue
 
getHybridization() - Method in class gov.nih.nci.caarray.domain.search.QuantitationTypeSearchCriteria
 
getHybridizationByName(String) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Return the hybridization with given name in this experiment.
getHybridizationData() - Method in class gov.nih.nci.caarray.domain.data.AbstractDataColumn
 
getHybridizationData() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
 
getHybridizationDataList() - Method in class gov.nih.nci.caarray.domain.data.DataSet
 
getHybridizations() - Method in class gov.nih.nci.caarray.domain.data.AbstractArrayData
 
getHybridizations() - Method in class gov.nih.nci.caarray.domain.data.DataRetrievalRequest
 
getHybridizations() - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
getHybridizations() - Method in class gov.nih.nci.caarray.domain.sample.LabeledExtract
Gets the hybridizations.
getId() - Method in class edu.georgetown.pir.AdditionalOrganismName
 
getId() - Method in class edu.georgetown.pir.Organism
 
getId() - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayObject
Returns the id.
getId() - Method in class gov.nih.nci.caarray.domain.audit.AuditLogSecurity
Returns the id.
getId() - Method in class gov.nih.nci.caarray.domain.BlobHolder
Returns the id.
getId() - Method in class gov.nih.nci.caarray.domain.data.DataRetrievalRequest
Deprecated. only exists to fulfill caDSR loading requirement
getId() - Method in class gov.nih.nci.caarray.domain.data.DesignElementReference
 
getId() - Method in class gov.nih.nci.caarray.domain.MultiPartBlob
Returns the id.
getId() - Method in class gov.nih.nci.caarray.domain.permissions.AccessProfile
 
getId() - Method in class gov.nih.nci.caarray.domain.permissions.CollaboratorGroup
 
getId() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getId() - Method in class gov.nih.nci.cabio.domain.ArrayReporter
 
getImageFile() - Method in class gov.nih.nci.caarray.domain.data.Image
Gets the imageFile.
getImages() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Gets the images.
getImportDescription() - Method in class gov.nih.nci.caarray.domain.project.Project
 
getImportedFiles() - Method in class gov.nih.nci.caarray.domain.project.Project
Get the files.
getImportingFiles() - Method in class gov.nih.nci.caarray.domain.project.Project
Get the files.
getIndex() - Method in class gov.nih.nci.caarray.domain.data.DesignElementReference
 
getInvocationCredential() - Static method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
getIso3() - Method in class gov.nih.nci.caarray.domain.country.Country
 
getIssue() - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
getJobEntityId() - Method in interface gov.nih.nci.caarray.domain.project.BaseJob
 
getJobEntityId() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
getJobEntityId() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
getJobEntityName() - Method in interface gov.nih.nci.caarray.domain.project.BaseJob
 
getJobEntityName() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
getJobEntityName() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
getJobId() - Method in interface gov.nih.nci.caarray.domain.project.BaseJob
 
getJobId() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
getJobId() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
getJobsProcessed() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
 
getJobStatus() - Method in interface gov.nih.nci.caarray.domain.project.BaseJob
 
getJobStatus() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
getJobStatus() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
getJobType() - Method in interface gov.nih.nci.caarray.domain.project.BaseJob
 
getJobType() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
getJobType() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
getJoin() - Method in enum gov.nih.nci.caarray.domain.search.BrowseCategory
 
getJoins() - Method in class gov.nih.nci.caarray.domain.search.AdHocSortCriterion
Get list of join tables for this search order.
getJoins() - Method in interface gov.nih.nci.caarray.domain.search.BiomaterialSearchCategory
These are the fields to join against in the HQL query.
getJoins() - Method in enum gov.nih.nci.caarray.domain.search.ExternalBiomaterialSearchCategory
These are the fields to join against in the HQL query.
getJoins() - Method in interface gov.nih.nci.caarray.domain.search.JoinableSortCriterion
Get list of join tables for this search order.
getJoins() - Method in enum gov.nih.nci.caarray.domain.search.SampleJoinableSortCriterion
Get list of join tables for this search order.
getJoins() - Method in enum gov.nih.nci.caarray.domain.search.SearchCategory
These are the fields to join against in the HQL query.
getJoins() - Method in enum gov.nih.nci.caarray.domain.search.SearchSampleCategory
These are the fields to join against in the HQL query.
getJoins() - Method in enum gov.nih.nci.caarray.domain.search.SearchSourceCategory
These are the fields to join against in the HQL query.
getJoins() - Method in enum gov.nih.nci.caarray.domain.search.SourceJoinableSortCriterion
Get list of join tables for this search order.
getLabel() - Method in class gov.nih.nci.caarray.domain.sample.LabeledExtract
Gets the label.
getLabel() - Method in class gov.nih.nci.caarray.util.LabelValue
get label.
getLabeledExtract() - Method in class gov.nih.nci.caarray.domain.data.HybridizationData
 
getLabeledExtractByName(String) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Return the labeled extract with given name in this experiment.
getLabeledExtracts() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Gets the labeledExtract.
getLabeledExtracts() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the labeledExtracts.
getLabeledExtracts() - Method in class gov.nih.nci.caarray.domain.sample.Extract
Gets the labeledExtracts.
getLastDataModificationDate() - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
getLastModifiedDataTime() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
getLastName() - Method in class gov.nih.nci.caarray.domain.contact.Person
Gets the lastName.
getLastName() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getLastUpdated() - Method in class gov.nih.nci.caarray.domain.project.Project
Gets the last updated date.
getLeftJoinField() - Method in enum gov.nih.nci.caarray.domain.search.AbstractBioMaterialSortCriterion
getLeftJoinField() - Method in class gov.nih.nci.caarray.domain.search.AdHocSortCriterion
getLeftJoinField() - Method in enum gov.nih.nci.caarray.domain.search.AuditLogSortCriterion
getLeftJoinField() - Method in enum gov.nih.nci.caarray.domain.search.ExtractSortCriterion
getLeftJoinField() - Method in enum gov.nih.nci.caarray.domain.search.FactorSortCriterion
getLeftJoinField() - Method in enum gov.nih.nci.caarray.domain.search.HybridizationSortCriterion
getLeftJoinField() - Method in enum gov.nih.nci.caarray.domain.search.JobSortCriterion
getLeftJoinField() - Method in enum gov.nih.nci.caarray.domain.search.LabeledExtractSortCriterion
getLeftJoinField() - Method in enum gov.nih.nci.caarray.domain.search.PersonSortCriterion
getLeftJoinField() - Method in enum gov.nih.nci.caarray.domain.search.ProjectSortCriterion
getLeftJoinField() - Method in enum gov.nih.nci.caarray.domain.search.PublicationSortCriterion
getLeftJoinField() - Method in enum gov.nih.nci.caarray.domain.search.SampleJoinableSortCriterion
getLeftJoinField() - Method in enum gov.nih.nci.caarray.domain.search.SampleSortCriterion
getLeftJoinField() - Method in enum gov.nih.nci.caarray.domain.search.SourceJoinableSortCriterion
getLeftJoinField() - Method in enum gov.nih.nci.caarray.domain.search.SourceSortCriterion
getLogicalProbes() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesignDetails
 
getLoginName() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getLsid() - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
Returns the concatenated the LSID for this entity.
getLsidAuthority() - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
Returns the LSID authority.
getLsidNamespace() - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
Returns the LSID namespace.
getLsidObjectId() - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
Returns the LSID object ID.
getMageTabTypes() - Method in interface gov.nih.nci.caarray.domain.file.FileTypeRegistry
 
getMageTabTypes() - Method in class gov.nih.nci.caarray.domain.file.FileTypeRegistryImpl
getMailSession() - Method in class gov.nih.nci.caarray.util.EmailUtil
Returns a handle on the populated mail session object.
getMainPointOfContact() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the ExperimentContact corresponding to the Main POC for the experiment.
getManufacturer() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the manufacturer for this Experiment.
getMatchMode() - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
 
getMaterialType() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Gets the materialType.
getMessage() - Method in class gov.nih.nci.caarray.domain.search.AuditLogSearchCriteria
 
getMiddleInitial() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getMiddleInitials() - Method in class gov.nih.nci.caarray.domain.contact.Person
Gets the middleInitials.
getMultipleResourceProperties(GetMultipleResourceProperties_Element) - Method in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
getMultipleResourceProperties(GetMultipleResourceProperties_Element) - Method in interface gov.nih.nci.cagrid.caarray.common.CaArraySvcI
 
getName() - Method in class gov.nih.nci.caarray.domain.array.AbstractProbe
 
getName() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Gets the name.
getName() - Method in class gov.nih.nci.caarray.domain.array.ArrayGroup
 
getName() - Method in class gov.nih.nci.caarray.domain.array.ProbeGroup
 
getName() - Method in class gov.nih.nci.caarray.domain.contact.Organization
Gets the name.
getName() - Method in class gov.nih.nci.caarray.domain.contact.Person
 
getName() - Method in class gov.nih.nci.caarray.domain.country.Country
 
getName() - Method in class gov.nih.nci.caarray.domain.data.AbstractArrayData
Gets the name.
getName() - Method in class gov.nih.nci.caarray.domain.data.ArrayDataType
 
getName() - Method in interface gov.nih.nci.caarray.domain.data.ArrayDataTypeDescriptor
Returns the name of this data type for display in the application (e.g.
getName() - Method in enum gov.nih.nci.caarray.domain.data.DataType
 
getName() - Method in class gov.nih.nci.caarray.domain.data.Image
Gets the name.
getName() - Method in class gov.nih.nci.caarray.domain.data.QuantitationType
 
getName() - Method in interface gov.nih.nci.caarray.domain.data.QuantitationTypeDescriptor
Returns the name of the type.
getName() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
Gets the name.
getName() - Method in enum gov.nih.nci.caarray.domain.file.FileCategory
 
getName() - Method in class gov.nih.nci.caarray.domain.file.FileType
 
getName() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Gets the name.
getName() - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
 
getName() - Method in class gov.nih.nci.caarray.domain.project.AssayType
Gets the name.
getName() - Method in class gov.nih.nci.caarray.domain.project.Factor
Gets the name.
getName() - Method in class gov.nih.nci.caarray.domain.protocol.Parameter
Gets the name.
getName() - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Gets the name.
getName() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Gets the name.
getName() - Method in class gov.nih.nci.caarray.domain.state.State
 
getName() - Method in class gov.nih.nci.caarray.domain.vocabulary.Category
Gets the name.
getName() - Method in class gov.nih.nci.caarray.domain.vocabulary.TermSource
Gets the name.
getName() - Method in class gov.nih.nci.cabio.domain.ArrayReporter
 
getNameAndSource() - Method in class edu.georgetown.pir.Organism
 
getNameAndVersion() - Method in class gov.nih.nci.caarray.domain.vocabulary.TermSource
 
getNames() - Method in class gov.nih.nci.caarray.domain.search.BiomaterialSearchCriteria
 
getNames() - Method in class gov.nih.nci.caarray.domain.search.HybridizationSearchCriteria
 
getNamespace() - Method in class gov.nih.nci.caarray.domain.LSID
 
getNcbiTaxonomyId() - Method in class edu.georgetown.pir.Organism
 
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
getNodeClass() - Method in enum gov.nih.nci.caarray.domain.protocol.ProtocolTypeAssociation
 
getNodeType() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
getNodeType() - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
 
getNodeType() - Method in class gov.nih.nci.caarray.domain.sample.Extract
getNodeType() - Method in class gov.nih.nci.caarray.domain.sample.LabeledExtract
getNodeType() - Method in class gov.nih.nci.caarray.domain.sample.Sample
getNodeType() - Method in class gov.nih.nci.caarray.domain.sample.Source
getNormalizationTypes() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the normalizationTypes.
getNotes() - Method in class gov.nih.nci.caarray.domain.protocol.ProtocolApplication
 
getNumberOfFeatures() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Gets the numberOfFeatures.
getNumcode() - Method in class gov.nih.nci.caarray.domain.country.Country
 
getObjectId() - Method in class gov.nih.nci.caarray.domain.LSID
 
getOntology() - Method in enum gov.nih.nci.caarray.domain.project.ExperimentOntologyCategory
 
getOntologyName() - Method in enum gov.nih.nci.caarray.domain.project.ExperimentOntology
 
getOrderField() - Method in enum gov.nih.nci.caarray.domain.search.AbstractBioMaterialSortCriterion
getOrderField() - Method in class gov.nih.nci.caarray.domain.search.AdHocSortCriterion
getOrderField() - Method in enum gov.nih.nci.caarray.domain.search.AuditLogSortCriterion
getOrderField() - Method in enum gov.nih.nci.caarray.domain.search.ExtractSortCriterion
getOrderField() - Method in enum gov.nih.nci.caarray.domain.search.FactorSortCriterion
getOrderField() - Method in enum gov.nih.nci.caarray.domain.search.HybridizationSortCriterion
getOrderField() - Method in enum gov.nih.nci.caarray.domain.search.JobSortCriterion
getOrderField() - Method in enum gov.nih.nci.caarray.domain.search.LabeledExtractSortCriterion
getOrderField() - Method in enum gov.nih.nci.caarray.domain.search.PersonSortCriterion
getOrderField() - Method in enum gov.nih.nci.caarray.domain.search.ProjectSortCriterion
getOrderField() - Method in enum gov.nih.nci.caarray.domain.search.PublicationSortCriterion
getOrderField() - Method in enum gov.nih.nci.caarray.domain.search.SampleJoinableSortCriterion
getOrderField() - Method in enum gov.nih.nci.caarray.domain.search.SampleSortCriterion
getOrderField() - Method in enum gov.nih.nci.caarray.domain.search.SourceJoinableSortCriterion
getOrderField() - Method in enum gov.nih.nci.caarray.domain.search.SourceSortCriterion
getOrganism() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
 
getOrganism() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the organism for this Experiment.
getOrganism() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
getOrganism() - Method in class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
getOrganismCollection() - Method in class edu.georgetown.pir.AdditionalOrganismName
 
getOrganization() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getOriginalJob() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
 
getOwner() - Method in class gov.nih.nci.caarray.domain.permissions.CollaboratorGroup
 
getOwnerName() - Method in interface gov.nih.nci.caarray.domain.project.BaseJob
 
getOwnerName() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
getOwnerName() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
getOwners() - Method in class gov.nih.nci.caarray.domain.project.Project
 
getPages() - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
getParameter() - Method in class gov.nih.nci.caarray.domain.protocol.AbstractParameterValue
Gets the parameter.
getParameters() - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Gets the parameters.
getParent() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
getParent() - Method in interface gov.nih.nci.caarray.domain.project.BaseJob
 
getParent() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
getParent() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
getParents() - Method in class gov.nih.nci.caarray.domain.vocabulary.Category
Gets the parent.
getParseableArrayDataTypes() - Method in interface gov.nih.nci.caarray.domain.file.FileTypeRegistry
 
getParseableArrayDataTypes() - Method in class gov.nih.nci.caarray.domain.file.FileTypeRegistryImpl
getParseableArrayDesignTypes() - Method in interface gov.nih.nci.caarray.domain.file.FileTypeRegistry
 
getParseableArrayDesignTypes() - Method in class gov.nih.nci.caarray.domain.file.FileTypeRegistryImpl
getPartialSize() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
getPermSearchCategories() - Static method in enum gov.nih.nci.caarray.domain.search.SearchSampleCategory
 
getPerson() - Method in class gov.nih.nci.caarray.domain.project.ExperimentContact
Gets the person.
getPhastConservation() - Method in class gov.nih.nci.cabio.domain.SNPArrayReporter
 
getPhone() - Method in class gov.nih.nci.caarray.domain.contact.AbstractContact
Gets the phone.
getPhone() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getPhysicalPosition() - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
getPolicy(Node) - Method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
getPolicyNames() - Method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
getPolymerType() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Gets the polymerType.
getPosition() - Method in interface gov.nih.nci.caarray.domain.project.Job
 
