Index (ice 5.3.1 API)

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

A

ABIParser - Class in org.jbei.ice.lib.parsers: Parse ABI sequence trace file by wrapping BioJava.
ABIParser() - Constructor for class org.jbei.ice.lib.parsers.ABIParser
ABITrace - Class in org.jbei.ice.lib.parsers.abi: Title: ABITrace

ABITrace is a class for managing ABI file information, it is capable of opening an ABI file and storing the most important fields, which can be recalled as simple java types.
ABITrace(File) - Constructor for class org.jbei.ice.lib.parsers.abi.ABITrace: The File constructor opens a local ABI file and parses the content.
ABITrace(URL) - Constructor for class org.jbei.ice.lib.parsers.abi.ABITrace: The URL constructor opens an ABI file from any URL.
ABITrace(byte[]) - Constructor for class org.jbei.ice.lib.parsers.abi.ABITrace: The byte[] constructor parses an ABI file represented as a byte array.
AbstractFolder - Class in org.jbei.ice.lib.folder: Represents a grouping, in this case of folders / collections
AbstractFolder() - Constructor for class org.jbei.ice.lib.folder.AbstractFolder
AbstractFolder(long) - Constructor for class org.jbei.ice.lib.folder.AbstractFolder
AbstractFormatter - Class in org.jbei.ice.lib.entry.sequence.composers.formatters: Abstract formatter implementing IFormatter interface.
AbstractFormatter() - Constructor for class org.jbei.ice.lib.entry.sequence.composers.formatters.AbstractFormatter
AbstractParser - Class in org.jbei.ice.lib.parsers
AbstractParser(String, String) - Constructor for class org.jbei.ice.lib.parsers.AbstractParser
AbstractParser() - Constructor for class org.jbei.ice.lib.parsers.AbstractParser
ACCESSION_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
AccessKey - Class in org.jbei.ice.lib.dto.access
AccessKey() - Constructor for class org.jbei.ice.lib.dto.access.AccessKey
AccessPermission - Class in org.jbei.ice.lib.dto.access: Data transfer object for permissions
AccessPermission() - Constructor for class org.jbei.ice.lib.dto.access.AccessPermission
AccessPermission(AccessPermission.Article, long, AccessPermission.Type, long, String) - Constructor for class org.jbei.ice.lib.dto.access.AccessPermission
AccessPermission.Article - Enum in org.jbei.ice.lib.dto.access
AccessPermission.Type - Enum in org.jbei.ice.lib.dto.access
AccessStatus - Enum in org.jbei.ice.lib.access: Status of an account
AccessTokenResource - Class in org.jbei.ice.services.rest: API for access tokens (also session id for the user interface)
AccessTokenResource() - Constructor for class org.jbei.ice.services.rest.AccessTokenResource
AccessTokens - Class in org.jbei.ice.lib.access: Wrapper around mapping of a resource identifier to an access token generated for it
AccessTokens() - Constructor for class org.jbei.ice.lib.access.AccessTokens
AccessType - Enum in org.jbei.ice.lib.access: Used with the access permission classes to indicate the type of access that is being granted.
Account - Class in org.jbei.ice.storage.model: Store the account information for a single user.
Account() - Constructor for class org.jbei.ice.storage.model.Account: Constructor.
AccountController - Class in org.jbei.ice.lib.account: ABI to manipulate Account objects.
AccountController() - Constructor for class org.jbei.ice.lib.account.AccountController: Default constructor.
accountDAO - Variable in class org.jbei.ice.lib.entry.HasEntry
AccountDAO - Class in org.jbei.ice.storage.hibernate.dao: Data accessor object to manipulate Account objects in the database.
AccountDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.AccountDAO
accountHasReadPermission(Account, Set<Folder>) - Method in class org.jbei.ice.lib.access.PermissionsController
accountHasWritePermission(Account, Set<Folder>) - Method in class org.jbei.ice.lib.access.PermissionsController
AccountPreferences - Class in org.jbei.ice.storage.model: Store preferences for a user for an Account object.
AccountPreferences() - Constructor for class org.jbei.ice.storage.model.AccountPreferences
AccountResults - Class in org.jbei.ice.lib.dto: Wrapper around a list of user accounts
AccountResults() - Constructor for class org.jbei.ice.lib.dto.AccountResults
Accounts - Class in org.jbei.ice.lib.account: ICE user accounts
Accounts() - Constructor for class org.jbei.ice.lib.account.Accounts
AccountTransfer - Class in org.jbei.ice.lib.account: Data transfer object for user account
AccountTransfer() - Constructor for class org.jbei.ice.lib.account.AccountTransfer
AccountTransfer(String, String) - Constructor for class org.jbei.ice.lib.account.AccountTransfer
AccountType - Enum in org.jbei.ice.lib.account: Type of account managed by the system
AccountUtils - Class in org.jbei.ice.lib.account: Utility class for account management
AccountUtils() - Constructor for class org.jbei.ice.lib.account.AccountUtils
add(RegistryPartner, AccessPermission) - Method in class org.jbei.ice.lib.access.RemoteAccess: Add access privileges for a user on this instance to enable access to a (currently folder only) resource on a remote ICE instance
add() - Method in class org.jbei.ice.lib.entry.EntryHistory: Adds a read history object for the specified user and entry
add(AccessPermission) - Method in class org.jbei.ice.lib.entry.EntryPermissions: Adds a new permission to the specified entry.
add(Manuscript) - Method in class org.jbei.ice.lib.manuscript.Manuscripts
addArabidopsisSeedHeaders(List<EntryField>) - Static method in class org.jbei.ice.lib.bulkupload.BulkCSVUploadHeaders
addArabidopsisSeedHeaders(List<EntryField>) - Static method in class org.jbei.ice.lib.entry.EntryFields
addAttachment(String, long, long, InputStream, String) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController
addAttachment(long, AttachmentInfo) - Method in class org.jbei.ice.services.rest.PartResource
addAttachmentToEntry(String, long, AttachmentInfo) - Method in class org.jbei.ice.lib.entry.attachment.Attachments
addChildEntry(Entry) - Method in class org.jbei.ice.lib.entry.EntryLinks: Adds specified entry as a child of the entry associated with this
adddFileHeaders(List<EntryField>) - Static method in class org.jbei.ice.lib.bulkupload.BulkCSVUploadHeaders
addEntriesToFolders(String, List<Long>, List<FolderDetails>) - Method in class org.jbei.ice.lib.folder.FolderContents: Attempts to add the specified list of entries to the specified folder destinations.
addEntriesToTransferredFolder(List<Long>, Folder) - Method in class org.jbei.ice.lib.folder.FolderContents
addEntrySelection(String, EntrySelection) - Method in class org.jbei.ice.lib.folder.FolderContents: Adds entries in the selection context, to specified folders
addFolderContents(Folder, List<Entry>) - Method in class org.jbei.ice.storage.hibernate.dao.FolderDAO
addGroup(UserGroup) - Method in class org.jbei.ice.lib.group.Groups: Adds group to the list of groups for current user
addHeaders(Response.ResponseBuilder, String) - Method in class org.jbei.ice.services.rest.RestResource
addLink(PartData, LinkType) - Method in class org.jbei.ice.lib.entry.EntryLinks: Adds a link for the specified entry (or creates a new entry) of the type specified
addNewPartner(String, RegistryPartner, String) - Method in class org.jbei.ice.lib.net.WebPartners: Adds the registry instance specified by the url to the list of existing partners (if not already in there) and sends a request to the remote instance that includes a security token that the remote instance can use to communicate with this instance.
addNewPartner(RegistryPartner) - Method in class org.jbei.ice.services.rest.PartnerResource: Adds a remote instance as a registry partner.
addNote(DNAFeatureNote) - Method in class org.jbei.ice.lib.dto.DNAFeature
addParentEntry(Entry) - Method in class org.jbei.ice.lib.entry.EntryLinks
addPermission(AccessPermission, Entry, Folder, BulkUpload) - Method in class org.jbei.ice.lib.access.Permissions
addPermission(String, AccessPermission) - Method in class org.jbei.ice.lib.access.PermissionsController
addPermission(AccessPermission, Entry, Folder, BulkUpload) - Method in class org.jbei.ice.lib.access.PermissionsController
addPermission(String, long, AccessPermission) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController: Adds specified access permission to the bulk upload.
addPermission(long, AccessPermission) - Method in class org.jbei.ice.services.rest.BulkUploadResource: Add upload permission
addPermission(long, AccessPermission) - Method in class org.jbei.ice.services.rest.FolderResource: Add new permission to list of permissions for specified folder
addPermissions(Entry) - Method in class org.jbei.ice.lib.entry.EntryPermissionTask
addPlasmidHeaders(List<EntryField>) - Static method in class org.jbei.ice.lib.bulkupload.BulkCSVUploadHeaders
addPlasmidHeaders(List<EntryField>) - Static method in class org.jbei.ice.lib.entry.EntryFields
addReadPermission(Account, Group, Entry) - Method in class org.jbei.ice.lib.entry.EntryCreator
addRemoteAccess(RemoteAccessPermission) - Method in class org.jbei.ice.services.rest.PermissionResource: Add a remote access from a partner in the web of registries
addRemoteEntries(String, List<PartData>, List<FolderDetails>) - Method in class org.jbei.ice.lib.folder.FolderContents
addRequest(SampleRequest) - Method in class org.jbei.ice.services.rest.SampleResource
addSample(String, String, PartSample) - Method in class org.jbei.ice.services.rest.PartResource
addSelectedEntriesToFolders(EntrySelection, String, String, long) - Method in class org.jbei.ice.services.rest.FolderResource: Adds contents referenced in the entrySelection object to the folders also referenced in the same object