getPosition() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
getPosition() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
getPostLoadSecurityPolicies(User) - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayObject
Return the set of security policies that should be applied to this object at hibernate load time.
getPredecesorType() - Method in enum gov.nih.nci.caarray.domain.project.ExperimentDesignNodeType
 
getPredecessorsOfType(ExperimentDesignNodeType) - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
 
getPrimaryInvestigator() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the ExperimentContact corresponding to the PI for the experiment.
getPrimaryInvestigatorCount() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the number of PI for the experiment.
getPrincipalInvestigators() - Method in class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
getPrintableName() - Method in class gov.nih.nci.caarray.domain.country.Country
 
getPrinting() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Gets the printing.
getPrivilegeId() - Method in class gov.nih.nci.caarray.domain.audit.AuditLogSecurity
 
getPrivilegeNames() - Method in class gov.nih.nci.caarray.domain.permissions.Privileges
 
getProbeCount() - Method in class gov.nih.nci.cabio.domain.ExonArrayReporter
 
getProbeGroup() - Method in class gov.nih.nci.caarray.domain.array.PhysicalProbe
 
getProbeGroups() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesignDetails
 
getProbes() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesignDetails
 
getProbes() - Method in class gov.nih.nci.caarray.domain.array.LogicalProbe
 
getProbes() - Method in class gov.nih.nci.caarray.domain.array.ProbeGroup
 
getProbeSelectionRegionId() - Method in class gov.nih.nci.cabio.domain.ExonArrayReporter
 
getProcessor() - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
 
getProduction() - Method in class gov.nih.nci.caarray.domain.array.Array
Gets the production.
getProject() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
getProject() - Method in class gov.nih.nci.caarray.domain.permissions.AccessProfile
 
getProject() - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
getProjectId() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFileSet
 
getProtocol() - Method in class gov.nih.nci.caarray.domain.protocol.Parameter
 
getProtocol() - Method in class gov.nih.nci.caarray.domain.protocol.ProtocolApplication
Gets the protocol.
getProtocolApplication() - Method in class gov.nih.nci.caarray.domain.protocol.AbstractParameterValue
 
getProtocolApplications() - Method in class gov.nih.nci.caarray.domain.data.AbstractArrayData
Gets the protocolApplications.
getProtocolApplications() - Method in class gov.nih.nci.caarray.domain.data.Image
Gets the protocolApplications.
getProtocolApplications() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
getProtocolApplications() - Method in interface gov.nih.nci.caarray.domain.protocol.ProtocolApplicable
 
getProtocolApplications() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
getProvider() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Gets the provider.
getProviders() - Method in class gov.nih.nci.caarray.domain.sample.Source
Gets the providers.
getProvince() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getPublication() - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
getPublications() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the samples.
getPublicIdentifier() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets a human readable public identifier for this project.
getPublicIdentifier() - Method in class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
getPublicProfile() - Method in class gov.nih.nci.caarray.domain.project.Project
 
getPublicReleaseDate() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the publicReleaseDate.
getPublisher() - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
getPubMedId() - Method in class gov.nih.nci.caarray.domain.publication.Publication
Gets the pubMedId.
getQualityControlDescription() - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
getQualityControlTypes() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the qualityControlTypes.
getQuantitationType() - Method in class gov.nih.nci.caarray.domain.data.AbstractDataColumn
 
getQuantitationTypes() - Method in class gov.nih.nci.caarray.domain.data.ArrayDataType
 
getQuantitationTypes() - Method in interface gov.nih.nci.caarray.domain.data.ArrayDataTypeDescriptor
Returns the complete set of quantitation types that might be returned from a data file of this type.
getQuantitationTypes() - Method in class gov.nih.nci.caarray.domain.data.DataRetrievalRequest
 
getQuantitationTypes() - Method in class gov.nih.nci.caarray.domain.data.DataSet
 
getQueryProcessorClass() - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
getQueryProcessorClass() - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
getRawArrayData() - Method in class gov.nih.nci.caarray.domain.data.Image
 
getRawArrayDataTypes() - Method in interface gov.nih.nci.caarray.domain.file.FileTypeRegistry
 
getRawArrayDataTypes() - Method in class gov.nih.nci.caarray.domain.file.FileTypeRegistryImpl
getRawDataCollection() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Gets the rawArrayDatas.
getRecord() - Method in class gov.nih.nci.caarray.domain.audit.AuditLogSecurity
 
getRefseqAccession() - Method in class gov.nih.nci.caarray.domain.array.Gene
 
getRegistrationTemplateFile() - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceConfiguration
 
getRegistrationTemplateFile() - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.ResourceConfiguration
 
getRelatedHybridizations() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
getRelatedHybridizations() - Method in class gov.nih.nci.caarray.domain.sample.LabeledExtract
getRelatedHybridizations() - Method in class gov.nih.nci.caarray.domain.sample.Sample
getRelatedHybridizations() - Method in class gov.nih.nci.caarray.domain.sample.Source
getRemoteApiSecurityPolicies(User) - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayObject
Return the set of security policies that should be applied to this object prior to it being returned as part of a return value for a remote API call.
getRemoteApiSecurityPolicies(User) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Return the set of security policies that should be applied to this object prior to it being returned as part of a return value for a remote API call.
getRemoteApiSecurityPolicies(User) - Method in class gov.nih.nci.caarray.domain.project.Project
Return the set of security policies that should be applied to this object prior to it being returned as part of a return value for a remote API call.
getReplicateDescription() - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
getReplicateTypes() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the replicateTypes.
getRequiredParameters() - Method in class gov.nih.nci.cagrid.caarray.stubs.cql.StubCQLQueryProcessor
Deprecated.  
getResourceHome() - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcImplBase
 
getResourceHome(String) - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcImplBase
 
getResourceKey() - Method in enum gov.nih.nci.caarray.domain.permissions.SampleSecurityLevel
getResourceKey() - Method in enum gov.nih.nci.caarray.domain.permissions.SecurityLevel
getResourceKey() - Method in enum gov.nih.nci.caarray.domain.project.ServiceType
 
getResourceKey() - Method in interface gov.nih.nci.caarray.domain.ResourceBasedEnum
 
getResourceKey() - Method in interface gov.nih.nci.caarray.domain.search.BiomaterialSearchCategory
 
getResourceKey() - Method in enum gov.nih.nci.caarray.domain.search.BrowseCategory
 
getResourceKey() - Method in enum gov.nih.nci.caarray.domain.search.ExternalBiomaterialSearchCategory
getResourceKey() - Method in enum gov.nih.nci.caarray.domain.search.SearchCategory
 
getResourceKey() - Method in enum gov.nih.nci.caarray.domain.search.SearchSampleCategory
getResourceKey() - Method in enum gov.nih.nci.caarray.domain.search.SearchSourceCategory
getResourceKey() - Method in enum gov.nih.nci.caarray.domain.search.SearchTypeSelection
 
getResourceProperty(QName) - Method in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
getResourceProperty(QName) - Method in interface gov.nih.nci.cagrid.caarray.common.CaArraySvcI
 
getRole() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getRoleNames() - Method in class gov.nih.nci.caarray.domain.project.ExperimentContact
 
getRoles() - Method in class gov.nih.nci.caarray.domain.project.ExperimentContact
Gets the roles.
getRow() - Method in class gov.nih.nci.caarray.domain.array.Feature
 
getSampleByName(String) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Return the sample with given name in this experiment.
getSampleCount() - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
getSamples() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the samples.
getSamples() - Method in class gov.nih.nci.caarray.domain.sample.Extract
Gets the samples.
getSamples() - Method in class gov.nih.nci.caarray.domain.sample.Source
Gets the samples.
getSampleSecurityLevels() - Method in class gov.nih.nci.caarray.domain.permissions.AccessProfile
 
getSampleSecurityLevels() - Method in enum gov.nih.nci.caarray.domain.permissions.SecurityLevel
 
getScientificName() - Method in class edu.georgetown.pir.Organism
 
getSearchService() - Method in class gov.nih.nci.caarray.services.CaArrayServer
 
getSearchService() - Method in class gov.nih.nci.caarray.services.external.v1_0.CaArrayServer
 
getSecurityDescriptor() - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceBase
 
getSecurityEntries() - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogProcessor
Returns a mapping of audit records with their associated security entries.
getSecurityLevel() - Method in class gov.nih.nci.caarray.domain.permissions.AccessProfile
 
getSequenceSource() - Method in class gov.nih.nci.cabio.domain.ExpressionArrayReporter
 
getSequenceType() - Method in class gov.nih.nci.cabio.domain.ExpressionArrayReporter
 
getSerialNumber() - Method in class gov.nih.nci.caarray.domain.array.Array
Gets the serialNumber.
getServerConfigLocation() - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
getServerConfigLocation() - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
getServiceMetadata() - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceBase
 
getServiceMetadataFile() - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceConfiguration
 
getServiceMetadataFile() - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.ResourceConfiguration
 
getServiceNamespace() - Method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
getSessionFactory() - Method in interface gov.nih.nci.caarray.util.CaArrayHibernateHelper
 
getSessionFactory() - Method in class gov.nih.nci.caarray.util.CaArrayHibernateHelperUnsupportedOperationImpl
getSnpArrayReporter() - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
getSoftware() - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Gets the software.
getSource() - Method in class edu.georgetown.pir.AdditionalOrganismName
 
getSource() - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
 
getSource() - Method in enum gov.nih.nci.caarray.domain.protocol.ProtocolTypeAssociation
 
getSource() - Method in class gov.nih.nci.caarray.domain.vocabulary.Category
 
getSource() - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
Gets the source.
getSourceByName(String) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Return the source with given name in this experiment.
getSourceImages() - Method in class gov.nih.nci.caarray.domain.data.RawArrayData
 
getSources() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the sources.
getSources() - Method in class gov.nih.nci.caarray.domain.sample.Sample
Gets the sources.
getSpecialCharacteristics() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Returns the characteristics that are handled specially and have their own fields in AbstractBioMaterial or one of its subclasses, rather than being placed in the general characteristics collection.
getSpecialCharacteristics() - Method in class gov.nih.nci.caarray.domain.sample.LabeledExtract
Returns the characteristics that are handled specially and have their own fields in AbstractBioMaterial or one of its subclasses, rather than being placed in the general characteristics collection.
getStart() - Method in class gov.nih.nci.caarray.domain.array.ExonProbeAnnotation
 
getState() - Method in class gov.nih.nci.caarray.domain.contact.Address
Gets the state.
getState() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getStatus() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
getStatus() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFileSet
Returns the aggregate status of the file set.
getStatus() - Method in class gov.nih.nci.caarray.domain.publication.Publication
Gets the status.
getStatusCounts() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
 
getStop() - Method in class gov.nih.nci.caarray.domain.array.ExonProbeAnnotation
 
getStrand() - Method in class gov.nih.nci.caarray.domain.array.ExonProbeAnnotation
 
getStrand() - Method in class gov.nih.nci.cabio.domain.ExonArrayReporter
 
getStreet1() - Method in class gov.nih.nci.caarray.domain.contact.Address
Gets the street1.
getStreet2() - Method in class gov.nih.nci.caarray.domain.contact.Address
Gets the street2.
getSubstrateType() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Gets the substrateType.
getSuccessorsOfType(ExperimentDesignNodeType) - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
 
getSuccessorType() - Method in enum gov.nih.nci.caarray.domain.project.ExperimentDesignNodeType
 
getSurfaceType() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Gets the surfaceType.
getSymbol() - Method in class gov.nih.nci.caarray.domain.array.Gene
 
getTargetDescription() - Method in class gov.nih.nci.cabio.domain.ExpressionArrayReporter
 
getTargetId() - Method in class gov.nih.nci.cabio.domain.ExpressionArrayReporter
 
getTaxonomyRank() - Method in class edu.georgetown.pir.Organism
 
getTechnologyType() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Gets the technologyType.
getter() - Method in class gov.nih.nci.caarray.util.PropertyAccessor
 
getTerm() - Method in class gov.nih.nci.caarray.domain.project.TermBasedFactorValue
Gets the term.
getTerm() - Method in class gov.nih.nci.caarray.domain.protocol.TermBasedParameterValue
Gets the term.
getTerm() - Method in class gov.nih.nci.caarray.domain.sample.TermBasedCharacteristic
Gets the term.
getTerm() - Method in interface gov.nih.nci.caarray.domain.TermBasedValue
 
getTermCache() - Method in class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
 
getTermSource() - Method in class edu.georgetown.pir.Organism
 
getTermSource() - Method in class gov.nih.nci.caarray.util.owlparser.AbstractOntologyOwlParser
 
getThcAccession() - Method in class gov.nih.nci.caarray.domain.array.Gene
 
getTimeRequested() - Method in interface gov.nih.nci.caarray.domain.project.BaseJob
The time requested is never null.
getTimeRequested() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
The time requested is never null.
getTimeRequested() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
The time requested is never null.
getTimeStarted() - Method in interface gov.nih.nci.caarray.domain.project.BaseJob
 
getTimeStarted() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
getTimeStarted() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
getTissueSite() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
getTitle() - Method in class gov.nih.nci.caarray.domain.project.Experiment
Gets the title.
getTitle() - Method in class gov.nih.nci.caarray.domain.publication.Publication
Gets the title.
getTitle() - Method in class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
getType() - Method in class gov.nih.nci.caarray.domain.data.AbstractArrayData
 
getType() - Method in class gov.nih.nci.caarray.domain.data.QuantitationType
 
getType() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
getType() - Method in class gov.nih.nci.caarray.domain.project.Factor
Gets the type.
getType() - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Gets the type.
getType() - Method in class gov.nih.nci.caarray.domain.publication.Publication
Gets the type.
getType() - Method in class gov.nih.nci.caarray.util.PropertyAccessor
 
getTypeByName(String) - Method in interface gov.nih.nci.caarray.domain.file.FileTypeRegistry
Look up a type based on its name.
getTypeByName(String) - Method in class gov.nih.nci.caarray.domain.file.FileTypeRegistryImpl
Look up a type based on its name.
getTypeClass() - Method in enum gov.nih.nci.caarray.domain.data.DataType
Returns the Java class that corresponds to the data type.
getTypeClass() - Method in class gov.nih.nci.caarray.domain.data.QuantitationType
 
getTypeFromExtension(String) - Method in interface gov.nih.nci.caarray.domain.file.FileTypeRegistry
Determine a file's type based on its extension.
getTypeFromExtension(String) - Method in class gov.nih.nci.caarray.domain.file.FileTypeRegistryImpl
Determine a file's type based on its extension.
getTypes() - Method in class gov.nih.nci.caarray.domain.search.FileSearchCriteria
 
getUncompressedSize() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
getUncompressedSize() - Method in class gov.nih.nci.caarray.domain.MultiPartBlob
 
getUncompressedSizeOfDataFiles() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
 
getUnexpectedErrorPreparedStatement(Connection) - Method in interface gov.nih.nci.caarray.domain.project.ExecutableJob
Returns a prepared statement for the executer of the job to run if the job fails with an unexpected error.
getUnigeneclusterID() - Method in class gov.nih.nci.caarray.domain.array.Gene
 
getUnImportedFiles() - Method in class gov.nih.nci.caarray.domain.project.Project
Get the files.
getUniprotId() - Method in class gov.nih.nci.caarray.domain.array.ExonProbeAnnotation
 
getUnit() - Method in class gov.nih.nci.caarray.domain.project.AbstractFactorValue
Gets the unit.
getUnit() - Method in class gov.nih.nci.caarray.domain.protocol.AbstractParameterValue
Gets the unit.
getUnit() - Method in class gov.nih.nci.caarray.domain.sample.AbstractCharacteristic
Gets the unit.
getUnit() - Method in interface gov.nih.nci.caarray.domain.UnitableValue
Gets the unit.
getUri() - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
getUrl() - Method in class gov.nih.nci.caarray.domain.contact.AbstractContact
Gets the url.
getUrl() - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Gets the url.
getUrl() - Method in class gov.nih.nci.caarray.domain.vocabulary.Category
 
getUrl() - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
Gets the url at which this term can be accessed, if available.
getUrl() - Method in class gov.nih.nci.caarray.domain.vocabulary.TermSource
Gets the url.
getUser() - Method in interface gov.nih.nci.caarray.util.UsernameHolder
 
getUser() - Method in class gov.nih.nci.caarray.util.UsernameHolderImpl
getUserCanCancelJob() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
getUserCanCancelJob() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
A user can only cancel a job which is in_queue, or one of its children is in_queue.
getUserHasOwnership() - Method in interface gov.nih.nci.caarray.domain.project.Job
 
getUserHasOwnership() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
getUserHasOwnership() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
getUserHasReadAccess() - Method in interface gov.nih.nci.caarray.domain.project.Job
 
getUserHasReadAccess() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
getUserHasReadAccess() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
getUserHasWriteAccess() - Method in interface gov.nih.nci.caarray.domain.project.Job
 
getUserHasWriteAccess() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
getUserHasWriteAccess() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
getUsername() - Method in class gov.nih.nci.caarray.domain.search.AuditLogSearchCriteria
 
getUserVisibleFiles() - Method in class gov.nih.nci.caarray.domain.project.Project
Get user visible imported files.
getUserVisibleImportedFiles() - Method in class gov.nih.nci.caarray.domain.project.Project
Get user visible imported files.
getUserVisibleSupplementalFiles() - Method in class gov.nih.nci.caarray.domain.project.Project
Get user visible supplemental files.
getUserVisibleUnImportedFiles() - Method in class gov.nih.nci.caarray.domain.project.Project
Get user visible unimported files.
getValidationResult() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
getValue() - Method in class edu.georgetown.pir.AdditionalOrganismName
 
getValue() - Method in enum gov.nih.nci.caarray.domain.data.DesignElementType
 
getValue() - Method in interface gov.nih.nci.caarray.domain.MeasurementValue
 
getValue() - Method in class gov.nih.nci.caarray.domain.project.MeasurementFactorValue
 
getValue() - Method in class gov.nih.nci.caarray.domain.project.UserDefinedFactorValue
 
getValue() - Method in class gov.nih.nci.caarray.domain.protocol.MeasurementParameterValue
 
getValue(String) - Method in class gov.nih.nci.caarray.domain.protocol.ProtocolApplication
Return the parameter value for the parameter with given name in this protocol application.
getValue() - Method in enum gov.nih.nci.caarray.domain.protocol.ProtocolTypeAssociation
 
getValue() - Method in class gov.nih.nci.caarray.domain.protocol.UserDefinedParameterValue
 
getValue() - Method in class gov.nih.nci.caarray.domain.sample.MeasurementCharacteristic
 
getValue() - Method in class gov.nih.nci.caarray.domain.sample.UserDefinedCharacteristic
 
getValue() - Method in class gov.nih.nci.caarray.domain.search.AnnotationCriterion
 
getValue() - Method in interface gov.nih.nci.caarray.domain.UserDefinedValue
 
getValue() - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
Gets the value.
getValue() - Method in class gov.nih.nci.caarray.util.LabelValue
get value.
getValueAndSource() - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
 
getValues() - Method in class gov.nih.nci.caarray.domain.data.BooleanColumn
 
getValues() - Method in class gov.nih.nci.caarray.domain.data.DoubleColumn
 
getValues() - Method in class gov.nih.nci.caarray.domain.data.FloatColumn
 
getValues() - Method in class gov.nih.nci.caarray.domain.data.IntegerColumn
 
getValues() - Method in class gov.nih.nci.caarray.domain.data.LongColumn
 
getValues() - Method in class gov.nih.nci.caarray.domain.data.ShortColumn
 
getValues() - Method in class gov.nih.nci.caarray.domain.data.StringColumn
 
getValues() - Method in class gov.nih.nci.caarray.domain.protocol.ProtocolApplication
Gets the values.
getValuesAsArray() - Method in class gov.nih.nci.caarray.domain.data.AbstractDataColumn
Serialized values, from the DataStorageFacade.
getValuesAsArray() - Method in class gov.nih.nci.caarray.domain.data.BooleanColumn
Serialized values, from the DataStorageFacade.
getValuesAsArray() - Method in class gov.nih.nci.caarray.domain.data.DoubleColumn
Serialized values, from the DataStorageFacade.
getValuesAsArray() - Method in class gov.nih.nci.caarray.domain.data.FloatColumn
Serialized values, from the DataStorageFacade.
getValuesAsArray() - Method in class gov.nih.nci.caarray.domain.data.IntegerColumn
Serialized values, from the DataStorageFacade.
getValuesAsArray() - Method in class gov.nih.nci.caarray.domain.data.LongColumn
Serialized values, from the DataStorageFacade.
getValuesAsArray() - Method in class gov.nih.nci.caarray.domain.data.ShortColumn
Serialized values, from the DataStorageFacade.
getValuesAsArray() - Method in class gov.nih.nci.caarray.domain.data.StringColumn
Serialized values, from the DataStorageFacade.
getValuesAsString() - Method in class gov.nih.nci.caarray.domain.data.AbstractDataColumn
 
getValuesAsString() - Method in class gov.nih.nci.caarray.domain.data.BooleanColumn
getValuesAsString() - Method in class gov.nih.nci.caarray.domain.data.DoubleColumn
getValuesAsString() - Method in class gov.nih.nci.caarray.domain.data.FloatColumn
 
getValuesAsString() - Method in class gov.nih.nci.caarray.domain.data.IntegerColumn
 
getValuesAsString() - Method in class gov.nih.nci.caarray.domain.data.LongColumn
 
getValuesAsString() - Method in class gov.nih.nci.caarray.domain.data.ShortColumn
 
getValuesAsString() - Method in class gov.nih.nci.caarray.domain.data.StringColumn
 
getVersion() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Gets the version.
getVersion() - Method in class gov.nih.nci.caarray.domain.data.ArrayDataType
 
getVersion() - Method in interface gov.nih.nci.caarray.domain.data.ArrayDataTypeDescriptor
Returns the version of this data type.
getVersion() - Method in enum gov.nih.nci.caarray.domain.project.ExperimentOntology
 
getVersion() - Method in class gov.nih.nci.caarray.domain.vocabulary.TermSource
Gets the version.
getVolume() - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
getWhereClause() - Method in interface gov.nih.nci.caarray.domain.search.BiomaterialSearchCategory
 
getWhereClause() - Method in enum gov.nih.nci.caarray.domain.search.ExternalBiomaterialSearchCategory
getWhereClause() - Method in enum gov.nih.nci.caarray.domain.search.SearchCategory
 
getWhereClause() - Method in enum gov.nih.nci.caarray.domain.search.SearchSampleCategory
getWhereClause() - Method in enum gov.nih.nci.caarray.domain.search.SearchSourceCategory
getX_Coordinate() - Method in class gov.nih.nci.caarray.domain.array.Feature
 
getY_Coordinate() - Method in class gov.nih.nci.caarray.domain.array.Feature
 
getYear() - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
getZip() - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
getZipCode() - Method in class gov.nih.nci.caarray.domain.contact.Address
Gets the zipCode.
gov.nih.nci.caarray.domain - package gov.nih.nci.caarray.domain
 
gov.nih.nci.caarray.domain.array - package gov.nih.nci.caarray.domain.array
 
gov.nih.nci.caarray.domain.audit - package gov.nih.nci.caarray.domain.audit
 
gov.nih.nci.caarray.domain.contact - package gov.nih.nci.caarray.domain.contact
 
gov.nih.nci.caarray.domain.country - package gov.nih.nci.caarray.domain.country
 
gov.nih.nci.caarray.domain.data - package gov.nih.nci.caarray.domain.data
 
gov.nih.nci.caarray.domain.file - package gov.nih.nci.caarray.domain.file
 
gov.nih.nci.caarray.domain.hybridization - package gov.nih.nci.caarray.domain.hybridization
 
gov.nih.nci.caarray.domain.permissions - package gov.nih.nci.caarray.domain.permissions
 
gov.nih.nci.caarray.domain.project - package gov.nih.nci.caarray.domain.project
 
gov.nih.nci.caarray.domain.protocol - package gov.nih.nci.caarray.domain.protocol
 
gov.nih.nci.caarray.domain.publication - package gov.nih.nci.caarray.domain.publication
 
gov.nih.nci.caarray.domain.register - package gov.nih.nci.caarray.domain.register
 
gov.nih.nci.caarray.domain.sample - package gov.nih.nci.caarray.domain.sample
 
gov.nih.nci.caarray.domain.search - package gov.nih.nci.caarray.domain.search
 
gov.nih.nci.caarray.domain.state - package gov.nih.nci.caarray.domain.state
 
gov.nih.nci.caarray.domain.vocabulary - package gov.nih.nci.caarray.domain.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.util - package gov.nih.nci.caarray.util
 
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.cabio.domain - package gov.nih.nci.cabio.domain
 
gov.nih.nci.cagrid.caarray.client - package gov.nih.nci.cagrid.caarray.client
 
gov.nih.nci.cagrid.caarray.common - package gov.nih.nci.cagrid.caarray.common
 
gov.nih.nci.cagrid.caarray.service - package gov.nih.nci.cagrid.caarray.service
 
gov.nih.nci.cagrid.caarray.service.globus - package gov.nih.nci.cagrid.caarray.service.globus
 
gov.nih.nci.cagrid.caarray.service.globus.resource - package gov.nih.nci.cagrid.caarray.service.globus.resource
 
gov.nih.nci.cagrid.caarray.stubs.cql - package gov.nih.nci.cagrid.caarray.stubs.cql
 
gov.nih.nci.cagrid.caarray.util - package gov.nih.nci.cagrid.caarray.util
 
GridTransferResultHandler - Interface in gov.nih.nci.cagrid.caarray.util
An interface to be implemented by clients who which to to process data retrieved via a Grid Transfer enabled service as a stream.
GROUP - Static variable in class gov.nih.nci.caarray.domain.audit.AuditLogSecurity
Security based on group membership.
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

handleChildCancelled() - Method in interface gov.nih.nci.caarray.domain.project.ParentJob
Indicate a child job has been cancelled to the parent.
handleChildProcessed() - Method in interface gov.nih.nci.caarray.domain.project.ParentJob
Indicate a child job has been processed to the parent.
hasChildren() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
Indicates if the CaArrayFile has children (child CaArrayFile's) or not.
hashCode() - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayObject
Default hashCode goes off of id.
hashCode() - Method in class gov.nih.nci.caarray.domain.array.Accession
hashCode() - Method in class gov.nih.nci.caarray.domain.contact.AbstractContact
Default hashCode goes off of id.
hashCode() - Method in class gov.nih.nci.caarray.domain.contact.Address
Default hashCode goes off of id.
hashCode() - Method in class gov.nih.nci.caarray.domain.contact.Organization
Default hashCode goes off of id.
hashCode() - Method in class gov.nih.nci.caarray.domain.contact.Person
Default hashCode goes off of id.
hashCode() - Method in class gov.nih.nci.caarray.domain.file.FileType
hashCode() - Method in class gov.nih.nci.caarray.domain.protocol.Parameter
Default hashCode goes off of id.
hashCode() - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Default hashCode goes off of id.
hashCode() - Method in class gov.nih.nci.caarray.domain.publication.Publication
Default hashCode goes off of id.
hashCode() - Method in class gov.nih.nci.caarray.domain.vocabulary.Category
Default hashCode goes off of id.
hashCode() - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
Default hashCode goes off of id.
hashCode() - Method in class gov.nih.nci.caarray.domain.vocabulary.TermSource
Default hashCode goes off of id.
hashCode(Object) - Method in class gov.nih.nci.caarray.util.URIUserType
hasParsedArrayDesigns() - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
hasReadPermission(User) - Method in class gov.nih.nci.caarray.domain.project.Project
Returns whether the given user has read permissions to this project.
hasWritePermission(User) - Method in class gov.nih.nci.caarray.domain.project.Project
Returns whether the given user has write permissions to this project.
Hybridization - Class in gov.nih.nci.caarray.domain.hybridization
The act of hybridizing extracted genetic material to the probes on a microarray.
Hybridization() - Constructor for class gov.nih.nci.caarray.domain.hybridization.Hybridization
 
HybridizationData - Class in gov.nih.nci.caarray.domain.data
Value holder for all the data values associated with a specific hybridization.
HybridizationData() - Constructor for class gov.nih.nci.caarray.domain.data.HybridizationData
 
HybridizationSearchCriteria - Class in gov.nih.nci.caarray.domain.search
Simple bean to hold search criteria for hybridizations.
HybridizationSearchCriteria() - Constructor for class gov.nih.nci.caarray.domain.search.HybridizationSearchCriteria
 
HybridizationSortCriterion - Enum in gov.nih.nci.caarray.domain.search
Enum of possible sort criterions for hybridizations.

I

Image - Class in gov.nih.nci.caarray.domain.data
 
Image() - Constructor for class gov.nih.nci.caarray.domain.data.Image
 
IMPORTABLE_FILE_STATUSES - Static variable in enum gov.nih.nci.caarray.domain.file.FileStatus
The set of FileStatuses in which a file can be imported.
includeNulls() - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
Set this criteria to include null properties in the comparison.
includeProperties(String...) - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
Set this criteria to include given properties from comparison.
includeZeroes() - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
Set this criteria to include zero-valued properties in the comparison.
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.caarray.client.CaArraySvcClientBase
 
initialize(PDPConfig, String, String) - Method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
initialize(Object, QName, Object) - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceBase
 
initialize() - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceHome
Initialze the singleton resource, when the home is initialized.
initializeArray(int) - Method in class gov.nih.nci.caarray.domain.data.AbstractDataColumn
Initializes this column to hold the number of values given.
initializeArray(int) - Method in class gov.nih.nci.caarray.domain.data.BooleanColumn
Initializes this column to hold the number of values given.
initializeArray(int) - Method in class gov.nih.nci.caarray.domain.data.DoubleColumn
Initializes this column to hold the number of values given.
initializeArray(int) - Method in class gov.nih.nci.caarray.domain.data.FloatColumn
Initializes this column to hold the number of values given.
initializeArray(int) - Method in class gov.nih.nci.caarray.domain.data.IntegerColumn
Initializes this column to hold the number of values given.
initializeArray(int) - Method in class gov.nih.nci.caarray.domain.data.LongColumn
Initializes this column to hold the number of values given.
initializeArray(int) - Method in class gov.nih.nci.caarray.domain.data.ShortColumn
Initializes this column to hold the number of values given.
initializeArray(int) - Method in class gov.nih.nci.caarray.domain.data.StringColumn
Initializes this column to hold the number of values given.
IntegerColumn - Class in gov.nih.nci.caarray.domain.data
Contains a column of int values.
IntegerColumn() - Constructor for class gov.nih.nci.caarray.domain.data.IntegerColumn
 
isAllowsRead() - Method in enum gov.nih.nci.caarray.domain.permissions.SampleSecurityLevel
 
isAllowsRead() - Method in enum gov.nih.nci.caarray.domain.permissions.SecurityLevel
 
isAllowsWrite() - Method in enum gov.nih.nci.caarray.domain.permissions.SampleSecurityLevel
 
isAllowsWrite() - Method in enum gov.nih.nci.caarray.domain.permissions.SecurityLevel
 