addSequence(String, long, long, String, String) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController
addShotgunSequence(long, InputStream, FormDataContentDisposition) - Method in class org.jbei.ice.services.rest.PartResource
addStrainHeaders(List<EntryField>) - Static method in class org.jbei.ice.lib.bulkupload.BulkCSVUploadHeaders
addStrainHeaders(List<EntryField>) - Static method in class org.jbei.ice.lib.entry.EntryFields
addToRemoteFolder(Account, Folder, List<Long>) - Method in class org.jbei.ice.lib.folder.FolderContents
addToTotalCount(long) - Method in class org.jbei.ice.lib.search.IndexerProgressMonitor
addTraceSequence(File, String) - Method in class org.jbei.ice.lib.entry.sequence.TraceSequences
addTraceSequence(long, InputStream, FormDataContentDisposition) - Method in class org.jbei.ice.services.rest.PartResource
addTransferredEntriesToFolder(String, EntrySelection) - Method in class org.jbei.ice.lib.net.RemoteContact
addTransferredEntriesToFolder(String, String, EntrySelection, long, String, String) - Method in class org.jbei.ice.lib.net.RemoteContact
addType - Variable in class org.jbei.ice.lib.bulkupload.BulkCSVUpload
addWritePermission(Account, Entry) - Method in class org.jbei.ice.lib.bulkupload.BulkEntryCreator
addWritePermission(Account, Entry) - Method in class org.jbei.ice.lib.entry.EntryCreator
AnnotationLocation - Class in org.jbei.ice.storage.model: Store the basepair location annotation for a SequenceFeature object.
AnnotationLocation() - Constructor for class org.jbei.ice.storage.model.AnnotationLocation
AnnotationLocation(int, int, SequenceFeature) - Constructor for class org.jbei.ice.storage.model.AnnotationLocation
AnnotationResource - Class in org.jbei.ice.services.rest: REST resource for annotations
AnnotationResource() - Constructor for class org.jbei.ice.services.rest.AnnotationResource
Annotations - Class in org.jbei.ice.lib.entry.sequence.annotation: ICE Annotations with support for generating potential annotations for a specified entry
Annotations(String) - Constructor for class org.jbei.ice.lib.entry.sequence.annotation.Annotations
API_KEY_CLIENT_ID - Static variable in class org.jbei.ice.services.rest.Headers
API_KEY_CLIENT_ID - Variable in class org.jbei.ice.services.rest.RestResource
API_KEY_TOKEN - Static variable in class org.jbei.ice.services.rest.Headers
API_KEY_TOKEN - Variable in class org.jbei.ice.services.rest.RestResource
API_KEY_USER - Static variable in class org.jbei.ice.services.rest.Headers
API_KEY_USER - Variable in class org.jbei.ice.services.rest.RestResource
apiClientId - Variable in class org.jbei.ice.services.rest.RestResource
ApiKey - Class in org.jbei.ice.storage.model
ApiKey() - Constructor for class org.jbei.ice.storage.model.ApiKey
ApiKeyDAO - Class in org.jbei.ice.storage.hibernate.dao: Data Accessor object for retrieving ApiKey objects
ApiKeyDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.ApiKeyDAO
ApiKeyResource - Class in org.jbei.ice.services.rest: REST Resource for api-keys that enable third-party application access to ice
ApiKeyResource() - Constructor for class org.jbei.ice.services.rest.ApiKeyResource
apiKeyValidates(String, RegistryPartner) - Method in class org.jbei.ice.lib.net.RemoteContact: Contacts the registry partner at the specified url, to ensure that the API key validates.
apiToken - Variable in class org.jbei.ice.services.rest.RestResource
apiUser - Variable in class org.jbei.ice.services.rest.RestResource
ApplicationInitialize - Class in org.jbei.ice: Responsible for initializing the ICE application on startup
ApplicationInitialize() - Constructor for class org.jbei.ice.ApplicationInitialize
approveBulkImport(String, long) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController
ArabidopsisSeed - Class in org.jbei.ice.storage.model: Store Arabidopsis Seed specific fields.
ArabidopsisSeed() - Constructor for class org.jbei.ice.storage.model.ArabidopsisSeed
ArabidopsisSeedData - Class in org.jbei.ice.lib.dto.entry
ArabidopsisSeedData() - Constructor for class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
aroundReadFrom(ReaderInterceptorContext) - Method in class org.jbei.ice.services.rest.AuthenticationInterceptor
ArrayDataJSONHandler - Class in org.jbei.ice.services.rest
ArrayDataJSONHandler() - Constructor for class org.jbei.ice.services.rest.ArrayDataJSONHandler
Article - Enum in org.jbei.ice.lib.access: Item or object that the permission acts on.
Attachment - Class in org.jbei.ice.storage.model: Store information about attachments.
Attachment() - Constructor for class org.jbei.ice.storage.model.Attachment
Attachment(String, String, Entry) - Constructor for class org.jbei.ice.storage.model.Attachment: Attachment constructor.
AttachmentDAO - Class in org.jbei.ice.storage.hibernate.dao: Data accessor object for Attachments
AttachmentDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.AttachmentDAO
attachmentDirName - Static variable in class org.jbei.ice.lib.entry.attachment.Attachments
AttachmentInfo - Class in org.jbei.ice.lib.dto.entry
AttachmentInfo() - Constructor for class org.jbei.ice.lib.dto.entry.AttachmentInfo
AttachmentInfo(String) - Constructor for class org.jbei.ice.lib.dto.entry.AttachmentInfo
Attachments - Class in org.jbei.ice.lib.entry.attachment: ICE Entry Attachments
Attachments() - Constructor for class org.jbei.ice.lib.entry.attachment.Attachments
Audit - Class in org.jbei.ice.storage.model: Audit object for keep track of actions affecting entries.
Audit() - Constructor for class org.jbei.ice.storage.model.Audit
AuditDAO - Class in org.jbei.ice.storage.hibernate.dao: Accessor for Audit objects
AuditDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.AuditDAO
AuditType - Enum in org.jbei.ice.lib.dto
authenticate(String, String, String) - Method in class org.jbei.ice.lib.account.AccountController: Authenticate a user in the database.
authenticate(AccountTransfer) - Method in class org.jbei.ice.lib.account.AccountController: Authenticate a user in the database.
authenticated - Variable in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
authenticates(String, String) - Method in interface org.jbei.ice.lib.account.authentication.IAuthentication: Authenticates a user's name and password against the system's stored credentials
authenticates(String, String) - Method in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
authenticates(String, String) - Method in class org.jbei.ice.lib.account.authentication.LocalAuthentication
authenticates(String, String) - Method in class org.jbei.ice.lib.account.authentication.UserIdAuthentication
authenticateWithLDAP(String, String) - Method in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication: Authenticate user to the ldap server.
AUTHENTICATION_PARAM_NAME - Static variable in class org.jbei.ice.services.rest.Headers
AUTHENTICATION_PARAM_NAME - Variable in class org.jbei.ice.services.rest.RestResource
AuthenticationException - Exception in org.jbei.ice.lib.account.authentication: Exception class for the Authentication
AuthenticationException(String) - Constructor for exception org.jbei.ice.lib.account.authentication.AuthenticationException
AuthenticationException(Throwable) - Constructor for exception org.jbei.ice.lib.account.authentication.AuthenticationException
AuthenticationException(String, Throwable) - Constructor for exception org.jbei.ice.lib.account.authentication.AuthenticationException
AuthenticationInterceptor - Class in org.jbei.ice.services.rest: Filter watches for Authorization headers on incoming requests, and passes along data to build an HmacSignature to validate the request.
AuthenticationInterceptor() - Constructor for class org.jbei.ice.services.rest.AuthenticationInterceptor
authenticationURL - Variable in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
Authorization - Interface in org.jbei.auth: An object specifying if a request is valid, and for which user.
Authorization<T extends DataModel> - Class in org.jbei.ice.lib.access: Used in instances where access permissions are to be enforced.
Authorization(IRepository<T>) - Constructor for class org.jbei.ice.lib.access.Authorization
AuthorizationException - Exception in org.jbei.ice.lib.access: Exception used in cases where authorization is required but lacking for access (i.e.
AuthorizationException(String) - Constructor for exception org.jbei.ice.lib.access.AuthorizationException
AutoAnnotationBlastDbBuildTask - Class in org.jbei.ice.lib.entry.sequence.annotation: Task to rebuild blast database of features for auto annotation
AutoAnnotationBlastDbBuildTask(boolean) - Constructor for class org.jbei.ice.lib.entry.sequence.annotation.AutoAnnotationBlastDbBuildTask
AutoAnnotationBlastDbBuildTask() - Constructor for class org.jbei.ice.lib.entry.sequence.annotation.AutoAnnotationBlastDbBuildTask
AutoCompleteField - Enum in org.jbei.ice.lib.dto.entry: Fields in the registry entry that have autocomplete enabled
AutoCompleteFieldValues - Class in org.jbei.ice.lib.dto.entry: Values for auto complete fields
AutoCompleteFieldValues(String) - Constructor for class org.jbei.ice.lib.dto.entry.AutoCompleteFieldValues: Each instance of this object is tied to a specified field
autoUpdateBulkUpload(String, BulkUploadAutoUpdate, EntryType) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController
autoUpdateSetting(String, Setting) - Method in class org.jbei.ice.lib.config.ConfigurationController