isArrayData() - Method in class gov.nih.nci.caarray.domain.file.FileType
 
isArrayDesign() - Method in class gov.nih.nci.caarray.domain.file.FileType
 
isAuditableEntity(Object) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogProcessor
isAvailableToGroups() - Method in enum gov.nih.nci.caarray.domain.permissions.SecurityLevel
 
isAvailableToPublic() - Method in enum gov.nih.nci.caarray.domain.permissions.SampleSecurityLevel
 
isAvailableToPublic() - Method in enum gov.nih.nci.caarray.domain.permissions.SecurityLevel
 
isBrowse() - Method in class gov.nih.nci.caarray.domain.permissions.Privileges
 
isCollaborator(User) - Method in class gov.nih.nci.caarray.domain.project.Project
Returns whether the given user is a collaborator on this project, ie whether he is in any of the collaborator groups that have an access profile with a security level greater than "None" configured for this project.
isDataMatrix() - Method in class gov.nih.nci.caarray.domain.file.FileType
 
isDeletable() - Method in enum gov.nih.nci.caarray.domain.file.FileStatus
 
isDerivedArrayData() - Method in class gov.nih.nci.caarray.domain.file.FileType
 
isDirectPredecessorOf(ExperimentDesignNodeType) - Method in enum gov.nih.nci.caarray.domain.project.ExperimentDesignNodeType
Return whether this node type is to the immediate left of the given node type in a hybridization channel or experiment design graph.
isDirectSuccessorOf(ExperimentDesignNodeType) - Method in enum gov.nih.nci.caarray.domain.project.ExperimentDesignNodeType
Return whether this node type is immediately to the right of the given node type in a hybridization channel or experiment design graph.
isEquivalent(ArrayDataType) - Method in interface gov.nih.nci.caarray.domain.data.ArrayDataTypeDescriptor
Indicates whether the ArrayDataType given is equivalent to this descriptor, matching on name and version.
isExcludeNulls() - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
 
isExcludeZeroes() - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
 
isGroupProfile() - Method in class gov.nih.nci.caarray.domain.permissions.AccessProfile
 
isImportable() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
Check whether this file is eligible to be imported.
isImportable() - Method in enum gov.nih.nci.caarray.domain.file.FileStatus
 
isImportedAndParsed() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Check whether this is a array design that has been imported imported but not parsed.
isImportingData() - Method in class gov.nih.nci.caarray.domain.project.Project
 
isInProgress() - Method in interface gov.nih.nci.caarray.domain.project.BaseJob
 
isInProgress() - Method in class gov.nih.nci.caarray.domain.project.JobSnapshot
isInProgress() - Method in class gov.nih.nci.caarray.domain.project.UserVisibleJob
isLoaded() - Method in class gov.nih.nci.caarray.domain.data.AbstractDataColumn
Indicates whether this column is already loaded, meaning its populated with an array of values.
isLoaded() - Method in class gov.nih.nci.caarray.domain.data.BooleanColumn
Indicates whether this column is already loaded, meaning its populated with an array of values.
isLoaded() - Method in class gov.nih.nci.caarray.domain.data.DoubleColumn
Indicates whether this column is already loaded, meaning its populated with an array of values.
isLoaded() - Method in class gov.nih.nci.caarray.domain.data.FloatColumn
Indicates whether this column is already loaded, meaning its populated with an array of values.
isLoaded() - Method in class gov.nih.nci.caarray.domain.data.IntegerColumn
Indicates whether this column is already loaded, meaning its populated with an array of values.
isLoaded() - Method in class gov.nih.nci.caarray.domain.data.LongColumn
Indicates whether this column is already loaded, meaning its populated with an array of values.
isLoaded() - Method in class gov.nih.nci.caarray.domain.data.ShortColumn
Indicates whether this column is already loaded, meaning its populated with an array of values.
isLoaded() - Method in class gov.nih.nci.caarray.domain.data.StringColumn
Indicates whether this column is already loaded, meaning its populated with an array of values.
isLocked() - Method in class gov.nih.nci.caarray.domain.project.Project
Gets the workflow status of this project.
isMageTab() - Method in class gov.nih.nci.caarray.domain.file.FileType
 
isMainPointOfContact() - Method in class gov.nih.nci.caarray.domain.project.ExperimentContact
Returns whether this contact is the main POC for the experiment (based on whether he has the appropriate role).
isMutable() - Method in class gov.nih.nci.caarray.util.URIUserType
isOwner(User) - Method in class gov.nih.nci.caarray.domain.project.Project
Checks whether a given user is an owner of this project.
isParseableArrayDesign() - Method in class gov.nih.nci.caarray.domain.file.FileType
 
isParseableData() - Method in class gov.nih.nci.caarray.domain.file.FileType
 
isParsed() - Method in class gov.nih.nci.caarray.domain.file.FileType
 
isPartial() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
isPartialRead() - Method in class gov.nih.nci.caarray.domain.permissions.Privileges
 
isPartialRead() - Method in enum gov.nih.nci.caarray.domain.permissions.SecurityLevel
 
isPartialWrite() - Method in class gov.nih.nci.caarray.domain.permissions.Privileges
 
isPartialWrite() - Method in enum gov.nih.nci.caarray.domain.permissions.SecurityLevel
 
isPermissions() - Method in class gov.nih.nci.caarray.domain.permissions.Privileges
 
isPermitted(Subject, MessageContext, QName) - Method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
isPredecessorOf(ExperimentDesignNodeType) - Method in enum gov.nih.nci.caarray.domain.project.ExperimentDesignNodeType
Return whether this node type is to the left of the given node type in a hybridization channel or experiment design graph.
isPrimaryInvestigator() - Method in class gov.nih.nci.caarray.domain.project.ExperimentContact
Returns whether this contact is the PI for the experiment (based on whether he has the appropriate role).
isProvider() - Method in class gov.nih.nci.caarray.domain.contact.Organization
 
isPublicProfile() - Method in class gov.nih.nci.caarray.domain.permissions.AccessProfile
 
isRawArrayData() - Method in class gov.nih.nci.caarray.domain.file.FileType
 
isRead() - Method in class gov.nih.nci.caarray.domain.permissions.Privileges
 
isSampleLevelPermissionsAllowed() - Method in enum gov.nih.nci.caarray.domain.permissions.SecurityLevel
 
isSuccessorOf(ExperimentDesignNodeType) - Method in enum gov.nih.nci.caarray.domain.project.ExperimentDesignNodeType
Return whether this node type is to the right of the given node type in a hybridization channel or experiment design graph.
isUnparsedAndReimportable() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Check whether this is a array design that was previously imported but not parsed, but now can be imported and parsed (due to a new parsing FileHandler being implemented for it, or because it was previously canceled from the job queue).
isUnparsedAndReimportable() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
Check whether this is a file that was previously imported but not parsed, but now can be imported and parsed (due to a parsing FileHandler being implemented for it).
isUnparsedAndReimportable() - Method in class gov.nih.nci.caarray.domain.project.Project
Check whether this is a experiment that was previously imported but not parsed, but now can be imported and parsed (due to a parsing FileHandler being implemented for it).
isUnsupported(String) - Static method in enum gov.nih.nci.caarray.domain.file.UnsupportedAffymetrixCdfFiles
Check if the given filename is on the list of unsupported files.
isValidatable() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
Check whether this file is eligible to be validated.
isValidatable() - Method in enum gov.nih.nci.caarray.domain.file.FileStatus
 
isValidated() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFileSet
Returns a value to indicate if the fileset has been validated or not.
isWrite() - Method in class gov.nih.nci.caarray.domain.permissions.Privileges
 

J

JNDI_NAME - Static variable in interface gov.nih.nci.caarray.services.arraydesign.ArrayDesignDetailsService
The JNDI name to look up the remote ArrayDesignDetailsService service.
JNDI_NAME - Static variable in interface gov.nih.nci.caarray.services.data.DataRetrievalService
The JNDI name to look up the remote ArrayDesignDetailsService service.
JNDI_NAME - Static variable in interface gov.nih.nci.caarray.services.file.FileRetrievalService
The JNDI name to look up the remote FileRetrievalService service.
JNDI_NAME - Static variable in interface gov.nih.nci.caarray.services.search.CaArraySearchService
The JNDI name to look up the remote CaArraySearch service.
Job - Interface in gov.nih.nci.caarray.domain.project
 
JobMessageSender - Interface in gov.nih.nci.caarray.domain.project
Sends messages to subscribers interested in events on the job queue.
JobSnapshot - Class in gov.nih.nci.caarray.domain.project
Represents the read-only state of another job at the time an instance of this class is created.
JobSnapshot(User, ExecutableJob, int) - Constructor for class gov.nih.nci.caarray.domain.project.JobSnapshot
 
JobSortCriterion - Enum in gov.nih.nci.caarray.domain.search
Enum of possible sort criterions for job queue.
JobStatus - Enum in gov.nih.nci.caarray.domain.project
Indicates the status of aJob.
JobType - Enum in gov.nih.nci.caarray.domain.project
Indicates the type of a Job.
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.
JoinableSortCriterion<T> - Interface in gov.nih.nci.caarray.domain.search
SortCriterion where the orderBy field must be used with the joins field because the orderBy field depends on an alias established in the joins.
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

L

LABELED_EXTRACTS_FILTER - Static variable in class gov.nih.nci.caarray.domain.project.Experiment
 
LabeledExtract - Class in gov.nih.nci.caarray.domain.sample
 
LabeledExtract() - Constructor for class gov.nih.nci.caarray.domain.sample.LabeledExtract
 
LabeledExtractSortCriterion - Enum in gov.nih.nci.caarray.domain.search
Enum of possible sort criterions for labeled extracts.
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.
LARGE_TEXT_FIELD_LENGTH - Static variable in class gov.nih.nci.caarray.domain.AbstractCaArrayObject
The column size for large string columns in the db.
LOG - Static variable in class gov.nih.nci.cagrid.caarray.stubs.cql.CaArrayCQLQueryProcessor
 
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
LogicalProbe - Class in gov.nih.nci.caarray.domain.array
A logical probe corresponding to a sequence that is composed of multiple physical probes.
LogicalProbe(ArrayDesignDetails) - Constructor for class gov.nih.nci.caarray.domain.array.LogicalProbe
Creates a new LogicalProbe with its LSID initialized.
LogicalProbe() - Constructor for class gov.nih.nci.caarray.domain.array.LogicalProbe
Deprecated. hibernate & castor only
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).
LogUtil - Class in gov.nih.nci.caarray.util.io.logging
Utility methods for logging functionality.
LongColumn - Class in gov.nih.nci.caarray.domain.data
Contains a column of long values.
LongColumn() - Constructor for class gov.nih.nci.caarray.domain.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.
LSID - Class in gov.nih.nci.caarray.domain
Life Science Identifier -- a unique identifier for entities.
LSID(String, String, String) - Constructor for class gov.nih.nci.caarray.domain.LSID
Instantiates a complete, populated LSID.
LSID(String) - Constructor for class gov.nih.nci.caarray.domain.LSID
Sets the LSID components for this entity.

M

MAGE_TAB_IDF - Static variable in interface gov.nih.nci.caarray.domain.file.FileTypeRegistry
The FileType for MAGE-TAB IDF files.
MAGE_TAB_SDRF - Static variable in interface gov.nih.nci.caarray.domain.file.FileTypeRegistry
The FileType for MAGE-TAB SDRF files.
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.caarray.client.CaArraySvcClient
 
MAIN_POC_ROLE - Static variable in class gov.nih.nci.caarray.domain.project.ExperimentContact
value of the Term for the POC Role.
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.
markAsCancelled() - Method in interface gov.nih.nci.caarray.domain.project.ExecutableJob
Set the appropriate fileset and job status values, indicating that the job has been cancelled.
markAsInProgress() - Method in interface gov.nih.nci.caarray.domain.project.ExecutableJob
Set the appropriate fileset and job status values, indicating that the job is in progress.
markAsInQueue() - Method in interface gov.nih.nci.caarray.domain.project.ExecutableJob
Set the appropriate fileset and job status values, indicating that the job is in the queue.
markAsProcessed() - Method in interface gov.nih.nci.caarray.domain.project.ExecutableJob
Set the appropriate job status values, indicating that the job has been processed.
matches(AbstractParameterValue) - Method in class gov.nih.nci.caarray.domain.protocol.AbstractParameterValue
Checks if two ParameterValues are the same, ignoring ProtocolApplications.
matches(AbstractParameterValue) - Method in class gov.nih.nci.caarray.domain.protocol.MeasurementParameterValue
Checks if two ParameterValues are the same, ignoring ProtocolApplications.
matches(AbstractParameterValue) - Method in class gov.nih.nci.caarray.domain.protocol.TermBasedParameterValue
Checks if two ParameterValues are the same, ignoring ProtocolApplications.
matches(AbstractParameterValue) - Method in class gov.nih.nci.caarray.domain.protocol.UserDefinedParameterValue
Checks if two ParameterValues are the same, ignoring ProtocolApplications.
matchUsing(MatchMode) - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
Set the match mode of this criteria to given match mode.
MaxSerializableSize - Annotation Type in gov.nih.nci.caarray.domain
The presence of this annotation indicates to the entity pruning algorithm used to prepare return results for remote API queries a maximum size for a collection that can be serialized.
MeasurementCharacteristic - Class in gov.nih.nci.caarray.domain.sample
 
MeasurementCharacteristic() - Constructor for class gov.nih.nci.caarray.domain.sample.MeasurementCharacteristic
Hibernate-only constructor.
MeasurementCharacteristic(Category, Float, Term) - Constructor for class gov.nih.nci.caarray.domain.sample.MeasurementCharacteristic
Create a new characteristic with given fields.
MeasurementFactorValue - Class in gov.nih.nci.caarray.domain.project
 
MeasurementFactorValue() - Constructor for class gov.nih.nci.caarray.domain.project.MeasurementFactorValue
Hibernate-only constructor.
MeasurementFactorValue(Float, Term) - Constructor for class gov.nih.nci.caarray.domain.project.MeasurementFactorValue
Create a new factor value with given fields.
MeasurementParameterValue - Class in gov.nih.nci.caarray.domain.protocol
a parameter value with a numeric value.
MeasurementParameterValue() - Constructor for class gov.nih.nci.caarray.domain.protocol.MeasurementParameterValue
Hibernate-only constructor.
MeasurementParameterValue(MeasurementParameterValue) - Constructor for class gov.nih.nci.caarray.domain.protocol.MeasurementParameterValue
Copy constructor.
MeasurementParameterValue(Float, Term) - Constructor for class gov.nih.nci.caarray.domain.protocol.MeasurementParameterValue
Create a new parameter value with given fields.
MeasurementValue - Interface in gov.nih.nci.caarray.domain
A UnitableValue with a numerical value.
merge(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Merges another AbstractExperimentDesignNode into this one.
merge(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
Merges another AbstractExperimentDesignNode into this one.
merge(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Merges another AbstractExperimentDesignNode into this one.
merge(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.sample.Extract
Merges another AbstractExperimentDesignNode into this one.
merge(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.sample.LabeledExtract
Merges another AbstractExperimentDesignNode into this one.
merge(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.sample.Sample
Merges another AbstractExperimentDesignNode into this one.
merge(AbstractExperimentDesignNode) - Method in class gov.nih.nci.caarray.domain.sample.Source
Merges another AbstractExperimentDesignNode into this one.
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.
MIR - Static variable in class gov.nih.nci.caarray.domain.array.MiRNAProbeAnnotation
Name of the miRNA database.
MiRNAProbeAnnotation - Class in gov.nih.nci.caarray.domain.array
 
MiRNAProbeAnnotation() - Constructor for class gov.nih.nci.caarray.domain.array.MiRNAProbeAnnotation
 