B

BASE_COUNT_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
BASE_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
beginTransaction() - Static method in class org.jbei.ice.storage.hibernate.HibernateUtil
BioSafetyOption - Enum in org.jbei.ice.lib.shared: BioSafety Option options
Bl2SeqResult - Class in org.jbei.ice.lib.parsers.bl2seq: Stores information about the bl2seq output.
Bl2SeqResult(int, int, int, String, int, int, String, int) - Constructor for class org.jbei.ice.lib.parsers.bl2seq.Bl2SeqResult
BLAST_FTP_DIR - Static variable in class org.jbei.ice.lib.config.ConfigurationController
BlastException - Exception in org.jbei.ice.lib.search.blast: Exception class to throw for Blast.
BlastException() - Constructor for exception org.jbei.ice.lib.search.blast.BlastException
BlastException(String, Throwable) - Constructor for exception org.jbei.ice.lib.search.blast.BlastException
BlastException(String) - Constructor for exception org.jbei.ice.lib.search.blast.BlastException
BlastException(Throwable) - Constructor for exception org.jbei.ice.lib.search.blast.BlastException
BlastPlus - Class in org.jbei.ice.lib.search.blast: Enables (command line) interaction with BLAST+
Current usage is for blast searches and auto-annotation support
BlastPlus() - Constructor for class org.jbei.ice.lib.search.blast.BlastPlus
BlastProgram - Enum in org.jbei.ice.lib.dto.search: Types of blast programs that this system supports for nucleotide search
BlastQuery - Class in org.jbei.ice.lib.dto.search: Blast query.
BlastQuery() - Constructor for class org.jbei.ice.lib.dto.search.BlastQuery
BOOLEAN_PROPERTY - Static variable in class org.jbei.ice.storage.hibernate.bridge.EntryBooleanPropertiesBridge
boostFieldForField(String) - Static method in enum org.jbei.ice.lib.dto.search.SearchBoostField
breakUpLines(String) - Static method in class org.jbei.ice.lib.utils.SequenceUtils: Format into 6 column, 10 basepairs per column display.
buildEntry(EntryType) - Static method in class org.jbei.ice.lib.entry.EntryFactory
buildOrRebuildAlignment(TraceSequence, Sequence) - Method in class org.jbei.ice.lib.entry.sequence.SequenceAnalysisController: Calculate sequence alignment between the given TraceSequence and Sequence using bl2seq, and save the result into the database.
buildOrRebuildAlignment(TraceSequence, Sequence) - Method in class org.jbei.ice.lib.entry.sequence.TraceSequences: Calculate sequence alignment between the given TraceSequence and Sequence using bl2seq, and save the result into the database.
buildSignature(HttpServletRequest, String, String) - Method in class org.jbei.auth.hmac.HmacSignatureFactory
buildSignature(HttpRequestBase, String, String) - Method in class org.jbei.auth.hmac.HmacSignatureFactory
buildSignature(String, String, String, String, String, Map<String, ? extends Iterable<String>>) - Method in class org.jbei.auth.hmac.HmacSignatureFactory: Builds initial signature object from raw individual components.
BulkCSVUpload - Class in org.jbei.ice.lib.bulkupload: Helper class for dealing with bulk CSV uploads
BulkCSVUpload(String, Path, EntryType) - Constructor for class org.jbei.ice.lib.bulkupload.BulkCSVUpload
BulkCSVUploadHeaders - Class in org.jbei.ice.lib.bulkupload: Headers for each of the entry add types for bulk csv upload
BulkCSVUploadHeaders() - Constructor for class org.jbei.ice.lib.bulkupload.BulkCSVUploadHeaders
BulkEntryCreator - Class in org.jbei.ice.lib.bulkupload: Creates entries for bulk uploads
BulkEntryCreator() - Constructor for class org.jbei.ice.lib.bulkupload.BulkEntryCreator
BulkFileSBOLUpload - Class in org.jbei.ice.lib.bulkupload: Bulk upload with multiple components in a single SBOL document
BulkFileSBOLUpload(String, Path, EntryType) - Constructor for class org.jbei.ice.lib.bulkupload.BulkFileSBOLUpload
BulkUpload - Class in org.jbei.ice.storage.model: Saved draft of bulk imports.
BulkUpload() - Constructor for class org.jbei.ice.storage.model.BulkUpload
BulkUploadAuthorization - Class in org.jbei.ice.lib.bulkupload
BulkUploadAuthorization() - Constructor for class org.jbei.ice.lib.bulkupload.BulkUploadAuthorization
BulkUploadAutoUpdate - Class in org.jbei.ice.lib.bulkupload: Data model for bulk upload auto updates
BulkUploadAutoUpdate(EntryType) - Constructor for class org.jbei.ice.lib.bulkupload.BulkUploadAutoUpdate
BulkUploadAutoUpdate(EntryType, EditMode) - Constructor for class org.jbei.ice.lib.bulkupload.BulkUploadAutoUpdate
BulkUploadController - Class in org.jbei.ice.lib.bulkupload: Controller for dealing with bulk imports (including drafts)
BulkUploadController() - Constructor for class org.jbei.ice.lib.bulkupload.BulkUploadController
BulkUploadDAO - Class in org.jbei.ice.storage.hibernate.dao: Hibernate Data accessor object for retrieving BulkUpload objects from the database
BulkUploadDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.BulkUploadDAO
BulkUploadDeleteTask - Class in org.jbei.ice.lib.bulkupload: Task to delete bulk uploads with a status of draft and their contents.
BulkUploadDeleteTask(String, long) - Constructor for class org.jbei.ice.lib.bulkupload.BulkUploadDeleteTask
BulkUploadInfo - Class in org.jbei.ice.lib.bulkupload: Data transfer model for bulk upload.
BulkUploadInfo() - Constructor for class org.jbei.ice.lib.bulkupload.BulkUploadInfo
BulkUploadResource - Class in org.jbei.ice.services.rest: Rest API for interacting with bulk upload resources
BulkUploadResource() - Constructor for class org.jbei.ice.services.rest.BulkUploadResource
BulkUploadStatus - Enum in org.jbei.ice.lib.bulkupload: Status used to indicate whether a bulk upload is pending approval or still being worked on.
BulkUploadValidation - Class in org.jbei.ice.lib.bulkupload: Validation class for Bulk Upload Entries
BulkUploadValidation(BulkUpload) - Constructor for class org.jbei.ice.lib.bulkupload.BulkUploadValidation
BulkZipUpload - Class in org.jbei.ice.lib.bulkupload: Bulk Upload with zip files.
BulkZipUpload(String, Path, EntryType) - Constructor for class org.jbei.ice.lib.bulkupload.BulkZipUpload
ByteArrayWrapper - Class in org.jbei.ice.lib.entry.sequence: Wrapper around an array of bytes representing file contents, and the name of the file.
ByteArrayWrapper(byte[], String) - Constructor for class org.jbei.ice.lib.entry.sequence.ByteArrayWrapper
bytesToHex(byte[]) - Static method in class org.jbei.ice.lib.account.AccountUtils