MultiPartBlob - Class in gov.nih.nci.caarray.domain
This class is used to get around a mysql issue where the mysql server uses memory extremely poorly on a connection where a blob is being used.
MultiPartBlob() - Constructor for class gov.nih.nci.caarray.domain.MultiPartBlob
 

N

namesForEnums(Iterable<E>) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Return the constant names of the given enum instances.
namesForTypes(Iterable<FileType>) - Static method in class gov.nih.nci.caarray.domain.file.FileTypeRegistryImpl
Return the names of the given FileType instances.
NamingStrategy - Class in gov.nih.nci.caarray.util
CaArray Naming Strategy.
NamingStrategy() - Constructor for class gov.nih.nci.caarray.util.NamingStrategy
 
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
onEndElement(String, String, DeserializationContext) - Method in class gov.nih.nci.cagrid.caarray.util.CaArrayDeserializer
 
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 edu.georgetown.pir
Organism that the sample or data comes from.
Organism() - Constructor for class edu.georgetown.pir.Organism
 
Organization - Class in gov.nih.nci.caarray.domain.contact
Represents an organization.
Organization() - Constructor for class gov.nih.nci.caarray.domain.contact.Organization
 

P

Parameter - Class in gov.nih.nci.caarray.domain.protocol
 
Parameter(String, Protocol) - Constructor for class gov.nih.nci.caarray.domain.protocol.Parameter
 
Parameter() - Constructor for class gov.nih.nci.caarray.domain.protocol.Parameter
Deprecated. for hibernate and castor only
ParentJob - Interface in gov.nih.nci.caarray.domain.project
Represents a job with children.
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.domain.contact
 
Person() - Constructor for class gov.nih.nci.caarray.domain.contact.Person
Default constructor.
Person(User) - Constructor for class gov.nih.nci.caarray.domain.contact.Person
Constructor for a Person based on a CSM User instance.
PersonSortCriterion - Enum in gov.nih.nci.caarray.domain.search
Enum of possible sort criterions for Person objects.
PhysicalProbe - Class in gov.nih.nci.caarray.domain.array
Represents a physical probe on a microarray.
PhysicalProbe(ArrayDesignDetails, ProbeGroup) - Constructor for class gov.nih.nci.caarray.domain.array.PhysicalProbe
Creates a new PhysicalProbe.
PhysicalProbe() - Constructor for class gov.nih.nci.caarray.domain.array.PhysicalProbe
Deprecated. hibernate & castor only
PI_ROLE - Static variable in class gov.nih.nci.caarray.domain.project.ExperimentContact
value of the Term for the PI Role.
portType - Variable in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClientBase
 
portTypeMutex - Variable in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClientBase
 
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.
prepareColumns(List<QuantitationType>, int) - Method in class gov.nih.nci.caarray.domain.data.DataSet
Initialize the columns of each HybridizationData in this DataSet with empty value sets of given size.
prepareColumns(List<QuantitationType>, int) - Method in class gov.nih.nci.caarray.domain.data.HybridizationData
Initialize the columns of this HybridizationData with empty value sets of given size.
printResults(CQLQueryResults, String) - Method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
Privileges - Class in gov.nih.nci.caarray.domain.permissions
A simple class to hold the privileges a user may have for a Protectable object.
Privileges(List<String>) - Constructor for class gov.nih.nci.caarray.domain.permissions.Privileges
Create a new Privileges with given privilege names.
Privileges() - Constructor for class gov.nih.nci.caarray.domain.permissions.Privileges
Create a new Privileges with no privilege names.
ProbeGroup - Class in gov.nih.nci.caarray.domain.array
A logical grouping of like probes, allowing the specification of a type.
ProbeGroup(ArrayDesignDetails) - Constructor for class gov.nih.nci.caarray.domain.array.ProbeGroup
 
ProbeGroup() - Constructor for class gov.nih.nci.caarray.domain.array.ProbeGroup
Deprecated. for castor & hibernate use only
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
processQuery(CQLQuery) - Method in class gov.nih.nci.cagrid.caarray.stubs.cql.CaArrayCQLQueryProcessor
 
processQuery(CQLQuery) - Method in class gov.nih.nci.cagrid.caarray.stubs.cql.StubCQLQueryProcessor
Deprecated.  
processRetrievedData(InputStream) - Method in interface gov.nih.nci.cagrid.caarray.util.GridTransferResultHandler
Process the data incoming via the grid transfer service.
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.
PROJECT - Static variable in class gov.nih.nci.caarray.domain.audit.AuditLogSecurity
Security based on project permissions.
Project - Class in gov.nih.nci.caarray.domain.project
A microarray project.
Project() - Constructor for class gov.nih.nci.caarray.domain.project.Project
Hibernate and caster constructor.
ProjectSortCriterion - Enum in gov.nih.nci.caarray.domain.search
Enum of possible sort criterions for projects.
propagateLastModifiedDataTime(Date) - Method in class gov.nih.nci.caarray.domain.project.AbstractExperimentDesignNode
Propagates the last modified data time up the chain.
propagateLastModifiedDataTime(Date) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Propagates the last modified data time up the chain.
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
Protocol - Class in gov.nih.nci.caarray.domain.protocol
Class representing a protocol.
Protocol() - Constructor for class gov.nih.nci.caarray.domain.protocol.Protocol
Deprecated. 
Protocol(String, Term, TermSource) - Constructor for class gov.nih.nci.caarray.domain.protocol.Protocol
Constructor taking all required fields.
ProtocolApplicable - Interface in gov.nih.nci.caarray.domain.protocol
Interface for entities to which Protocols can be applied.
ProtocolApplication - Class in gov.nih.nci.caarray.domain.protocol
Application of a protocol to an entity, such as a bio material or hybridization.
ProtocolApplication() - Constructor for class gov.nih.nci.caarray.domain.protocol.ProtocolApplication
Default constructor.
ProtocolApplication(ProtocolApplication) - Constructor for class gov.nih.nci.caarray.domain.protocol.ProtocolApplication
Constructs a new ProtocolApplication based on another.
ProtocolTypeAssociation - Enum in gov.nih.nci.caarray.domain.protocol
 
Publication - Class in gov.nih.nci.caarray.domain.publication
 
Publication() - Constructor for class gov.nih.nci.caarray.domain.publication.Publication
 
PublicationSortCriterion - Enum in gov.nih.nci.caarray.domain.search
Enum of possible sort criterions for publication.
publicLevels() - Static method in enum gov.nih.nci.caarray.domain.permissions.SampleSecurityLevel
 
publicLevels() - Static method in enum gov.nih.nci.caarray.domain.permissions.SecurityLevel
 
pullUpValidationMessages() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFileSet
Validation messages on files that have parents are copies to the respective parents.

Q

QuantitationType - Class in gov.nih.nci.caarray.domain.data
Represents the heading for a "column" of array data, indicating the name and primitive typeClass of the data.
QuantitationType() - Constructor for class gov.nih.nci.caarray.domain.data.QuantitationType
 
QuantitationTypeDescriptor - Interface in gov.nih.nci.caarray.domain.data
Interface that enums of specific quantitation types must implement in order to register potentially new QuantitationTypes with caArray.
QuantitationTypeSearchCriteria - Class in gov.nih.nci.caarray.domain.search
Simple bean to hold search criteria for a quantitation types.
QuantitationTypeSearchCriteria() - Constructor for class gov.nih.nci.caarray.domain.search.QuantitationTypeSearchCriteria
 
query(CQLQuery) - Method in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
query(CQLQuery) - Method in interface gov.nih.nci.cagrid.caarray.common.CaArraySvcI
The standard caGrid Data Service query method.
queryCaArrayService(CQLQuery) - Method in class gov.nih.nci.cagrid.caarray.stubs.cql.CaArrayCQLQueryProcessor
Call out to the remote EJB that actually processes the query.
queryResourceProperties(QueryResourceProperties_Element) - Method in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
queryResourceProperties(QueryResourceProperties_Element) - Method in interface gov.nih.nci.cagrid.caarray.common.CaArraySvcI
 

R

RawArrayData - Class in gov.nih.nci.caarray.domain.data
Represents the raw image quantitation extracted from an image.
RawArrayData() - Constructor for class gov.nih.nci.caarray.domain.data.RawArrayData
 
readCompressedContents() - Method in class gov.nih.nci.caarray.domain.MultiPartBlob
Returns an input stream to access the contents of this MultiPartBlob.
readFile(CaArrayFile) - Method in interface gov.nih.nci.caarray.services.file.FileRetrievalService
Returns the requested file's contents.
readFile(CaArrayFile) - Method in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
readFile(CaArrayFile) - Method in interface gov.nih.nci.cagrid.caarray.common.CaArraySvcI
 
readFile(CaArrayFile) - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcImpl
Returns the bytes of the requested file's contents.
readFile(gov.nih.nci.cagrid.caarray.stubs.ReadFileRequest) - Method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcProviderImpl
 
readFileUsingGridTransfer(CaArrayFile) - Method in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
readFileUsingGridTransfer(CaArrayFile, GridTransferResultHandler) - Method in class gov.nih.nci.cagrid.caarray.client.CaArraySvcClient
 
readUncompressedContents() - Method in class gov.nih.nci.caarray.domain.MultiPartBlob
Returns an input stream to access the contents of this MultiPartBlob.
REF_SEQ - Static variable in class gov.nih.nci.caarray.domain.array.Gene
Name of the RefSeq database.
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.cagrid.caarray.service.globus.resource.CaArraySvcResourceBase
This checks the configuration file, and attempts to register to the IndexService if shouldPerformRegistration==true.
RegistrationRequest - Class in gov.nih.nci.caarray.domain.register
 
RegistrationRequest() - Constructor for class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
RELATED_BATCH_SIZE - Static variable in class gov.nih.nci.caarray.domain.array.AbstractProbeAnnotation
Batch size for all associations for probe annotation subclasses.
relatedProtectables() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
relatedProtectables() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
relatedProtectables() - Method in class gov.nih.nci.caarray.domain.sample.Extract
relatedProtectables() - Method in class gov.nih.nci.caarray.domain.sample.LabeledExtract
removeArrayData(AbstractArrayData) - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Remove an array data from this hybridization.
removeChild(CaArrayFile) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
Removes a child CaArrayFile.
removeGroupProfile(CollaboratorGroup) - Method in class gov.nih.nci.caarray.domain.project.Project
remove the access profile for given collaborator group from this project.
replace(Object, Object, Object) - Method in class gov.nih.nci.caarray.util.URIUserType
RESOURCE_KEY - Static variable in interface gov.nih.nci.cagrid.caarray.common.CaArraySvcConstantsBase
 
RESOURCE_KEY - Static variable in interface gov.nih.nci.cagrid.caarray.service.globus.resource.ResourceConstants
 
RESOURCE_PROPERTY_SET - Static variable in interface gov.nih.nci.cagrid.caarray.common.CaArraySvcConstantsBase
 
RESOURCE_PROPERTY_SET - Static variable in interface gov.nih.nci.cagrid.caarray.service.globus.resource.ResourceConstants
 
ResourceBasedEnum - Interface in gov.nih.nci.caarray.domain
Interface to be implemented by Enums which have a field holding a resource key that represents the UI label for that enum.
ResourceConfiguration - Class in gov.nih.nci.cagrid.caarray.service.globus.resource
DO NOT EDIT: This class is autogenerated! This class is used by the resource to get configuration information about the resource.
ResourceConfiguration() - Constructor for class gov.nih.nci.cagrid.caarray.service.globus.resource.ResourceConfiguration
 
ResourceConstants - Interface in gov.nih.nci.cagrid.caarray.service.globus.resource
 
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

Sample - Class in gov.nih.nci.caarray.domain.sample
 
Sample() - Constructor for class gov.nih.nci.caarray.domain.sample.Sample
 
Sample.ByNameComparator - Class in gov.nih.nci.caarray.domain.sample
Comparator for samples by name.
Sample.ByNameComparator() - Constructor for class gov.nih.nci.caarray.domain.sample.Sample.ByNameComparator
 
SampleJoinableSortCriterion - Enum in gov.nih.nci.caarray.domain.search
Enum of possible sort criterions for samples.
SAMPLES_FILTER - Static variable in class gov.nih.nci.caarray.domain.project.Experiment
 
SampleSecurityLevel - Enum in gov.nih.nci.caarray.domain.permissions
Enum of access types for sample-level security.
SampleSortCriterion - Enum in gov.nih.nci.caarray.domain.search
Enum of possible sort criterions for samples.
search(T) - Method in interface gov.nih.nci.caarray.services.search.CaArraySearchService
Performs a query-by-example search based on the entity passed.
search(T, boolean, boolean) - Method in interface gov.nih.nci.caarray.services.search.CaArraySearchService
Performs a query-by-example search based on the entity passed.
search(CQLQuery) - Method in interface gov.nih.nci.caarray.services.search.CaArraySearchService
Searches for entities based on the given CQL query.
SearchCategory - Enum in gov.nih.nci.caarray.domain.search
 
SearchSampleCategory - Enum in gov.nih.nci.caarray.domain.search
 
SearchSourceCategory - Enum in gov.nih.nci.caarray.domain.search
 
SearchTypeSelection - Enum in gov.nih.nci.caarray.domain.search
 
SECURITY_FILTER_NAME - Static variable in class gov.nih.nci.caarray.domain.project.Experiment
Filter name used for instance level security filters.
SecurityLevel - Enum in gov.nih.nci.caarray.domain.permissions
For access profiles, what type of access is permitted.
sendEnqueueMessage() - Method in class gov.nih.nci.caarray.domain.project.DefaultJobMessageSenderImpl
Send a message to all subscribers that a new job has been placed in the queue.
sendEnqueueMessage() - Method in interface gov.nih.nci.caarray.domain.project.JobMessageSender
Send a message to all subscribers that a new job has been placed in the queue.
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.domain.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.
SerializationFactory - Class in gov.nih.nci.cagrid.caarray.util
Pass through to the grid serialization factory, but with the correct API to actually work.
SerializationFactory(Class, QName) - Constructor for class gov.nih.nci.cagrid.caarray.util.SerializationFactory
 
serialize(Serializable) - Static method in class gov.nih.nci.caarray.util.CaArrayUtils
Serializes the given object (zipped) to a byte array.
serialize(QName, Attributes, Object, SerializationContext) - Method in class gov.nih.nci.cagrid.caarray.util.CaArraySerializer
 
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.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
SERVICE_NS - Static variable in interface gov.nih.nci.cagrid.caarray.common.CaArraySvcConstantsBase
 
SERVICE_NS - Static variable in interface gov.nih.nci.cagrid.caarray.service.globus.resource.ResourceConstants
 
ServiceConfiguration - Class in gov.nih.nci.cagrid.caarray.service
DO NOT EDIT: This class is autogenerated! This class holds all service properties which were defined for the service to have access to.
ServiceConfiguration() - Constructor for class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
SERVICEMETADATA - Static variable in interface gov.nih.nci.cagrid.caarray.common.CaArraySvcConstantsBase
 
SERVICEMETADATA_Value_RP - Static variable in interface gov.nih.nci.cagrid.caarray.service.globus.resource.ResourceConstants
 
ServiceType - Enum in gov.nih.nci.caarray.domain.project
An enumeration of different lab service types that can be requested for an Experiment.
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.domain.vocabulary.Category
 
setAccession(String) - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
Sets the accession.
setAccessionNumber(String) - Method in class gov.nih.nci.caarray.domain.array.Accession
Deprecated. should only be used by castor and hibernate.
setAdditionalOrganismNameCollection(Set<AdditionalOrganismName>) - Method in class edu.georgetown.pir.Organism
 
setAddress(Address) - Method in class gov.nih.nci.caarray.domain.contact.AbstractContact
Sets the address.
setAddress1(String) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setAddress2(String) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setAlleleA(String) - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
setAlleleB(String) - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
setAmountOfMaterial(float) - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
 
setAmountOfMaterialUnit(Term) - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
 
setAnnotation(AbstractProbeAnnotation) - Method in class gov.nih.nci.caarray.domain.array.AbstractProbe
 
setAnnotationCriterions(Set<AnnotationCriterion>) - Method in class gov.nih.nci.caarray.domain.search.BiomaterialSearchCriteria
 
setAnnotationCriterions(Set<AnnotationCriterion>) - Method in class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
setAnnotationFile(CaArrayFile) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
 
setArray(Array) - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Sets the array.
setArrayData(AbstractArrayData) - Method in class gov.nih.nci.caarray.domain.data.DataSet
 
setArrayDataTypes(Set<ArrayDataType>) - Method in class gov.nih.nci.caarray.domain.data.QuantitationType
 
setArrayDataTypes(Set<ArrayDataType>) - Method in class gov.nih.nci.caarray.domain.search.QuantitationTypeSearchCriteria
 
setArrayDesigns(Set<ArrayDesign>) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Sets the arrayDesigns.
setArrayGroup(ArrayGroup) - Method in class gov.nih.nci.caarray.domain.array.Array
 
setArrayProvider(Organization) - Method in class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
setAssayType(AssayType) - Method in class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
setAssayTypes(SortedSet<AssayType>) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
 
setAssayTypes(SortedSet<AssayType>) - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
setAuthors(String) - Method in class gov.nih.nci.caarray.domain.publication.Publication
Sets the authors.
setBatch(String) - Method in class gov.nih.nci.caarray.domain.array.Array
Sets the batch.
setBigid(String) - Method in class gov.nih.nci.cabio.domain.ArrayReporter
 
setBioMaterial(AbstractBioMaterial) - Method in class gov.nih.nci.caarray.domain.sample.AbstractCharacteristic
 
setBiomaterialClasses(Set<Class<? extends AbstractBioMaterial>>) - Method in class gov.nih.nci.caarray.domain.search.BiomaterialSearchCriteria
 
setBiomaterials(Set<AbstractBioMaterial>) - Method in class gov.nih.nci.caarray.domain.search.HybridizationSearchCriteria
 
setBlockColumn(short) - Method in class gov.nih.nci.caarray.domain.array.Feature
 
setBlockRow(short) - Method in class gov.nih.nci.caarray.domain.array.Feature
 
setCaBigId(String) - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayObject
 
setCategories(Set<FileCategory>) - Method in class gov.nih.nci.caarray.domain.search.FileSearchCriteria
 
setCategory(FileCategory) - Method in class gov.nih.nci.caarray.domain.file.FileType
 
setCategory(Category) - Method in class gov.nih.nci.caarray.domain.sample.AbstractCharacteristic
Set the category.
setCategory(Category) - Method in class gov.nih.nci.caarray.domain.search.AnnotationCriterion
 
setCategory(Category) - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
Sets the categories of this term to be the singleton set with the given category.
setCellType(Term) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
setChromosome(String, long, long) - Method in class gov.nih.nci.caarray.domain.array.ExpressionProbeAnnotation
 
setChromosome(Integer) - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
setChromosomeEndPosition(Long) - Method in class gov.nih.nci.caarray.domain.array.ExpressionProbeAnnotation
 
setChromosomeName(String) - Method in class gov.nih.nci.caarray.domain.array.ExpressionProbeAnnotation
 
setChromosomeStartPosition(Long) - Method in class gov.nih.nci.caarray.domain.array.ExpressionProbeAnnotation
 
setCity(String) - Method in class gov.nih.nci.caarray.domain.contact.Address
Sets the city.
setCity(String) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setCode(String) - Method in class gov.nih.nci.caarray.domain.country.Country
 
setCode(String) - Method in class gov.nih.nci.caarray.domain.state.State
 
setColumn(short) - Method in class gov.nih.nci.caarray.domain.array.Feature
 
setComment(String) - Method in class edu.georgetown.pir.AdditionalOrganismName
 
setCommonName(String) - Method in class edu.georgetown.pir.Organism
 
setCompressedSize(long) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
This method should generally not be called directly, as file size is calculated when data is written to the file.
setCompressedSize(long) - Method in class gov.nih.nci.caarray.domain.MultiPartBlob
This method should generally not be called directly, as file size is calculated when data is written to the file.
setContact(Person) - Method in class gov.nih.nci.caarray.domain.project.ExperimentContact
Sets the contact.
setContact(String) - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Sets the contact.
setContents(Blob) - Method in class gov.nih.nci.caarray.domain.BlobHolder
 
setControlType(Term) - Method in class gov.nih.nci.caarray.domain.array.PhysicalProbe
 
setCoordinateUnits(Term) - Method in class gov.nih.nci.caarray.domain.array.Feature
 
setCountry(Country) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setCreationTimestamp(Date) - Method in class gov.nih.nci.caarray.domain.MultiPartBlob
 
setDatabaseName(String) - Method in class gov.nih.nci.caarray.domain.array.Accession
Deprecated. should only be used by castor and hibernate.
setDataFile(CaArrayFile) - Method in class gov.nih.nci.caarray.domain.data.AbstractArrayData
Sets the dataFile.
setDataHandle(URI) - Method in class gov.nih.nci.caarray.domain.data.AbstractDataColumn
 
setDataHandle(URI) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
setDataMatrix(boolean) - Method in class gov.nih.nci.caarray.domain.file.FileType
 
setDataService_auditorsConfigFile(String) - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
setDataService_auditorsConfigFile(String) - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
setDataService_classMappingsFilename(String) - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
setDataService_classMappingsFilename(String) - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
setDataService_cqlValidatorClass(String) - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
setDataService_cqlValidatorClass(String) - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
setDataService_domainModelValidatorClass(String) - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
setDataService_domainModelValidatorClass(String) - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
setDataService_validateCqlFlag(String) - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
setDataService_validateCqlFlag(String) - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
setDataService_validateDomainModelFlag(String) - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
setDataService_validateDomainModelFlag(String) - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
setDataSet(DataSet) - Method in class gov.nih.nci.caarray.domain.data.AbstractArrayData
 
setDataSet(DataSet) - Method in class gov.nih.nci.caarray.domain.data.HybridizationData
 
setDataType(DataType) - Method in class gov.nih.nci.caarray.domain.data.QuantitationType
Set the data type of this quantitation type as a DataType constant.
setDate(Date) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Sets the date of this Experiment.
setDbSNPId(String) - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
setDbSNPVersion(Integer) - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
setDefaultValue(AbstractParameterValue) - Method in class gov.nih.nci.caarray.domain.protocol.Parameter
Sets the defaultValue.
setDescription(String) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
 
setDescription(String) - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
 
setDescription(String) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Sets the description.
setDescription(String) - Method in class gov.nih.nci.caarray.domain.project.Factor
 
setDescription(String) - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Sets the description.
setDescription(String) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Sets the description.
setDescription(String) - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
Sets the description.
setDesign(ArrayDesign) - Method in class gov.nih.nci.caarray.domain.array.Array
Sets the design.
setDesignDescription(String) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Set the description of the experiment design.
setDesignDetails(ArrayDesignDetails) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
 
setDesignElement(AbstractDesignElement) - Method in class gov.nih.nci.caarray.domain.data.DesignElementReference
 
setDesignElementList(DesignElementList) - Method in class gov.nih.nci.caarray.domain.data.DataSet
 
setDesignElementList(DesignElementList) - Method in class gov.nih.nci.caarray.domain.data.DesignElementReference
 
setDesignElementReferences(List<DesignElementReference>) - Method in class gov.nih.nci.caarray.domain.data.DesignElementList
 
setDesignElements(List<AbstractDesignElement>) - Method in class gov.nih.nci.caarray.domain.data.DesignElementList
 
setDesignElementType(String) - Method in class gov.nih.nci.caarray.domain.data.DesignElementList
 
setDesignElementTypeEnum(DesignElementType) - Method in class gov.nih.nci.caarray.domain.data.DesignElementList
 
setDesignFileSet(CaArrayFileSet) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Set the design files of this array design to the ones contained in the given set.
setDiseaseState(Term) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
setDoi(String) - Method in class gov.nih.nci.caarray.domain.publication.Publication
Sets the doi.
setDomainModel(DomainModel) - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceBase
 
setDomainModelFile(String) - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceConfiguration
 
setDomainModelFile(String) - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.ResourceConfiguration
 
setEditor(String) - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
setEmail(String) - Method in class gov.nih.nci.caarray.domain.contact.AbstractContact
Sets the email.
setEmail(String) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setEnsemblgeneID(String) - Method in class gov.nih.nci.caarray.domain.array.Gene
 
setEntityId(Long) - Method in class gov.nih.nci.caarray.domain.audit.AuditLogSecurity
 
setEntityName(String) - Method in class gov.nih.nci.caarray.domain.audit.AuditLogSecurity
 
setEntrezgeneID(String) - Method in class gov.nih.nci.caarray.domain.array.Gene
 
setEtcDirectoryPath(String) - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
setEthnicityStrain(String) - Method in class edu.georgetown.pir.Organism
 
setExample(T) - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
 
setExcludeNulls(boolean) - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
 
setExcludeProperties(Collection<String>) - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
 
setExcludeZeroes(boolean) - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
 
setExonArrayReporter(ExonArrayReporter) - Method in class gov.nih.nci.caarray.domain.array.ExonProbeAnnotation
 
setExperiment(Experiment) - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
 
setExperiment(Experiment) - Method in class gov.nih.nci.caarray.domain.project.ExperimentContact
 
setExperiment(Experiment) - Method in class gov.nih.nci.caarray.domain.project.Factor
 
setExperiment(Experiment) - Method in class gov.nih.nci.caarray.domain.project.Project
Sets the experiment.
setExperiment(Experiment) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
setExperiment(Experiment) - Method in class gov.nih.nci.caarray.domain.search.BiomaterialSearchCriteria
 
setExperiment(Experiment) - Method in class gov.nih.nci.caarray.domain.search.FileSearchCriteria
 
setExperiment(Experiment) - Method in class gov.nih.nci.caarray.domain.search.HybridizationSearchCriteria
 
setExperimentDesignTypes(Set<Term>) - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
setExperimentNodes(Set<AbstractExperimentDesignNode>) - Method in class gov.nih.nci.caarray.domain.search.FileSearchCriteria
 
setExpressionArrayReporter(ExpressionArrayReporter) - Method in class gov.nih.nci.caarray.domain.array.ExpressionProbeAnnotation
 
setExtension(String) - Method in class gov.nih.nci.caarray.domain.search.FileSearchCriteria
 
setExtensions(Set<String>) - Method in class gov.nih.nci.caarray.domain.file.FileType
 
setExternalId(String) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
setExternalIds(Set<String>) - Method in class gov.nih.nci.caarray.domain.search.BiomaterialSearchCriteria
 
setFactor(Factor) - Method in class gov.nih.nci.caarray.domain.project.AbstractFactorValue
Sets the factor.
setFax(String) - Method in class gov.nih.nci.caarray.domain.contact.AbstractContact
Sets the fax.
setFax(String) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setFeatureNumber(Integer) - Method in class gov.nih.nci.caarray.domain.array.Feature
 
setFileCategories(Set<FileCategory>) - Method in class gov.nih.nci.caarray.domain.search.QuantitationTypeSearchCriteria
 
setFiles(SortedSet<CaArrayFile>) - Method in class gov.nih.nci.caarray.domain.project.Project
Sets the files.
setFileStatus(FileStatus) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
setFileType(FileType) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
setFileTypes(Set<FileType>) - Method in class gov.nih.nci.caarray.domain.search.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.domain.contact.Person
Sets the firstName.
setFirstName(String) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setFlank(String) - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
setFullName(String) - Method in class gov.nih.nci.caarray.domain.array.Gene
 
setGenbankAccession(String) - Method in class gov.nih.nci.caarray.domain.array.Gene
 
setGenbankAccessionVersion(String) - Method in class gov.nih.nci.caarray.domain.array.Gene
 
setGene(Gene) - Method in class gov.nih.nci.caarray.domain.array.ExonProbeAnnotation
 
setGene(Gene) - Method in class gov.nih.nci.caarray.domain.array.ExpressionProbeAnnotation
 
setGeoAccession(String) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
 
setGroup(CollaboratorGroup) - Method in class gov.nih.nci.caarray.domain.permissions.AccessProfile
 
setHardware(String) - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Sets the hardware.
setHibernateHelper(HibernateHelper) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
 
setHybridization(Hybridization) - Method in class gov.nih.nci.caarray.domain.data.HybridizationData
 
setHybridization(Hybridization) - Method in class gov.nih.nci.caarray.domain.data.Image
 
setHybridization(Hybridization) - Method in class gov.nih.nci.caarray.domain.project.AbstractFactorValue
 
setHybridization(Hybridization) - Method in class gov.nih.nci.caarray.domain.search.QuantitationTypeSearchCriteria
 
setHybridizationData(HybridizationData) - Method in class gov.nih.nci.caarray.domain.data.AbstractDataColumn
 
setHybridizationData(Set<HybridizationData>) - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
 
setId(Long) - Method in class edu.georgetown.pir.AdditionalOrganismName
 
setId(Long) - Method in class edu.georgetown.pir.Organism
 
setId(Long) - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayObject
Deprecated. should only be used by castor and hibernate
setId(Long) - Method in class gov.nih.nci.caarray.domain.audit.AuditLogSecurity
Deprecated. should only be used by castor and hibernate
setId(Long) - Method in class gov.nih.nci.caarray.domain.BlobHolder
Deprecated. should only be used by castor and hibernate
setId(Long) - Method in class gov.nih.nci.caarray.domain.data.DataRetrievalRequest
Deprecated. only exists to fulfill caDSR loading requirement
setId(Long) - Method in class gov.nih.nci.caarray.domain.MultiPartBlob
Deprecated. should only be used by castor and hibernate
setId(Long) - Method in class gov.nih.nci.caarray.domain.permissions.AccessProfile
Deprecated. should only be used by castor, hibernate and struts
setId(Long) - Method in class gov.nih.nci.caarray.domain.permissions.CollaboratorGroup
Deprecated. should only be used by castor, hibernate and struts
setId(Long) - Method in class gov.nih.nci.cabio.domain.ArrayReporter
 
setImageFile(CaArrayFile) - Method in class gov.nih.nci.caarray.domain.data.Image
Sets the imageFile.
setImportDescription(String) - Method in class gov.nih.nci.caarray.domain.project.Project
 
setIndex(int) - Method in class gov.nih.nci.caarray.domain.data.DesignElementReference
 
setIso3(String) - Method in class gov.nih.nci.caarray.domain.country.Country
 
setIssue(String) - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
setJobId(UUID) - Method in interface gov.nih.nci.caarray.domain.project.ExecutableJob
Set an uuid for the job.
setLabel(Term) - Method in class gov.nih.nci.caarray.domain.sample.LabeledExtract
Sets the label.
setLabel(String) - Method in class gov.nih.nci.caarray.util.LabelValue
set label.
setLabeledExtract(LabeledExtract) - Method in class gov.nih.nci.caarray.domain.data.HybridizationData
 
setLastDataModificationDate(Date) - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
setLastModifiedDataTime(Date) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
setLastName(String) - Method in class gov.nih.nci.caarray.domain.contact.Person
Sets the lastName.
setLastName(String) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setLastUpdated(Date) - Method in class gov.nih.nci.caarray.domain.project.Project
Sets the last updated date.
setLocked(boolean) - Method in class gov.nih.nci.caarray.domain.project.Project
Sets the workflow status of this project.
setLoginName(String) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setLsid(LSID) - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
Set the LSID for this entity.
setLsid(String) - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
Set the LSID for this entity.
setLsidForEntity(String) - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayEntity
Sets the LSID components for this entity.
setManufacturer(Organization) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Sets the manufacturer for this Experiment.
setMatchMode(MatchMode) - Method in class gov.nih.nci.caarray.domain.search.ExampleSearchCriteria
 