C

calculateReverseComplementSequenceHash(String) - Static method in class org.jbei.ice.lib.utils.SequenceUtils: Calculate the SHA-1 sequence hash of the reverse complement of the given sequence.
calculateSequenceHash(String) - Static method in class org.jbei.ice.lib.utils.SequenceUtils: Calculate the SHA-1 sequence hash of the given sequence.
call - Variable in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
canEdit(String, String, Entry) - Method in class org.jbei.ice.lib.entry.EntryController
canEdit(String, String, Entry) - Method in class org.jbei.ice.lib.entry.sequence.TraceSequences
canRead(String, T) - Method in class org.jbei.ice.lib.access.Authorization
canRead(String, Folder) - Method in class org.jbei.ice.lib.dto.folder.FolderAuthorization
canRead(String, Entry) - Method in class org.jbei.ice.lib.entry.EntryAuthorization
canWrite(String, T) - Method in class org.jbei.ice.lib.access.Authorization: Should either be an administrator or the owner of the object to be able to write
canWrite(String, Folder) - Method in class org.jbei.ice.lib.dto.folder.FolderAuthorization
canWrite(String, Entry) - Method in class org.jbei.ice.lib.entry.EntryAuthorization: Determine if the referenced userId has write permissions for the entry.
canWrite(String, Sample) - Method in class org.jbei.ice.lib.entry.sample.SampleAuthorization: Determines if the specified user has write privileges.
checkAddFilter(List<Predicate>, Root<Entry>, String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
checkEnableHasAttribute(FullTextQuery, SearchQuery.Parameters) - Method in class org.jbei.ice.storage.hibernate.search.HibernateSearch
checkEnableSecurityFilter(String, FullTextQuery) - Method in class org.jbei.ice.storage.hibernate.search.HibernateSearch: Enables the security filter if the account does not have administrative privileges
classesForTypes(List<EntryType>) - Static method in class org.jbei.ice.lib.search.filter.SearchFieldFactory
cleanQuery(String) - Static method in class org.jbei.ice.storage.hibernate.search.HibernateSearch
cleanSequence(String) - Method in class org.jbei.ice.lib.parsers.AbstractParser: Replace different line termination characters with the newline character (\n).
clearBulkEdits(String) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController: Removes any bulk edits belonging to the specified user
clearPermissions(Folder) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
clearPermissions(Group) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
close() - Static method in class org.jbei.ice.storage.hibernate.HibernateUtil
Collection - Class in org.jbei.ice.lib.folder.collection: Represents a collection of a specific type
Collection(String, CollectionType) - Constructor for class org.jbei.ice.lib.folder.collection.Collection
CollectionCounts - Class in org.jbei.ice.lib.folder: Wrapper around counts for collections
CollectionCounts() - Constructor for class org.jbei.ice.lib.folder.CollectionCounts
CollectionEntries - Class in org.jbei.ice.lib.folder.collection: Represents entries contained within a specified collection filtered by the permissions available to the person retrieving the entries
CollectionEntries(String, CollectionType) - Constructor for class org.jbei.ice.lib.folder.collection.CollectionEntries
CollectionResource - Class in org.jbei.ice.services.rest: Collections represent system defined sets of parts.
CollectionResource() - Constructor for class org.jbei.ice.services.rest.CollectionResource
Collections - Class in org.jbei.ice.lib.folder.collection: Represents the fixed collections supported in the eco-system
Collections(String) - Constructor for class org.jbei.ice.lib.folder.collection.Collections
CollectionType - Enum in org.jbei.ice.lib.folder.collection: Types of collections that are supported in ICE.
ColumnField - Enum in org.jbei.ice.lib.shared: Column fields for tables used on the ice platform UI
columnFieldToString(ColumnField) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
Comment - Class in org.jbei.ice.storage.model: Store comments about an Entry object, with the associated .lib.account.model.Account.
Comment() - Constructor for class org.jbei.ice.storage.model.Comment
Comment(Entry, Account, String) - Constructor for class org.jbei.ice.storage.model.Comment
COMMENT_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
CommentDAO - Class in org.jbei.ice.storage.hibernate.dao: DAO for comment objects
CommentDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.CommentDAO
commitTransaction() - Static method in class org.jbei.ice.storage.hibernate.HibernateUtil
compare(DNAFeature, DNAFeature) - Method in class org.jbei.ice.lib.bulkupload.DNAFeatureComparator
compare(SequenceFeature, SequenceFeature) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.SequenceFeatureComparator
compareEnds(DNAFeature, DNAFeature) - Method in class org.jbei.ice.lib.bulkupload.DNAFeatureComparator
compareEnds(SequenceFeature, SequenceFeature) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.SequenceFeatureComparator
compareTo(AbstractFolder) - Method in class org.jbei.ice.lib.folder.AbstractFolder
compose(Sequence, IFormatter) - Method in class org.jbei.ice.lib.entry.sequence.SequenceController: Generate a formatted text of a given IFormatter from the given Sequence.
concatSequence(String, String) - Method in class org.jbei.ice.lib.utils.PackageAssembler: Concatinate two DNA sequences.
ConfigResource - Class in org.jbei.ice.services.rest
ConfigResource() - Constructor for class org.jbei.ice.services.rest.ConfigResource
Configuration - Class in org.jbei.ice.storage.model: Site wide configuration values.
Configuration() - Constructor for class org.jbei.ice.storage.model.Configuration
Configuration(String, String) - Constructor for class org.jbei.ice.storage.model.Configuration
ConfigurationController - Class in org.jbei.ice.lib.config
ConfigurationController() - Constructor for class org.jbei.ice.lib.config.ConfigurationController
ConfigurationDAO - Class in org.jbei.ice.storage.hibernate.dao: Manage Configuration objects in the database.
ConfigurationDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.ConfigurationDAO
ConfigurationKey - Enum in org.jbei.ice.lib.dto: Types of configuration stored in the database.
contactPotentialPartner(RegistryPartner, String) - Method in class org.jbei.ice.lib.net.RemoteContact
contextDestroyed(ServletContextEvent) - Method in class org.jbei.ice.servlet.IceServletContextListener
contextInitialized(ServletContextEvent) - Method in class org.jbei.ice.servlet.IceServletContextListener
CONTIG_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
copyPart(String, String) - Method in class org.jbei.ice.lib.entry.EntryCreator: Creates a copy of
create(String, BulkUploadInfo) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController: Creates a new bulk upload.
create(AccountTransfer) - Method in class org.jbei.ice.services.rest.AccessTokenResource: Creates a new access token for the user referenced in the parameter, after the credentials (username and password) are validated.
create(BulkUploadInfo) - Method in class org.jbei.ice.services.rest.BulkUploadResource
create(long, CustomField) - Method in class org.jbei.ice.services.rest.CustomFieldResource: Creates a new custom field and associated it with the specified entry.
create(boolean, FolderDetails) - Method in class org.jbei.ice.services.rest.FolderResource: Creates a new folder with the details specified in the parameter.
create(Manuscript) - Method in class org.jbei.ice.services.rest.ManuscriptResource
create(String, PartData) - Method in class org.jbei.ice.services.rest.PartResource: Creates a new entry.
create(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
create(String, String, Entry, String, Date) - Method in class org.jbei.ice.storage.hibernate.dao.ShotgunSequenceDAO
create(Path, TraceSequence, InputStream) - Method in class org.jbei.ice.storage.hibernate.dao.TraceSequenceDAO: Create a new TraceSequence object in the database, and write the file data to disk.
create(T) - Method in class org.jbei.ice.storage.hibernate.HibernateRepository: Creates new object in the database
create(T) - Method in interface org.jbei.ice.storage.IRepository
createAdminAccount() - Method in class org.jbei.ice.lib.account.AccountController
createApiKey(String) - Method in class org.jbei.ice.services.rest.ApiKeyResource: creates an api-key for the specified client id
createBlastFilterQuery(FullTextSession, HashMap<String, SearchResult>, BooleanQuery.Builder) - Method in class org.jbei.ice.storage.hibernate.search.HibernateSearch
createBulkUpload(String, EntryType) - Method in class org.jbei.ice.lib.bulkupload.BulkEntryCreator
createChildrenStorage(StorageLocation, Storage, String) - Method in class org.jbei.ice.lib.entry.sample.SampleService: Creates storage for all children of given parent storage
createComment(long, UserComment) - Method in class org.jbei.ice.services.rest.PartResource
created - Variable in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
createEntries(String, long, List<PartWithSample>, HashMap<String, InputStream>) - Method in class org.jbei.ice.lib.bulkupload.BulkEntryCreator
createEntry(String, long, PartData) - Method in class org.jbei.ice.lib.bulkupload.BulkEntryCreator
createEntry(Account, Entry, ArrayList<AccessPermission>) - Method in class org.jbei.ice.lib.entry.EntryCreator: Create an entry in the database.
createEntry(long, PartData) - Method in class org.jbei.ice.services.rest.BulkUploadResource
createEntryComment(String, long, UserComment) - Method in class org.jbei.ice.lib.entry.EntryController
createEntryForUpload(String, PartData, BulkUpload) - Method in class org.jbei.ice.lib.bulkupload.BulkEntryCreator
createField(String, long, CustomField) - Method in class org.jbei.ice.lib.dto.entry.CustomFields
createGroup(String, UserGroup) - Method in class org.jbei.ice.lib.group.GroupController
createGroup(UserGroup) - Method in class org.jbei.ice.services.rest.GroupResource
createGroup(long, UserGroup) - Method in class org.jbei.ice.services.rest.UserResource
createICEComponentDefinitionRecord(SBOLDocument, ComponentDefinition) - Method in class org.jbei.ice.lib.parsers.sbol.SBOLParser
createICEModuleDefinitionRecord(SBOLDocument, ModuleDefinition) - Method in class org.jbei.ice.lib.parsers.sbol.SBOLParser
createKey() - Static method in class org.jbei.auth.hmac.HmacSignatureFactory: Convenience method to create a new random key for signing requests.
createLink(String, LinkType, PartData) - Method in class org.jbei.ice.services.rest.PartResource: Creates a new link between the referenced part id and the part in the parameter
createNewAccount(AccountTransfer, boolean) - Method in class org.jbei.ice.lib.account.AccountController: Creates a new account using the parameters passed.
createNewEntry(TopLevel, SBOLDocument) - Method in class org.jbei.ice.lib.parsers.sbol.SBOLParser
createNewSessionForUser(String) - Static method in class org.jbei.ice.lib.account.UserSessions: Creates a new session id for the specified user stores and returns it
createNewUser(boolean, AccountTransfer) - Method in class org.jbei.ice.services.rest.UserResource
createOrRetrieveBulkUpload(Account, BulkUploadAutoUpdate, EntryType) - Method in class org.jbei.ice.lib.bulkupload.BulkEntryCreator
createOrRetrievePublicGroup() - Method in class org.jbei.ice.lib.group.GroupController
createOrUpdateEntries(String, long, List<PartData>) - Method in class org.jbei.ice.lib.bulkupload.BulkEntryCreator
createOrUpdateEntry(String, BulkUploadAutoUpdate, EntryType) - Method in class org.jbei.ice.lib.bulkupload.BulkEntryCreator: Creates (or updates) entry based on information in parameters
createOrUpdatePreference(Account, String, String) - Method in class org.jbei.ice.storage.hibernate.dao.PreferencesDAO
createOrUpdateStudy(Study) - Method in class org.jbei.ice.lib.experiment.Experiments: Creates a new study for a particular entry.
createPart(String, PartData) - Method in class org.jbei.ice.lib.entry.EntryCreator: Creates a new entry using the passed data
createPartExperiment(String, Study) - Method in class org.jbei.ice.services.rest.PartResource
createPermission(AccessPermission) - Method in class org.jbei.ice.lib.folder.FolderPermissions: Creates a new access permission record to enable read or write privileges for a folder.
createPermission(String, AccessPermission) - Method in class org.jbei.ice.services.rest.PartResource
createPermissionModel(AccessPermission, Folder, Account) - Method in class org.jbei.ice.lib.access.RemoteAccess
createPermissionModel(AccessPermission, RemoteShareModel) - Method in class org.jbei.ice.lib.folder.FolderPermissions
createPermissionQuery(Entry, Folder, BulkUpload, Account, Group, boolean, boolean) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
createPersonalFolder(String, FolderDetails) - Method in class org.jbei.ice.lib.folder.FolderController
createPlate96Location(String, StorageLocation) - Method in class org.jbei.ice.lib.entry.sample.SampleService: Creates location records for a sample contained in a 96 well plate Provides support for 2-D barcoded systems.
createPredicates(Root<Request>, String, SampleRequestStatus) - Method in class org.jbei.ice.storage.hibernate.dao.RequestDAO
createPreference(Account, String, String) - Method in class org.jbei.ice.lib.account.PreferencesController
createRemoteAccessModel(AccessPermission, RemoteClientModel, Permission) - Method in class org.jbei.ice.lib.access.RemoteAccess
createRemotePartnerObject(RegistryPartner, String) - Method in class org.jbei.ice.lib.net.WebPartners
createRemotePermission(AccessPermission) - Method in class org.jbei.ice.lib.folder.FolderPermissions: Creates an access folder permission for a remote user
createSample(String, String, PartSample, String) - Method in class org.jbei.ice.lib.entry.sample.SampleService
createSampleObject(String, String, String) - Static method in class org.jbei.ice.lib.entry.sample.SampleCreator: Create a Sample object.
createSessionForUser(String, String) - Static method in class org.jbei.ice.lib.account.UserSessions: Uses the session id passed in the parameter and sets it as the session id for the user as long as it meets a specified criteria (currently must be at least 5 xters long)
createShelfStorage(String, StorageLocation) - Method in class org.jbei.ice.lib.entry.sample.SampleService
createStorage(String, String, SampleType) - Method in class org.jbei.ice.lib.entry.sample.SampleService
createTableViewData(String, Entry, boolean) - Static method in class org.jbei.ice.storage.ModelToInfoFactory
createTipView(Entry) - Static method in class org.jbei.ice.storage.ModelToInfoFactory
createTransferredFolder(FolderDetails) - Method in class org.jbei.ice.lib.folder.FolderController
createZip(long) - Method in class org.jbei.ice.services.rest.ManuscriptResource
csvFilePath - Variable in class org.jbei.ice.lib.bulkupload.BulkCSVUpload
curate(List<DNAFeature>) - Method in class org.jbei.ice.lib.entry.sequence.annotation.Annotations: Curates a specified set of annotations.
curate(List<DNAFeature>) - Method in class org.jbei.ice.services.rest.AnnotationResource: Curate available annotations to include or exclude them from auto-annotation feature
Curation - Class in org.jbei.ice.lib.dto
Curation() - Constructor for class org.jbei.ice.lib.dto.Curation
currentSession() - Static method in class org.jbei.ice.storage.hibernate.HibernateRepository: Obtain the current hibernate Session.
currentSession() - Static method in class org.jbei.ice.storage.hibernate.HibernateUtil
CustomEmail - Class in org.jbei.ice.lib.email
CustomEmail() - Constructor for class org.jbei.ice.lib.email.CustomEmail
customExport(EntrySelection) - Method in class org.jbei.ice.services.rest.PartResource
CustomField - Class in org.jbei.ice.lib.dto.entry: User created key/value pair fields for an entry.
CustomField() - Constructor for class org.jbei.ice.lib.dto.entry.CustomField
CustomField(String, String) - Constructor for class org.jbei.ice.lib.dto.entry.CustomField
CustomField(long, String, String) - Constructor for class org.jbei.ice.lib.dto.entry.CustomField
CustomField(long, long, String, String) - Constructor for class org.jbei.ice.lib.dto.entry.CustomField
CustomFieldResource - Class in org.jbei.ice.services.rest: REST API for ICE custom fields (typically) associated with parts
CustomFieldResource() - Constructor for class org.jbei.ice.services.rest.CustomFieldResource
CustomFields - Class in org.jbei.ice.lib.dto.entry
CustomFields() - Constructor for class org.jbei.ice.lib.dto.entry.CustomFields
customize(EntrySelection) - Method in class org.jbei.ice.lib.entry.EntriesAsCSV

D

DAOException - Exception in org.jbei.ice.storage: Unchecked exception for DAO operations.
DAOException() - Constructor for exception org.jbei.ice.storage.DAOException
DAOException(String, Throwable) - Constructor for exception org.jbei.ice.storage.DAOException
DAOException(String) - Constructor for exception org.jbei.ice.storage.DAOException
DAOException(Throwable) - Constructor for exception org.jbei.ice.storage.DAOException
DAOFactory - Class in org.jbei.ice.storage
DAOFactory() - Constructor for class org.jbei.ice.storage.DAOFactory
DataModel - Interface in org.jbei.ice.storage
DBLINK_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
debug(String) - Static method in class org.jbei.ice.lib.common.logging.Logger
decodeKey(String) - Static method in class org.jbei.auth.hmac.HmacSignatureFactory: Convenience method to decode a key stored in Base64 encoding.
DEFAULT_NAMESPACE - Static variable in class org.jbei.ice.lib.entry.sequence.composers.formatters.AbstractFormatter
DefaultHmacSignature - Class in org.jbei.auth.hmac: TODO
DefaultHmacSignature(Mac, String) - Constructor for class org.jbei.auth.hmac.DefaultHmacSignature
DEFINITION_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
delete(String, long, long) - Method in class org.jbei.ice.lib.entry.attachment.Attachments
delete(long) - Method in class org.jbei.ice.lib.entry.EntryHistory
delete(String, long, long) - Method in class org.jbei.ice.lib.entry.sample.SampleService: Deletes specified sample for entry and all associated storage locations
delete(String, long, FolderType) - Method in class org.jbei.ice.lib.folder.FolderController: Deletes either a user folder or bulk upload (which is represented as a folder to the user)
delete(long) - Method in class org.jbei.ice.lib.manuscript.Manuscripts
delete(long) - Method in class org.jbei.ice.services.rest.CustomFieldResource
delete(String, String, String) - Method in class org.jbei.ice.services.rest.IceRestClient
delete(long) - Method in class org.jbei.ice.services.rest.ManuscriptResource
delete(long, long) - Method in class org.jbei.ice.services.rest.PartResource
delete(File, Attachment) - Method in class org.jbei.ice.storage.hibernate.dao.AttachmentDAO
delete(Path, ShotgunSequence) - Method in class org.jbei.ice.storage.hibernate.dao.ShotgunSequenceDAO
delete(Path, TraceSequence) - Method in class org.jbei.ice.storage.hibernate.dao.TraceSequenceDAO: Delete the trace file from the referenced directory and if that succeeds, deletes the given TraceSequence object in the database
delete(T) - Method in class org.jbei.ice.storage.hibernate.HibernateRepository: Deletes an DataModel from the database.
delete(T) - Method in interface org.jbei.ice.storage.IRepository
deleteAll() - Method in class org.jbei.ice.lib.entry.EntryHistory: Delete all available history for a specified entry Due to the destructive nature, it is required that the user be the owner or an administrator
deleteAll(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.AuditDAO
deleteApiKey(String, String, long) - Method in class org.jbei.ice.services.rest.ApiKeyResource: Delete a specified API key
deleteAttachment(String, long, long) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController
deleteAttachment(long, long) - Method in class org.jbei.ice.services.rest.PartResource
deleteDraftById(String, long) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController: Deletes a bulk import draft referenced by a unique identifier.
deleteEntry(String, long, long) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController
deleteEntry(long, long) - Method in class org.jbei.ice.services.rest.BulkUploadResource
deleteEntryAttachment(long, long) - Method in class org.jbei.ice.services.rest.BulkUploadResource
deleteEntrySequence(long, long) - Method in class org.jbei.ice.services.rest.BulkUploadResource
deleteField(String, long) - Method in class org.jbei.ice.lib.dto.entry.CustomFields: Deletes the custom field specified by the unique identifier in the parameter.
deleteFile(File, Attachment) - Method in class org.jbei.ice.storage.hibernate.dao.AttachmentDAO
deleteFolder(long, String) - Method in class org.jbei.ice.services.rest.FolderResource: Deletes the specified folder resource
deleteGroup(String, long) - Method in class org.jbei.ice.lib.group.GroupController
deleteInstanceFromMaster(String) - Method in class org.jbei.ice.lib.net.RemoteContact: Deletes this instance of ICE from the web of registries master list
deleteKey(long, String) - Method in class org.jbei.ice.lib.account.UserApiKeys: Deletes an api key
deleteLink(String, LinkType, long) - Method in class org.jbei.ice.services.rest.PartResource: Removes the linkId from id
deletePartExperiment(String, long) - Method in class org.jbei.ice.services.rest.PartResource
deletePermission(String, long, long) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController: Removes specified permission from bulk upload
deleteSample(UriInfo, long, long) - Method in class org.jbei.ice.services.rest.PartResource
deleteSampleRequest(long) - Method in class org.jbei.ice.services.rest.SampleResource
deleteSequence(String, long) - Method in class org.jbei.ice.lib.entry.sequence.SequenceController
deleteSequence(long) - Method in class org.jbei.ice.services.rest.PartResource
deleteSequence(Sequence, String) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceDAO: Delete the given Sequence object in the database.
deleteShotgunSequence(String, long, long) - Method in class org.jbei.ice.lib.entry.EntryController
deleteShotgunSequence(UriInfo, long, long) - Method in class org.jbei.ice.services.rest.PartResource
deleteStudy(long) - Method in class org.jbei.ice.lib.experiment.Experiments: Deletes a study associated with the specified part and with the specified unique identifier.
deleteToken() - Method in class org.jbei.ice.services.rest.AccessTokenResource: Invalidates the current session information.
deleteTrace(UriInfo, long, long) - Method in class org.jbei.ice.services.rest.PartResource
deleteTraceSequence(String, long, long) - Method in class org.jbei.ice.lib.entry.EntryController
deleteUserGroup(long) - Method in class org.jbei.ice.services.rest.GroupResource
demoteFolder(String, Folder) - Method in class org.jbei.ice.lib.folder.FolderController: Opposite of FolderController#demoteFolder(userId, long) Removes the folder from being a featured collections
depositor - Variable in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
description - Variable in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
description - Variable in class org.jbei.ice.storage.model.Group
destroy() - Method in class org.jbei.ice.servlet.filter.IceFilter
detectFormat(String) - Method in class org.jbei.ice.lib.entry.sequence.PartSequence: Attempts to detect the sequence format from the first line of a stream using the following heuristics If line starts with LOCUS then assumed to be a genbank file If line starts with > then assumed to be a fasta file If line starts with < then assumed to be an sbol file Anything else is assumed to be plain nucleotides
dirContext - Variable in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
disablePublicAccess(long) - Method in class org.jbei.ice.services.rest.FolderResource
disablePublicAccess(String) - Method in class org.jbei.ice.services.rest.PartResource
disablePublicReadAccess() - Method in class org.jbei.ice.lib.entry.EntryPermissions
disablePublicReadAccess() - Method in class org.jbei.ice.lib.folder.FolderPermissions
displayToEnum(String) - Static method in enum org.jbei.ice.lib.shared.StatusType
displayValueOf(String) - Static method in enum org.jbei.ice.lib.shared.StatusType
DNAFeature - Class in org.jbei.ice.lib.dto: Data transfer object for Sequence Features
DNAFeature() - Constructor for class org.jbei.ice.lib.dto.DNAFeature
DNAFeatureComparator - Class in org.jbei.ice.lib.bulkupload
DNAFeatureComparator() - Constructor for class org.jbei.ice.lib.bulkupload.DNAFeatureComparator
DNAFeatureLocation - Class in org.jbei.ice.lib.dto: Value object to hold AnnotationLocation data.
DNAFeatureLocation() - Constructor for class org.jbei.ice.lib.dto.DNAFeatureLocation
DNAFeatureLocation(int, int) - Constructor for class org.jbei.ice.lib.dto.DNAFeatureLocation
DNAFeatureNote - Class in org.jbei.ice.lib.dto: Value object to hold SequenceFeatureAttribute data.
DNAFeatureNote() - Constructor for class org.jbei.ice.lib.dto.DNAFeatureNote
DNAFeatureNote(String, String) - Constructor for class org.jbei.ice.lib.dto.DNAFeatureNote
DNAFeatures - Class in org.jbei.ice.lib.dto: Wrapper around a list of DNAFeatures that have the same label
DNAFeatures(String) - Constructor for class org.jbei.ice.lib.dto.DNAFeatures
DNASequence - Class in org.jbei.ice.lib.dto: Value object to hold DNA sequence.
DNASequence() - Constructor for class org.jbei.ice.lib.dto.DNASequence
DNASequence(String) - Constructor for class org.jbei.ice.lib.dto.DNASequence
dnaSequenceToSequence(DNASequence) - Static method in class org.jbei.ice.lib.entry.sequence.SequenceController: Create a Sequence object from an DNASequence object.
documentsAdded(long) - Method in class org.jbei.ice.lib.search.IndexerProgressMonitor
documentsBuilt(int) - Method in class org.jbei.ice.lib.search.IndexerProgressMonitor
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.jbei.ice.servlet.filter.IceFilter
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.jbei.ice.servlet.SBOLVisualDownloadServlet
doUpdate(String, Entry, PartData) - Method in class org.jbei.ice.lib.bulkupload.BulkEntryCreator
downloadCSV(List<String>, List<String>, EntrySelection) - Method in class org.jbei.ice.services.rest.FileResource: Extracts the csv information and writes it to the temp dir and returns the file uuid.
downloadSequence(long, String, long, String) - Method in class org.jbei.ice.services.rest.FileResource