setMaterialType(Term) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Sets the materialType.
setMessage(String) - Method in class gov.nih.nci.caarray.domain.search.AuditLogSearchCriteria
 
setMiddleInitial(String) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setMiddleInitials(String) - Method in class gov.nih.nci.caarray.domain.contact.Person
Sets the middleInitials.
setName(String) - Method in class gov.nih.nci.caarray.domain.array.AbstractProbe
 
setName(String) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Sets the name.
setName(String) - Method in class gov.nih.nci.caarray.domain.array.ArrayGroup
 
setName(String) - Method in class gov.nih.nci.caarray.domain.array.ProbeGroup
 
setName(String) - Method in class gov.nih.nci.caarray.domain.contact.Organization
Sets the name.
setName(String) - Method in class gov.nih.nci.caarray.domain.country.Country
 
setName(String) - Method in class gov.nih.nci.caarray.domain.data.AbstractArrayData
Sets the name.
setName(String) - Method in class gov.nih.nci.caarray.domain.data.ArrayDataType
 
setName(String) - Method in class gov.nih.nci.caarray.domain.data.Image
Sets the name.
setName(String) - Method in class gov.nih.nci.caarray.domain.data.QuantitationType
 
setName(String) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
Sets the name.
setName(String) - Method in class gov.nih.nci.caarray.domain.file.FileType
 
setName(String) - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
Sets the name.
setName(String) - Method in class gov.nih.nci.caarray.domain.project.AssayType
Sets the name.
setName(String) - Method in class gov.nih.nci.caarray.domain.project.Factor
Sets the name.
setName(String) - Method in class gov.nih.nci.caarray.domain.protocol.Parameter
Sets the name.
setName(String) - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Sets the name.
setName(String) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
Sets the name.
setName(String) - Method in class gov.nih.nci.caarray.domain.state.State
 
setName(String) - Method in class gov.nih.nci.caarray.domain.vocabulary.Category
Sets the name.
setName(String) - Method in class gov.nih.nci.caarray.domain.vocabulary.TermSource
Sets the name.
setName(String) - Method in class gov.nih.nci.cabio.domain.ArrayReporter
 
setNames(Set<String>) - Method in class gov.nih.nci.caarray.domain.search.BiomaterialSearchCriteria
 
setNames(Set<String>) - Method in class gov.nih.nci.caarray.domain.search.HybridizationSearchCriteria
 
setNcbiTaxonomyId(Long) - Method in class edu.georgetown.pir.Organism
 
setNotes(String) - Method in class gov.nih.nci.caarray.domain.protocol.ProtocolApplication
 
setNumberOfFeatures(Integer) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Sets the numberOfFeatures.
setNumcode(String) - Method in class gov.nih.nci.caarray.domain.country.Country
 
setOrganism(Organism) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
 
setOrganism(Organism) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Sets the organism for this Experiment.
setOrganism(Organism) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
setOrganism(Organism) - Method in class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
setOrganismCollection(Set<Organism>) - Method in class edu.georgetown.pir.AdditionalOrganismName
 
setOrganization(String) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setOwner(User) - Method in class gov.nih.nci.caarray.domain.permissions.CollaboratorGroup
 
setPages(String) - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
setParameter(Parameter) - Method in class gov.nih.nci.caarray.domain.protocol.AbstractParameterValue
Sets the parameter.
setParsed(boolean) - Method in class gov.nih.nci.caarray.domain.file.FileType
 
setPartialSize(long) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
setPerformRegistration(boolean) - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceConfiguration
 
setPerformRegistration(boolean) - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.ResourceConfiguration
 
setPerson(Person) - Method in class gov.nih.nci.caarray.domain.project.ExperimentContact
Sets the person.
setPhastConservation(String) - Method in class gov.nih.nci.cabio.domain.SNPArrayReporter
 
setPhone(String) - Method in class gov.nih.nci.caarray.domain.contact.AbstractContact
Sets the phone.
setPhone(String) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setPhysicalPosition(Long) - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
setPolicy(Node) - Method in class gov.nih.nci.cagrid.caarray.service.globus.CaArraySvcAuthorization
 
setPolymerType(Term) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Sets the polymerType.
setPrincipalInvestigators(Set<Person>) - Method in class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
setPrintableName(String) - Method in class gov.nih.nci.caarray.domain.country.Country
 
setPrinting(ProtocolApplication) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Sets the printing.
setPrivilegeId(Long) - Method in class gov.nih.nci.caarray.domain.audit.AuditLogSecurity
 
setProbeCount(Long) - Method in class gov.nih.nci.cabio.domain.ExonArrayReporter
 
setProbeGroup(ProbeGroup) - Method in class gov.nih.nci.caarray.domain.array.PhysicalProbe
 
setProbeSelectionRegionId(Long) - Method in class gov.nih.nci.cabio.domain.ExonArrayReporter
 
setProcessor(DefaultProcessor) - Method in class gov.nih.nci.caarray.util.CaArrayAuditLogInterceptor
 
setProduction(ProtocolApplication) - Method in class gov.nih.nci.caarray.domain.array.Array
Sets the production.
setProject(Project) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
setProject(Project) - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
setProjectForGroupProfile(Project) - Method in class gov.nih.nci.caarray.domain.permissions.AccessProfile
 
setProjectForPublicProfile(Project) - Method in class gov.nih.nci.caarray.domain.permissions.AccessProfile
 
setProtocol(Protocol) - Method in class gov.nih.nci.caarray.domain.protocol.Parameter
 
setProtocol(Protocol) - Method in class gov.nih.nci.caarray.domain.protocol.ProtocolApplication
Sets the protocol.
setProtocolApplication(ProtocolApplication) - Method in class gov.nih.nci.caarray.domain.protocol.AbstractParameterValue
 
setProvider(Organization) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Sets the provider.
setProvider(boolean) - Method in class gov.nih.nci.caarray.domain.contact.Organization
Sets whether this organization represents an array provider.
setProvince(String) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setPublication(String) - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
setPublicIdentifier(String) - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
setPublicIdentifier(String) - Method in class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
setPublicReleaseDate(Date) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Sets the publicReleaseDate.
setPublisher(String) - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
setPubMedId(String) - Method in class gov.nih.nci.caarray.domain.publication.Publication
Sets the pubMedId.
setQualityControlDescription(String) - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
setQualityControlTypes(Set<Term>) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Sets the qualityControlTypes.
setQuantitationType(QuantitationType) - Method in class gov.nih.nci.caarray.domain.data.AbstractDataColumn
 
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.
setQueryProcessorClass(String) - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
setQueryProcessorClass(String) - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
setRawArrayData(RawArrayData) - Method in class gov.nih.nci.caarray.domain.data.Image
 
setRecord(AuditLogRecord) - Method in class gov.nih.nci.caarray.domain.audit.AuditLogSecurity
 
setRefseqAccession(String) - Method in class gov.nih.nci.caarray.domain.array.Gene
 
setRegistrationTemplateFile(String) - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceConfiguration
 
setRegistrationTemplateFile(String) - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.ResourceConfiguration
 
setReplicateDescription(String) - Method in class gov.nih.nci.caarray.domain.project.Experiment
 
setReplicateTypes(Set<Term>) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Sets the replicateTypes.
setRole(String) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setRoles(Set<Term>) - Method in class gov.nih.nci.caarray.domain.project.ExperimentContact
Sets the roles.
setRow(short) - Method in class gov.nih.nci.caarray.domain.array.Feature
 
setSampleSecurityLevels(Map<Sample, SampleSecurityLevel>) - Method in class gov.nih.nci.caarray.domain.permissions.AccessProfile
 
setScientificName(String) - Method in class edu.georgetown.pir.Organism
 
setSecurityDescriptor(ResourceSecurityDescriptor) - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceBase
Sets the security descriptor for this resource.
setSecurityLevel(SecurityLevel) - Method in class gov.nih.nci.caarray.domain.permissions.AccessProfile
 
setSequenceSource(String) - Method in class gov.nih.nci.cabio.domain.ExpressionArrayReporter
 
setSequenceType(String) - Method in class gov.nih.nci.cabio.domain.ExpressionArrayReporter
 
setSerialNumber(String) - Method in class gov.nih.nci.caarray.domain.array.Array
Sets the serialNumber.
setServerConfigLocation(String) - Method in class gov.nih.nci.cagrid.caarray.service.CaArraySvcConfiguration
 
setServerConfigLocation(String) - Method in class gov.nih.nci.cagrid.caarray.service.ServiceConfiguration
 
setServiceMetadata(gov.nih.nci.cagrid.metadata.ServiceMetadata) - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceBase
 
setServiceMetadataFile(String) - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceConfiguration
 
setServiceMetadataFile(String) - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.ResourceConfiguration
 
setSnpArrayReporter(SNPArrayReporter) - Method in class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
setSoftware(String) - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Sets the software.
setSource(String) - Method in class edu.georgetown.pir.AdditionalOrganismName
 
setSource(TermSource) - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
 
setSource(TermSource) - Method in class gov.nih.nci.caarray.domain.vocabulary.Category
Set the termSource.
setSource(TermSource) - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
Sets the source.
setStart(Long) - Method in class gov.nih.nci.caarray.domain.array.ExonProbeAnnotation
 
setState(String) - Method in class gov.nih.nci.caarray.domain.contact.Address
Sets the state.
setState(State) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setStatus(Term) - Method in class gov.nih.nci.caarray.domain.publication.Publication
Sets the status.
setStop(Long) - Method in class gov.nih.nci.caarray.domain.array.ExonProbeAnnotation
 
setStrand(String) - Method in class gov.nih.nci.caarray.domain.array.ExonProbeAnnotation
 
setStrand(String) - Method in class gov.nih.nci.cabio.domain.ExonArrayReporter
 
setStreet1(String) - Method in class gov.nih.nci.caarray.domain.contact.Address
Sets the street1.
setStreet2(String) - Method in class gov.nih.nci.caarray.domain.contact.Address
Sets the street2.
setSubstrateType(Term) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Sets the substrateType.
setSurfaceType(Term) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Sets the surfaceType.
setSymbol(String) - Method in class gov.nih.nci.caarray.domain.array.Gene
 
setTargetDescription(String) - Method in class gov.nih.nci.cabio.domain.ExpressionArrayReporter
 
setTargetId(String) - Method in class gov.nih.nci.cabio.domain.ExpressionArrayReporter
 
setTaxonomyRank(String) - Method in class edu.georgetown.pir.Organism
 
setTechnologyType(Term) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Sets the technologyType.
setter() - Method in class gov.nih.nci.caarray.util.PropertyAccessor
 
setTerm(Term) - Method in class gov.nih.nci.caarray.domain.project.TermBasedFactorValue
Sets the term.
setTerm(Term) - Method in class gov.nih.nci.caarray.domain.protocol.TermBasedParameterValue
Sets the term.
setTerm(Term) - Method in class gov.nih.nci.caarray.domain.sample.TermBasedCharacteristic
Sets the term.
setTerm(Term) - Method in interface gov.nih.nci.caarray.domain.TermBasedValue
 
setTermSource(TermSource) - Method in class edu.georgetown.pir.Organism
Set the termSource.
setThcAccession(String) - Method in class gov.nih.nci.caarray.domain.array.Gene
 
setTissueSite(Term) - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
 
setTitle(String) - Method in class gov.nih.nci.caarray.domain.project.Experiment
Sets the title.
setTitle(String) - Method in class gov.nih.nci.caarray.domain.publication.Publication
Sets the title.
setTitle(String) - Method in class gov.nih.nci.caarray.domain.search.ExperimentSearchCriteria
 
setType(ArrayDataType) - Method in class gov.nih.nci.caarray.domain.data.AbstractArrayData
 
setType(String) - Method in class gov.nih.nci.caarray.domain.data.QuantitationType
 
setType(String) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
setType(Term) - Method in class gov.nih.nci.caarray.domain.project.Factor
Sets the type.
setType(Term) - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Sets the type.
setType(Term) - Method in class gov.nih.nci.caarray.domain.publication.Publication
Sets the type.
setTypeClass(Class<?>) - Method in class gov.nih.nci.caarray.domain.data.QuantitationType
 
setTypes(Set<FileType>) - Method in class gov.nih.nci.caarray.domain.search.FileSearchCriteria
 
setUncompressedSize(long) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
This method should generally not be called directly, as file size is calculated when data is written to the file.
setUncompressedSize(long) - Method in class gov.nih.nci.caarray.domain.MultiPartBlob
This method should generally not be called directly, as file size is calculated when data is written to the file.
setUnigeneclusterID(String) - Method in class gov.nih.nci.caarray.domain.array.Gene
 
setUniprotId(String) - Method in class gov.nih.nci.caarray.domain.array.ExonProbeAnnotation
 
setUnit(Term) - Method in class gov.nih.nci.caarray.domain.project.AbstractFactorValue
Sets the unit.
setUnit(Term) - Method in class gov.nih.nci.caarray.domain.protocol.AbstractParameterValue
Sets the unit.
setUnit(Term) - Method in class gov.nih.nci.caarray.domain.sample.AbstractCharacteristic
Sets the unit.
setUnit(Term) - Method in interface gov.nih.nci.caarray.domain.UnitableValue
Sets the unit.
setUp() - Method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
setUri(String) - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
setUrl(String) - Method in class gov.nih.nci.caarray.domain.contact.AbstractContact
Sets the url.
setUrl(String) - Method in class gov.nih.nci.caarray.domain.protocol.Protocol
Sets the url.
setUrl(String) - Method in class gov.nih.nci.caarray.domain.vocabulary.Category
 
setUrl(String) - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
Sets the url.
setUrl(String) - Method in class gov.nih.nci.caarray.domain.vocabulary.TermSource
Sets the url.
setUser(String) - Method in interface gov.nih.nci.caarray.util.UsernameHolder
 
setUser(String) - Method in class gov.nih.nci.caarray.util.UsernameHolderImpl
setUsername(String) - Method in class gov.nih.nci.caarray.domain.search.AuditLogSearchCriteria
 
setValidationResult(FileValidationResult) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
 
setValue(String) - Method in class edu.georgetown.pir.AdditionalOrganismName
 
setValue(Float) - Method in interface gov.nih.nci.caarray.domain.MeasurementValue
 
setValue(Float) - Method in class gov.nih.nci.caarray.domain.project.MeasurementFactorValue
 
setValue(String) - Method in class gov.nih.nci.caarray.domain.project.UserDefinedFactorValue
 
setValue(Float) - Method in class gov.nih.nci.caarray.domain.protocol.MeasurementParameterValue
 
setValue(String) - Method in class gov.nih.nci.caarray.domain.protocol.UserDefinedParameterValue
 
setValue(Float) - Method in class gov.nih.nci.caarray.domain.sample.MeasurementCharacteristic
 
setValue(String) - Method in class gov.nih.nci.caarray.domain.sample.UserDefinedCharacteristic
 
setValue(String) - Method in class gov.nih.nci.caarray.domain.search.AnnotationCriterion
 
setValue(String) - Method in interface gov.nih.nci.caarray.domain.UserDefinedValue
 
setValue(String) - Method in class gov.nih.nci.caarray.domain.vocabulary.Term
Sets the value.
setValue(String) - Method in class gov.nih.nci.caarray.util.LabelValue
set value.
setValues(boolean[]) - Method in class gov.nih.nci.caarray.domain.data.BooleanColumn
 
setValues(double[]) - Method in class gov.nih.nci.caarray.domain.data.DoubleColumn
 