E

EditMode - Enum in org.jbei.ice.lib.dto.bulkupload: Sheet edit mode that is used to determine the sheet view to show to users
email - Variable in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
Email - Class in org.jbei.ice.lib.email: Parent class for custom Email types used to send emails
Email() - Constructor for class org.jbei.ice.lib.email.Email
EmailFactory - Class in org.jbei.ice.lib.email: Factory for instantiation the specified email object for use
EmailFactory() - Constructor for class org.jbei.ice.lib.email.EmailFactory
enablePublicAccess(long) - Method in class org.jbei.ice.services.rest.FolderResource
enablePublicAccess(String) - Method in class org.jbei.ice.services.rest.PartResource
enablePublicReadAccess() - Method in class org.jbei.ice.lib.entry.EntryPermissions
enablePublicReadAccess() - Method in class org.jbei.ice.lib.folder.FolderPermissions
encodeKey(Key) - Static method in class org.jbei.auth.hmac.HmacSignatureFactory: Convenience method to encode a key to a Base64 String.
encrypt(String, String) - Method in class org.jbei.ice.lib.account.TokenHash
encryptNewUserPassword(String, String) - Static method in class org.jbei.ice.lib.account.AccountUtils
encryptPassword(String, String) - Static method in class org.jbei.ice.lib.account.AccountUtils: Return the encrypted version of the given password, using the salt from the settings file.
encryptSHA(String) - Static method in class org.jbei.ice.lib.utils.Utils: Calculate the SHA-1 hash of the given string.
END_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
entitiesLoaded(int) - Method in class org.jbei.ice.lib.search.IndexerProgressMonitor
Entries - Class in org.jbei.ice.lib.entry
Entries(String) - Constructor for class org.jbei.ice.lib.entry.Entries
EntriesAsCSV - Class in org.jbei.ice.lib.entry: Representation of a list of entries as a CSV file with option to include associated sequences
EntriesAsCSV(String, String...) - Constructor for class org.jbei.ice.lib.entry.EntriesAsCSV
entry - Variable in class org.jbei.ice.lib.parsers.AbstractParser
Entry - Class in org.jbei.ice.storage.model: Entry class is the most important class in gd-ice.
Entry() - Constructor for class org.jbei.ice.storage.model.Entry
EntryAuthorization - Class in org.jbei.ice.lib.entry
EntryAuthorization() - Constructor for class org.jbei.ice.lib.entry.EntryAuthorization
EntryBooleanPropertiesBridge - Class in org.jbei.ice.storage.hibernate.bridge
EntryBooleanPropertiesBridge() - Constructor for class org.jbei.ice.storage.hibernate.bridge.EntryBooleanPropertiesBridge
EntryController - Class in org.jbei.ice.lib.entry: ABI to manipulate Entrys.
EntryController() - Constructor for class org.jbei.ice.lib.entry.EntryController
EntryCreator - Class in org.jbei.ice.lib.entry
EntryCreator() - Constructor for class org.jbei.ice.lib.entry.EntryCreator
entryDAO - Variable in class org.jbei.ice.lib.entry.HasEntry
EntryDAO - Class in org.jbei.ice.storage.hibernate.dao: DAO to manipulate Entry objects in the database.
EntryDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.EntryDAO
EntryFactory - Class in org.jbei.ice.lib.entry: Factory class for creating new entry object depending on type
EntryFactory() - Constructor for class org.jbei.ice.lib.entry.EntryFactory
EntryField - Enum in org.jbei.ice.lib.dto.entry: Represents the complete list of fields for parts.
EntryFields - Class in org.jbei.ice.lib.entry
EntryFields() - Constructor for class org.jbei.ice.lib.entry.EntryFields
entryFields(List<EntryType>) - Static method in class org.jbei.ice.lib.search.filter.SearchFieldFactory
entryFieldToValue(Entry, EntryField) - Static method in class org.jbei.ice.lib.entry.EntryUtil
entryFieldToValue(PartData, EntryField) - Static method in class org.jbei.ice.lib.entry.PartDataUtil
EntryFolders - Class in org.jbei.ice.lib.entry: Folders that an entry is contained in
EntryFolders(String, String) - Constructor for class org.jbei.ice.lib.entry.EntryFolders
EntryHasFilterFactory - Class in org.jbei.ice.storage.hibernate.filter
EntryHasFilterFactory() - Constructor for class org.jbei.ice.storage.hibernate.filter.EntryHasFilterFactory
EntryHeaderValue - Class in org.jbei.ice.lib.bulkupload
EntryHeaderValue(boolean, EntryField) - Constructor for class org.jbei.ice.lib.bulkupload.EntryHeaderValue
EntryHistory - Class in org.jbei.ice.lib.entry: History information for a specified entry
EntryHistory(String, long) - Constructor for class org.jbei.ice.lib.entry.EntryHistory
EntryLinks - Class in org.jbei.ice.lib.entry: Represents a main part and the hierarchical links that it is involved in.
EntryLinks(String, String) - Constructor for class org.jbei.ice.lib.entry.EntryLinks
EntryPermissions - Class in org.jbei.ice.lib.entry: Permissions associated with a specified entry
EntryPermissions(String, String) - Constructor for class org.jbei.ice.lib.entry.EntryPermissions
EntryPermissionTask - Class in org.jbei.ice.lib.entry: Task to update the permissions for a provided list of entries
EntryPermissionTask(String, List<Long>, List<AccessPermission>, boolean) - Constructor for class org.jbei.ice.lib.entry.EntryPermissionTask
EntrySecurityFilterFactory - Class in org.jbei.ice.storage.hibernate.filter
EntrySecurityFilterFactory() - Constructor for class org.jbei.ice.storage.hibernate.filter.EntrySecurityFilterFactory
EntrySelection - Class in org.jbei.ice.lib.entry: Represents entry selection in a specific context and by type (e.g.
EntrySelection() - Constructor for class org.jbei.ice.lib.entry.EntrySelection
EntrySelectionType - Enum in org.jbei.ice.lib.entry: Represents the context that entries can be selected from.
EntryType - Enum in org.jbei.ice.lib.dto.entry
EntryUtil - Class in org.jbei.ice.lib.entry: Utility class for operating on entries
EntryUtil() - Constructor for class org.jbei.ice.lib.entry.EntryUtil
equals(AccessPermission) - Method in class org.jbei.ice.lib.dto.access.AccessPermission
equals(Object) - Method in class org.jbei.ice.storage.model.Account
equals(Object) - Method in class org.jbei.ice.storage.model.Entry
error(String) - Static method in class org.jbei.ice.lib.common.logging.Logger
error(String, Throwable) - Static method in class org.jbei.ice.lib.common.logging.Logger
error(Throwable) - Static method in class org.jbei.ice.lib.common.logging.Logger
ErrorResponse - Class in org.jbei.ice.services.rest
ErrorResponse() - Constructor for class org.jbei.ice.services.rest.ErrorResponse
execute() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadDeleteTask
execute() - Method in class org.jbei.ice.lib.entry.EntryPermissionTask
execute() - Method in class org.jbei.ice.lib.entry.sequence.annotation.AutoAnnotationBlastDbBuildTask
execute() - Method in class org.jbei.ice.lib.executor.Task
execute() - Method in class org.jbei.ice.lib.executor.TransferTask
execute() - Method in class org.jbei.ice.lib.net.WebOfRegistriesTask
execute() - Method in class org.jbei.ice.lib.search.blast.RebuildBlastIndexTask
execute() - Method in class org.jbei.ice.lib.search.RebuildLuceneIndexTask
execute() - Method in class org.jbei.ice.lib.search.WebSearch.SearchTask
executeSearch(String, HashMap<String, QueryType>, SearchQuery, HashMap<String, SearchResult>) - Method in class org.jbei.ice.storage.hibernate.search.HibernateSearch
executeSearchNoTerms(String, HashMap<String, SearchResult>, SearchQuery) - Method in class org.jbei.ice.storage.hibernate.search.HibernateSearch
expectAdmin(String) - Method in class org.jbei.ice.lib.access.Authorization
EXPECTED_SIGNATURE - Static variable in class org.jbei.ice.services.rest.AuthenticationInterceptor: Property/Attribute name for mapping the expected value of the generated signature.
expectRead(String, T) - Method in class org.jbei.ice.lib.access.Authorization
expectWrite(String, T) - Method in class org.jbei.ice.lib.access.Authorization
Experiment - Class in org.jbei.ice.storage.model: Storage entity for experimental data
Experiment() - Constructor for class org.jbei.ice.storage.model.Experiment
ExperimentDAO - Class in org.jbei.ice.storage.hibernate.dao
ExperimentDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.ExperimentDAO
Experiments - Class in org.jbei.ice.lib.experiment: Links to experimental data associated with entries
Experiments(String, String) - Constructor for class org.jbei.ice.lib.experiment.Experiments
ExtensionToMimeType - Class in org.jbei.ice.services.rest: Helper class which provides utility methods for converting extensions to mime types
ExtensionToMimeType() - Constructor for class org.jbei.ice.services.rest.ExtensionToMimeType