setValues(float[]) - Method in class gov.nih.nci.caarray.domain.data.FloatColumn
 
setValues(int[]) - Method in class gov.nih.nci.caarray.domain.data.IntegerColumn
 
setValues(long[]) - Method in class gov.nih.nci.caarray.domain.data.LongColumn
 
setValues(short[]) - Method in class gov.nih.nci.caarray.domain.data.ShortColumn
 
setValues(String[]) - Method in class gov.nih.nci.caarray.domain.data.StringColumn
 
setValuesAsString(String) - Method in class gov.nih.nci.caarray.domain.data.AbstractDataColumn
Set values from a String representation.
setValuesAsString(String) - Method in class gov.nih.nci.caarray.domain.data.BooleanColumn
Set values from a String representation.
setValuesAsString(String) - Method in class gov.nih.nci.caarray.domain.data.DoubleColumn
Set values from a String representation.
setValuesAsString(String) - Method in class gov.nih.nci.caarray.domain.data.FloatColumn
Set values from a String representation.
setValuesAsString(String) - Method in class gov.nih.nci.caarray.domain.data.IntegerColumn
Set values from a String representation.
setValuesAsString(String) - Method in class gov.nih.nci.caarray.domain.data.LongColumn
Set values from a String representation.
setValuesAsString(String) - Method in class gov.nih.nci.caarray.domain.data.ShortColumn
Set values from a String representation.
setValuesAsString(String) - Method in class gov.nih.nci.caarray.domain.data.StringColumn
Sets the values of this column from a string, which must contain a comma-separated list of strings.
setValuesFromArray(Serializable) - Method in class gov.nih.nci.caarray.domain.data.AbstractDataColumn
Set the values of this column from a value array.
setValuesFromArray(Serializable) - Method in class gov.nih.nci.caarray.domain.data.BooleanColumn
Set the values of this column from a value array.
setValuesFromArray(Serializable) - Method in class gov.nih.nci.caarray.domain.data.DoubleColumn
Set the values of this column from a value array.
setValuesFromArray(Serializable) - Method in class gov.nih.nci.caarray.domain.data.FloatColumn
Set the values of this column from a value array.
setValuesFromArray(Serializable) - Method in class gov.nih.nci.caarray.domain.data.IntegerColumn
Set the values of this column from a value array.
setValuesFromArray(Serializable) - Method in class gov.nih.nci.caarray.domain.data.LongColumn
Set the values of this column from a value array.
setValuesFromArray(Serializable) - Method in class gov.nih.nci.caarray.domain.data.ShortColumn
Set the values of this column from a value array.
setValuesFromArray(Serializable) - Method in class gov.nih.nci.caarray.domain.data.StringColumn
Set the values of this column from a value array.
setVersion(String) - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
Sets the version.
setVersion(String) - Method in class gov.nih.nci.caarray.domain.data.ArrayDataType
 
setVersion(String) - Method in class gov.nih.nci.caarray.domain.vocabulary.TermSource
Sets the version.
setVolume(String) - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
setX_Coordinate(Double) - Method in class gov.nih.nci.caarray.domain.array.Feature
 
setY_Coordinate(Double) - Method in class gov.nih.nci.caarray.domain.array.Feature
 
setYear(String) - Method in class gov.nih.nci.caarray.domain.publication.Publication
 
setZip(String) - Method in class gov.nih.nci.caarray.domain.register.RegistrationRequest
 
setZipCode(String) - Method in class gov.nih.nci.caarray.domain.contact.Address
Sets the zipCode.
ShortColumn - Class in gov.nih.nci.caarray.domain.data
Contains a column of short values.
ShortColumn() - Constructor for class gov.nih.nci.caarray.domain.data.ShortColumn
 
shouldPerformRegistration() - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.CaArraySvcResourceConfiguration
 
shouldPerformRegistration() - Method in class gov.nih.nci.cagrid.caarray.service.globus.resource.ResourceConfiguration
 
SNPArrayReporter - Class in gov.nih.nci.cabio.domain
 
SNPArrayReporter() - Constructor for class gov.nih.nci.cabio.domain.SNPArrayReporter
 
SNPProbeAnnotation - Class in gov.nih.nci.caarray.domain.array
 
SNPProbeAnnotation() - Constructor for class gov.nih.nci.caarray.domain.array.SNPProbeAnnotation
 
Source - Class in gov.nih.nci.caarray.domain.sample
 
Source() - Constructor for class gov.nih.nci.caarray.domain.sample.Source
 
SourceJoinableSortCriterion - Enum in gov.nih.nci.caarray.domain.search
Enum of possible sort criterions for sources.
SourceSortCriterion - Enum in gov.nih.nci.caarray.domain.search
Enum of possible sort criterions for sources.
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.
State - Class in gov.nih.nci.caarray.domain.state
 
State() - Constructor for class gov.nih.nci.caarray.domain.state.State
 
StringColumn - Class in gov.nih.nci.caarray.domain.data
Contains a column of String values.
StringColumn() - Constructor for class gov.nih.nci.caarray.domain.data.StringColumn
 
StubCQLQueryProcessor - Class in gov.nih.nci.cagrid.caarray.stubs.cql
Deprecated. The stub CQL query processor is a placeholder to provide a starting point for implementation of CQL against a backend data source.
StubCQLQueryProcessor() - Constructor for class gov.nih.nci.cagrid.caarray.stubs.cql.StubCQLQueryProcessor
Deprecated.  
suite() - Static method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 

T

tableName(String) - Method in class gov.nih.nci.caarray.util.NamingStrategy
Term - Class in gov.nih.nci.caarray.domain.vocabulary
 
Term() - Constructor for class gov.nih.nci.caarray.domain.vocabulary.Term
 
TermBasedCharacteristic - Class in gov.nih.nci.caarray.domain.sample
 
TermBasedCharacteristic() - Constructor for class gov.nih.nci.caarray.domain.sample.TermBasedCharacteristic
Hibernate-only constructor.
TermBasedCharacteristic(Category, Term, Term) - Constructor for class gov.nih.nci.caarray.domain.sample.TermBasedCharacteristic
Create a new characteristic with given category, term and unit.
TermBasedFactorValue - Class in gov.nih.nci.caarray.domain.project
 
TermBasedFactorValue() - Constructor for class gov.nih.nci.caarray.domain.project.TermBasedFactorValue
Hibernate-only constructor.
TermBasedFactorValue(Term, Term) - Constructor for class gov.nih.nci.caarray.domain.project.TermBasedFactorValue
Create a new factor value with given term and unit.
TermBasedParameterValue - Class in gov.nih.nci.caarray.domain.protocol
A parameter value with a controlled vocabulary term value.
TermBasedParameterValue() - Constructor for class gov.nih.nci.caarray.domain.protocol.TermBasedParameterValue
Hibernate-only constructor.
TermBasedParameterValue(TermBasedParameterValue) - Constructor for class gov.nih.nci.caarray.domain.protocol.TermBasedParameterValue
Copy constructor.
TermBasedParameterValue(Term, Term) - Constructor for class gov.nih.nci.caarray.domain.protocol.TermBasedParameterValue
Create a new protocol value with given term and unit.
TermBasedValue - Interface in gov.nih.nci.caarray.domain
A UnitableValue with a controlled vocabulary term value.
TermSource - Class in gov.nih.nci.caarray.domain.vocabulary
 
TermSource() - Constructor for class gov.nih.nci.caarray.domain.vocabulary.TermSource
 
testDomainModel() - Method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
testFindAllAbstractBioMaterials() - Method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
testFindAllAddresses() - Method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
testFindAllArrayDesigns() - Method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
testFindAllCategorys() - Method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
testFindAllExperiments() - Method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
testFindAllFactors() - Method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
testFindAllFiles() - Method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
testFindAllHybridizations() - Method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
testFindAllOrganizations() - Method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
testFindAllProjects() - Method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
testFindAllRawArrayData() - Method in class gov.nih.nci.cagrid.caarray.client.CaArray2xGrid
 
THC - Static variable in class gov.nih.nci.caarray.domain.array.Gene
Name of the THC database.
toString() - Method in class gov.nih.nci.caarray.domain.AbstractCaArrayObject
toString() - Method in class gov.nih.nci.caarray.domain.array.ArrayDesign
toString() - Method in class gov.nih.nci.caarray.domain.contact.AbstractContact
toString() - Method in class gov.nih.nci.caarray.domain.contact.Address
toString() - Method in class gov.nih.nci.caarray.domain.contact.Organization
toString() - Method in class gov.nih.nci.caarray.domain.contact.Person
toString() - Method in class gov.nih.nci.caarray.domain.data.AbstractArrayData
toString() - Method in class gov.nih.nci.caarray.domain.data.Image
toString() - Method in class gov.nih.nci.caarray.domain.data.QuantitationType
toString() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFile
toString() - Method in class gov.nih.nci.caarray.domain.file.CaArrayFileSet
toString() - Method in class gov.nih.nci.caarray.domain.file.FileType
toString() - Method in class gov.nih.nci.caarray.domain.hybridization.Hybridization
toString() - Method in class gov.nih.nci.caarray.domain.LSID
Returns the full formatted LSID string.
toString() - Method in class gov.nih.nci.caarray.domain.project.AssayType
toString() - Method in class gov.nih.nci.caarray.domain.project.Experiment
toString() - Method in class gov.nih.nci.caarray.domain.project.Project
toString() - Method in class gov.nih.nci.caarray.domain.protocol.Parameter
toString() - Method in class gov.nih.nci.caarray.domain.sample.AbstractBioMaterial
toString() - Method in class gov.nih.nci.caarray.domain.vocabulary.Category
toString() - Method in class gov.nih.nci.caarray.domain.vocabulary.TermSource
toString() - Method in class gov.nih.nci.caarray.util.LabelValue
Return a string representation of this object.
TranscriptArrayReporter - Class in gov.nih.nci.cabio.domain
 
TranscriptArrayReporter() - Constructor for class gov.nih.nci.cabio.domain.TranscriptArrayReporter
 

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
 
UNIGENE - Static variable in class gov.nih.nci.caarray.domain.array.Gene
Name of the UniGene database.
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.
UnitableValue - Interface in gov.nih.nci.caarray.domain
Interface for classes that store a value with an optional unit.
UnsupportedAffymetrixCdfFiles - Enum in gov.nih.nci.caarray.domain.file
A list of Affymetrix CDF files that the AffxFusion jar (and therefore caArray) cannot handle.
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.
updateStatus(FileStatus) - Method in class gov.nih.nci.caarray.domain.file.CaArrayFileSet
Update the status of each file in this file set to the given status.
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.cagrid.caarray.client.CaArraySvcClient
 
UserDefinedCharacteristic - Class in gov.nih.nci.caarray.domain.sample
A Characteristic with a free text value.
UserDefinedCharacteristic() - Constructor for class gov.nih.nci.caarray.domain.sample.UserDefinedCharacteristic
Hibernate-only constructor.
UserDefinedCharacteristic(Category, String, Term) - Constructor for class gov.nih.nci.caarray.domain.sample.UserDefinedCharacteristic
Create a new characteristic with given fields.
UserDefinedFactorValue - Class in gov.nih.nci.caarray.domain.project
A FactorValue with a free text value.
UserDefinedFactorValue() - Constructor for class gov.nih.nci.caarray.domain.project.UserDefinedFactorValue
Hibernate-only constructor.
UserDefinedFactorValue(String, Term) - Constructor for class gov.nih.nci.caarray.domain.project.UserDefinedFactorValue
Create a new factor value with given fields.
UserDefinedParameterValue - Class in gov.nih.nci.caarray.domain.protocol
a parameter value with a free text value.
UserDefinedParameterValue() - Constructor for class gov.nih.nci.caarray.domain.protocol.UserDefinedParameterValue
Hibernate-only constructor.
UserDefinedParameterValue(UserDefinedParameterValue) - Constructor for class gov.nih.nci.caarray.domain.protocol.UserDefinedParameterValue
Copy constructor.
UserDefinedParameterValue(String, Term) - Constructor for class gov.nih.nci.caarray.domain.protocol.UserDefinedParameterValue
Create a new parameter value with given fields.
UserDefinedValue - Interface in gov.nih.nci.caarray.domain
A UnitableValue with a free text value.
userHasReadAccess(User) - Method in interface gov.nih.nci.caarray.domain.project.ExecutableJob
 
userHasWriteAccess(User) - Method in interface gov.nih.nci.caarray.domain.project.ExecutableJob
 
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
 
UserVisibleJob - Class in gov.nih.nci.caarray.domain.project
This object is a synthetic "job" used to represent the aggregate of a set of split jobs.
UserVisibleJob(Job, int) - Constructor for class gov.nih.nci.caarray.domain.project.UserVisibleJob
Create an object representing the given job and all its siblings.

V

VALIDATABLE_FILE_STATUSES - Static variable in enum gov.nih.nci.caarray.domain.file.FileStatus
The set of FileStatuses in which a file can be validated.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.ConfigParamEnum
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.data.DataType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.data.DesignElementType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.file.FileCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.file.FileStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.file.UnsupportedAffymetrixCdfFiles
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.permissions.SampleSecurityLevel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.permissions.SecurityLevel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.project.ExperimentDesignNodeType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.project.ExperimentOntology
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.project.ExperimentOntologyCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.project.JobStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.project.JobType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.project.ServiceType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.protocol.ProtocolTypeAssociation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.AbstractBioMaterialSortCriterion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.AuditLogSortCriterion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.BrowseCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.ExternalBiomaterialSearchCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.ExtractSortCriterion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.FactorSortCriterion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.HybridizationSortCriterion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.JobSortCriterion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.LabeledExtractSortCriterion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.PersonSortCriterion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.ProjectSortCriterion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.PublicationSortCriterion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.SampleJoinableSortCriterion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.SampleSortCriterion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.SearchCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.SearchSampleCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.SearchSourceCategory
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.SearchTypeSelection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.SourceJoinableSortCriterion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum gov.nih.nci.caarray.domain.search.SourceSortCriterion
Returns the enum constant of this type with the specified name.
values() - Static method in enum gov.nih.nci.caarray.domain.ConfigParamEnum
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.domain.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.domain.data.DesignElementType
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.domain.file.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.domain.file.FileStatus
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.domain.file.UnsupportedAffymetrixCdfFiles
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.domain.permissions.SampleSecurityLevel
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.domain.permissions.SecurityLevel
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.domain.project.ExperimentDesignNodeType
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.domain.project.ExperimentOntology
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.domain.project.ExperimentOntologyCategory
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.domain.project.JobStatus
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.domain.project.JobType
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.domain.project.ServiceType
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.domain.protocol.ProtocolTypeAssociation
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.domain.search.AbstractBioMaterialSortCriterion
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.domain.search.AuditLogSortCriterion
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.domain.search.BrowseCategory
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.domain.search.ExternalBiomaterialSearchCategory
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.domain.search.ExtractSortCriterion
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.domain.search.FactorSortCriterion
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.domain.search.HybridizationSortCriterion
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.domain.search.JobSortCriterion
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.domain.search.LabeledExtractSortCriterion
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.domain.search.PersonSortCriterion
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.domain.search.ProjectSortCriterion
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.domain.search.PublicationSortCriterion
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.domain.search.SampleJoinableSortCriterion
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.domain.search.SampleSortCriterion
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.domain.search.SearchCategory
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.domain.search.SearchSampleCategory
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.domain.search.SearchSourceCategory
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.domain.search.SearchTypeSelection
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.domain.search.SourceJoinableSortCriterion
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.domain.search.SourceSortCriterion
Returns an array containing the constants of this enum type, in the order they are declared.
ValueUtils - Class in gov.nih.nci.caarray.domain
Utilities for working with UnitableValues.

W

writeData(InputStream, boolean, int) - Method in class gov.nih.nci.caarray.domain.MultiPartBlob
Method that takes an input stream and breaks it up in to multiple blobs.

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