F

FastaFormatter - Class in org.jbei.ice.lib.entry.sequence.composers.formatters: Formatter for creating a FASTA formatted output.
FastaFormatter() - Constructor for class org.jbei.ice.lib.entry.sequence.composers.formatters.FastaFormatter
FastaParser - Class in org.jbei.ice.lib.parsers.fasta: Parse FASTA files.
FastaParser() - Constructor for class org.jbei.ice.lib.parsers.fasta.FastaParser
Feature - Class in org.jbei.ice.storage.model: Represents a unique sequence annotation known to this instance of gd-ice.
Feature() - Constructor for class org.jbei.ice.storage.model.Feature
Feature(String, String, String, String) - Constructor for class org.jbei.ice.storage.model.Feature
FeatureCurationModel - Class in org.jbei.ice.storage.model
FeatureCurationModel() - Constructor for class org.jbei.ice.storage.model.FeatureCurationModel
FeatureCurationModelDAO - Class in org.jbei.ice.storage.hibernate.dao
FeatureCurationModelDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.FeatureCurationModelDAO
FeatureDAO - Class in org.jbei.ice.storage.hibernate.dao: Hibernate data accessor object for Features
FeatureDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.FeatureDAO
FeaturedDNASequence - Class in org.jbei.ice.lib.dto: Value object to hold DNAFeatures and some genbank file information.
FeaturedDNASequence() - Constructor for class org.jbei.ice.lib.dto.FeaturedDNASequence
FeaturedDNASequence(String, List<DNAFeature>) - Constructor for class org.jbei.ice.lib.dto.FeaturedDNASequence
FeaturedDNASequence(String, String, boolean, List<DNAFeature>, String) - Constructor for class org.jbei.ice.lib.dto.FeaturedDNASequence
FEATURES_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
FeaturesTag - Class in org.jbei.ice.lib.parsers.genbank
FeaturesTag() - Constructor for class org.jbei.ice.lib.parsers.genbank.FeaturesTag
FieldFilter - Class in org.jbei.ice.lib.dto.search: Filter a specified entry field
FieldFilter() - Constructor for class org.jbei.ice.lib.dto.search.FieldFilter
FileBulkUpload - Class in org.jbei.ice.lib.bulkupload: Processes bulk uploads.
FileBulkUpload(String, Path, EntryType) - Constructor for class org.jbei.ice.lib.bulkupload.FileBulkUpload
fileId - Variable in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
filename - Variable in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
fileName - Variable in class org.jbei.ice.lib.parsers.AbstractParser
FileResource - Class in org.jbei.ice.services.rest: Resource for accessing files both locally and remotely
FileResource() - Constructor for class org.jbei.ice.services.rest.FileResource
filter(int, int, String) - Method in class org.jbei.ice.lib.entry.sequence.annotation.Annotations
filter(String, int) - Method in class org.jbei.ice.lib.folder.Folders
filter(ContainerRequestContext) - Method in class org.jbei.ice.services.rest.AuthenticationInterceptor
filter(ContainerRequestContext) - Method in class org.jbei.ice.services.rest.IceRequestFilter
filter(ContainerRequestContext, ContainerResponseContext) - Method in class org.jbei.ice.services.rest.IceResponseFilter
filter(List<CustomField>) - Method in class org.jbei.ice.storage.hibernate.dao.ParameterDAO
filterAccount(String, String, int) - Method in class org.jbei.ice.lib.account.Accounts
filterBlastResults(String, int, int, SearchQuery, HashMap<String, SearchResult>) - Method in class org.jbei.ice.storage.hibernate.search.HibernateSearch: Intended to be called after running a blast search to filter the results.
filterByName(String, int) - Method in class org.jbei.ice.storage.hibernate.dao.FolderDAO
filterByUserId(String, List<Long>) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
filterInput(InputStream) - Method in class org.jbei.auth.hmac.DefaultHmacSignature
filterInput(InputStream) - Method in interface org.jbei.auth.hmac.HmacSignature
filterOutput(OutputStream) - Method in class org.jbei.auth.hmac.DefaultHmacSignature
filterOutput(OutputStream) - Method in interface org.jbei.auth.hmac.HmacSignature
Folder - Class in org.jbei.ice.storage.model: Encapsulates the notion of a collection of Entrys Each folder has an owner.
Folder() - Constructor for class org.jbei.ice.storage.model.Folder
Folder(String) - Constructor for class org.jbei.ice.storage.model.Folder
FolderAuthorization - Class in org.jbei.ice.lib.dto.folder: Authorization specific to folder objects
FolderAuthorization() - Constructor for class org.jbei.ice.lib.dto.folder.FolderAuthorization
FolderContents - Class in org.jbei.ice.lib.folder: Contents of a folder which could be other folders or biological parts (entries)
FolderContents() - Constructor for class org.jbei.ice.lib.folder.FolderContents
FolderController - Class in org.jbei.ice.lib.folder
FolderController() - Constructor for class org.jbei.ice.lib.folder.FolderController
FolderDAO - Class in org.jbei.ice.storage.hibernate.dao: Manipulate Folder objects in the database.
FolderDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.FolderDAO
FolderDetails - Class in org.jbei.ice.lib.dto.folder: Folder Transfer Object
FolderDetails() - Constructor for class org.jbei.ice.lib.dto.folder.FolderDetails
FolderDetails(long, String) - Constructor for class org.jbei.ice.lib.dto.folder.FolderDetails
FolderPermissions - Class in org.jbei.ice.lib.folder: Represents permissions for a specified folder with methods to manipulate them
FolderPermissions(String, long) - Constructor for class org.jbei.ice.lib.folder.FolderPermissions
FolderResource - Class in org.jbei.ice.services.rest: Rest resource for dealing with folders.
FolderResource() - Constructor for class org.jbei.ice.services.rest.FolderResource
Folders - Class in org.jbei.ice.lib.folder: ICE Folders
Folders(String) - Constructor for class org.jbei.ice.lib.folder.Folders
FolderType - Enum in org.jbei.ice.lib.dto.folder: Type of folder sharing, which indicates where it will be displayed and the kinds of operations that are permitted
format(Sequence, OutputStream) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.AbstractFormatter
format(Sequence, OutputStream) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.FastaFormatter
format(Sequence, OutputStream) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter
format(Sequence, OutputStream) - Method in interface org.jbei.ice.lib.entry.sequence.composers.formatters.IFormatter: Interface method to take a Sequence object and output the formatted file to the OutputStream.
format(Sequence, OutputStream) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.SBOL2Formatter
format(Sequence, OutputStream) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.SBOLFormatter
FormatterException - Exception in org.jbei.ice.lib.entry.sequence.composers.formatters: Exception class for Formatters.
FormatterException() - Constructor for exception org.jbei.ice.lib.entry.sequence.composers.formatters.FormatterException: Constructor.
FormatterException(String) - Constructor for exception org.jbei.ice.lib.entry.sequence.composers.formatters.FormatterException: Create a new FormatterException using the message.
FormatterException(String, Throwable) - Constructor for exception org.jbei.ice.lib.entry.sequence.composers.formatters.FormatterException: Create a new FormatterException using the message and a Throwable.
FormatterException(Throwable) - Constructor for exception org.jbei.ice.lib.entry.sequence.composers.formatters.FormatterException: Create a new FormatterException using a Throwable.
fromDTO(AccountTransfer) - Static method in class org.jbei.ice.lib.account.AccountUtils
fromString(String) - Static method in enum org.jbei.ice.lib.dto.bulkupload.SampleField
fromString(String) - Static method in enum org.jbei.ice.lib.dto.entry.EntryField
fromString(String) - Static method in enum org.jbei.ice.lib.dto.entry.Generation
fromString(String) - Static method in enum org.jbei.ice.lib.dto.entry.PlantType
fromString(String) - Static method in enum org.jbei.ice.lib.dto.user.PreferenceKey
fromString(String) - Static method in enum org.jbei.ice.lib.entry.sequence.SequenceFormat
fullDelete(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO

G

GenbankFormatter - Class in org.jbei.ice.lib.entry.sequence.composers.formatters: Formatter for the Genbank file format.
GenbankFormatter(String) - Constructor for class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter: Constructor using only the name.
GenbankFormatter(String, String, int, double) - Constructor for class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter: Constructor using the complete header fields.
GenbankLocation - Class in org.jbei.ice.lib.parsers.genbank: Represent a contiguous Genbank location, including a single base pair.
GenbankLocation(int, int) - Constructor for class org.jbei.ice.lib.parsers.genbank.GenbankLocation
GenBankParser - Class in org.jbei.ice.lib.parsers.genbank: Genbank parser and generator.
GenBankParser() - Constructor for class org.jbei.ice.lib.parsers.genbank.GenBankParser
GeneralParser - Class in org.jbei.ice.lib.parsers: Helper class to set up a list of parsers to iterate over, to try to parse the input file.
GeneralParser() - Constructor for class org.jbei.ice.lib.parsers.GeneralParser
generate(long, boolean) - Method in class org.jbei.ice.lib.entry.sequence.annotation.Annotations: Auto generate annotations for specified entry
generate(FeaturedDNASequence) - Method in class org.jbei.ice.lib.entry.sequence.annotation.Annotations: Using existing and potentially curated annotations on this ICE instance, this generates matching features for the passed sequence
generateCSVFile(String, ArrayList<Long>) - Method in class org.jbei.ice.lib.entry.sample.RequestRetriever
generateNextStrainNameForEntry(Entry, String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
generatePigeonScript(Sequence) - Static method in class org.jbei.ice.lib.entry.sequence.composers.pigeon.PigeonSBOLv
generatePigeonVisual(Sequence) - Static method in class org.jbei.ice.lib.entry.sequence.composers.pigeon.PigeonSBOLv
generateQueriesForType(FullTextSession, HashSet<String>, BooleanQuery.Builder, String, QueryType, BioSafetyOption) - Method in class org.jbei.ice.storage.hibernate.search.HibernateSearch
generateRandomToken() - Method in class org.jbei.ice.lib.account.TokenHash
generateRandomToken(int) - Method in class org.jbei.ice.lib.account.TokenHash
generateSalt() - Method in class org.jbei.ice.lib.account.TokenHash: Uses SecureRandom to generate a random bytes of size 32 which is converted to a string containing a lexical base64 representation
generateSaltForUserAccount() - Static method in class org.jbei.ice.lib.utils.Utils
generateSignature() - Method in class org.jbei.auth.hmac.DefaultHmacSignature
generateSignature() - Method in interface org.jbei.auth.hmac.HmacSignature
generateToken() - Static method in class org.jbei.ice.lib.utils.Utils
generateUUID() - Static method in class org.jbei.ice.lib.utils.Utils: Generate a random UUID.
generateZip(long) - Method in class org.jbei.ice.lib.manuscript.Manuscripts
Generation - Enum in org.jbei.ice.lib.dto.entry: Arabidopsis seed generation options
get(String, long) - Method in class org.jbei.ice.lib.access.Authorization
get(long, String) - Method in class org.jbei.ice.lib.dto.web.RemoteUsers
get(int, int, boolean, String) - Method in class org.jbei.ice.lib.entry.EntryHistory
get(LinkType) - Method in class org.jbei.ice.lib.entry.EntryLinks: Retrieves entry links that are parents or children depending on specified type
get(EntryType) - Method in class org.jbei.ice.lib.entry.PartDefaults: Retrieves and sets the default values for the entry.
get(int, int, String) - Method in class org.jbei.ice.lib.entry.sequence.annotation.Annotations: Retrieves list of annotations that are available
get() - Method in class org.jbei.ice.lib.entry.sequence.PartSequence
get() - Method in class org.jbei.ice.lib.folder.FolderPermissions: Retrieves list of available folder permissions (both local and remote)
get(long) - Method in class org.jbei.ice.lib.group.Groups: Retrieves groups that user is either a member of.
get(GroupType, int, int) - Method in class org.jbei.ice.lib.group.Groups
get(String, boolean, int, int, String) - Method in class org.jbei.ice.lib.manuscript.Manuscripts
get(int, int) - Method in class org.jbei.ice.lib.message.Messages
get(long) - Method in class org.jbei.ice.lib.message.Messages
get(String) - Method in class org.jbei.ice.lib.net.RemoteSequence
get(String) - Method in class org.jbei.ice.lib.net.WebPartners
get(String, String) - Method in class org.jbei.ice.lib.net.WebPartners: Retrieve a partner based on partner token and unique identifier This is mostly intended to validate the token associated with url
get() - Method in class org.jbei.ice.services.rest.AccessTokenResource: Retrieve account information for user referenced by session id
get() - Method in class org.jbei.ice.services.rest.ConfigResource: Retrieves list of system settings available
get(long) - Method in class org.jbei.ice.services.rest.CustomFieldResource
get(String, String, Class<T>, Map<String, Object>) - Method in class org.jbei.ice.services.rest.IceRestClient
get(int, int) - Method in class org.jbei.ice.services.rest.MessageResource
get(long) - Method in class org.jbei.ice.services.rest.MessageResource
get(String) - Method in class org.jbei.ice.services.rest.PartResource: Retrieves the defaults for the requested entry types.
get(String, String, Class<T>, Map<String, Object>) - Method in class org.jbei.ice.services.rest.RestClient
get(int, int, String, boolean, String) - Method in class org.jbei.ice.services.rest.UserResource: Retrieves list of users that are available to user making request.
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.AccountDAO: Retrieve Account by id from the database.
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.ApiKeyDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.AttachmentDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.AuditDAO: Retrieves audit referenced by unique identifier
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.BulkUploadDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.CommentDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.ConfigurationDAO
get(ConfigurationKey) - Method in class org.jbei.ice.storage.hibernate.dao.ConfigurationDAO: Retrieve the Configuration object with the given ConfigurationKey.
get(String) - Method in class org.jbei.ice.storage.hibernate.dao.ConfigurationDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO: Retrieve an Entry object from the database by id.
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.ExperimentDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.FeatureCurationModelDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.FeatureDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.FolderDAO: Retrieves stored folder by locally unique identifier
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.GroupDAO: Retrieve Group object from the database by its id.
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.ManuscriptModelDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.MessageDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.ParameterDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.PreferencesDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.RemoteAccessModelDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.RemoteClientModelDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.RemotePartnerDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.RemoteShareModelDAO
get(String, RemotePartner, Folder) - Method in class org.jbei.ice.storage.hibernate.dao.RemoteShareModelDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.RequestDAO
get(int, int, String, boolean, SampleRequestStatus, String) - Method in class org.jbei.ice.storage.hibernate.dao.RequestDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.SampleDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.SelectionMarkerDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceFeatureDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.ShotgunSequenceDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.StorageDAO
get(long) - Method in class org.jbei.ice.storage.hibernate.dao.TraceSequenceDAO
get(Class<T>, long) - Method in class org.jbei.ice.storage.hibernate.HibernateRepository: Retrieve an DataModel object from the database by Class and database id.
get(long) - Method in interface org.jbei.ice.storage.IRepository
getAbbrev() - Method in enum org.jbei.ice.lib.dto.AuditType
getAccessPermissions() - Method in class org.jbei.ice.lib.dto.entry.PartData
getAccessPermissions() - Method in class org.jbei.ice.lib.folder.AbstractFolder
getAccount(String) - Method in class org.jbei.ice.lib.access.Authorization
getAccount(String, String) - Method in class org.jbei.ice.lib.account.Accounts
getAccount() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
getAccount() - Method in class org.jbei.ice.lib.dto.access.AccessKey
getAccount() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
getAccount() - Method in class org.jbei.ice.lib.dto.History
getAccount(String) - Method in class org.jbei.ice.lib.folder.FolderController
getAccount() - Method in class org.jbei.ice.storage.model.AccountPreferences
getAccount() - Method in class org.jbei.ice.storage.model.BulkUpload
getAccount() - Method in class org.jbei.ice.storage.model.Comment
getAccount() - Method in class org.jbei.ice.storage.model.Permission
getAccount() - Method in class org.jbei.ice.storage.model.Preference
getAccount() - Method in class org.jbei.ice.storage.model.Request
getAccountBySessionKey(String) - Method in class org.jbei.ice.lib.account.AccountController
getAccountDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getAccountId(String) - Method in class org.jbei.ice.lib.account.AccountController
getAccountPreferences(Account, List<PreferenceKey>) - Method in class org.jbei.ice.storage.hibernate.dao.PreferencesDAO
getAccountRequests(Account, SampleRequestStatus, int, int, String, boolean) - Method in class org.jbei.ice.storage.hibernate.dao.RequestDAO
getAccounts() - Method in class org.jbei.ice.lib.dto.message.MessageInfo
getAccounts(int, int, String, boolean, String) - Method in class org.jbei.ice.storage.hibernate.dao.AccountDAO: Retrieves list of pageable accounts, matching the parameter values
getAccountsCount(String) - Method in class org.jbei.ice.storage.hibernate.dao.AccountDAO: Retrieves maximum number of distinct accounts available and, if specified, whose firstName, lastName and email fields match the filter token.
getAccountTransfer() - Method in class org.jbei.ice.lib.dto.comment.UserComment
getAccountType() - Method in class org.jbei.ice.lib.account.AccountTransfer
getAction() - Method in class org.jbei.ice.lib.dto.History
getAction() - Method in class org.jbei.ice.storage.model.Audit
getAdded() - Method in class org.jbei.ice.storage.model.RemotePartner
getAddTime() - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
getAlias() - Method in class org.jbei.ice.lib.dto.entry.PartData
getAlias() - Method in class org.jbei.ice.storage.model.Entry
getAlignment() - Method in class org.jbei.ice.lib.dto.search.SearchResult
getAll() - Method in class org.jbei.ice.lib.entry.sequence.TraceSequences: Retrieves all the trace sequence files, for the specified part, and places them in a zip file
getAllApiKeys(String, int, int, boolean) - Method in class org.jbei.ice.storage.hibernate.dao.ApiKeyDAO: Retrieves all available api keys restricted by the paging parameters
getAllCounts() - Method in class org.jbei.ice.lib.folder.collection.Collections
getAllEntryCount(String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
getAllGroups(Account) - Method in class org.jbei.ice.lib.group.GroupController: retrieves all parent groups for any group in the set.
getAllPublicGroupsForAccount(Account) - Method in class org.jbei.ice.lib.group.GroupController
getAllTraces(long, String) - Method in class org.jbei.ice.services.rest.PartResource
getAndFilterFolderPermissions(String, Folder) - Method in class org.jbei.ice.lib.folder.FolderContents: The permission(s) enabling the share for user is(are) included.
getAnnotationLocations() - Method in class org.jbei.ice.storage.model.SequenceFeature
getAnnotations(SequenceFeature) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter: Convert SequenceFeature into a RichAnnotation.
getAnnotationsForSequence(FeaturedDNASequence) - Method in class org.jbei.ice.services.rest.AnnotationResource: Generates annotations for the passed sequence
getAnnotationType() - Method in class org.jbei.ice.lib.dto.DNAFeature
getAnnotationType() - Method in class org.jbei.ice.storage.model.SequenceFeature
getApiKey() - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
getApiKey() - Method in class org.jbei.ice.storage.model.RemotePartner
getApiKeyDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getApiKeys(int, int, boolean, String, boolean) - Method in class org.jbei.ice.services.rest.ApiKeyResource: retrieves list of api keys created by user
getApiKeysCount(String) - Method in class org.jbei.ice.storage.hibernate.dao.ApiKeyDAO: Retrieves the maximum number of api keys that can be retrieved for a specified user
getApiKeysForUser(String, String, int, int, boolean) - Method in class org.jbei.ice.storage.hibernate.dao.ApiKeyDAO: Retrieves list of available api keys for specified user, using the paging parameters
getArabidopsisSeedData() - Method in class org.jbei.ice.lib.dto.entry.PartData
getArticle() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
getArticleId() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
getAsset(String) - Method in class org.jbei.ice.services.rest.FileResource
getAssetName() - Method in class org.jbei.ice.lib.config.SiteSettings
getAttachment(String) - Method in class org.jbei.ice.services.rest.FileResource
getAttachmentByFileId(String, String) - Method in class org.jbei.ice.lib.entry.attachment.Attachments: Retrieves a previously uploaded attachment to an entry by it's unique file identifier This file identifier is assigned on upload
getAttachmentDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getAttachmentList(String, long, String) - Method in class org.jbei.ice.lib.net.RemoteContact
getAttachments() - Method in class org.jbei.ice.lib.dto.entry.PartData
getAttachments(long, long) - Method in class org.jbei.ice.services.rest.PartnerResource
getAttachments(long) - Method in class org.jbei.ice.services.rest.PartResource
getAttachments(long, long) - Method in class org.jbei.ice.services.rest.WebResource
getAttachments() - Method in class org.jbei.ice.storage.model.Entry
getAttachments(List<Attachment>) - Static method in class org.jbei.ice.storage.ModelToInfoFactory
getAuditDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getAuditsForEntry(Entry, int, int, boolean, String) - Method in class org.jbei.ice.storage.hibernate.dao.AuditDAO
getAuditsForEntryCount(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.AuditDAO
getAuthenticatedContext(String, String) - Method in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication: Get authenticated context from the ldap server.
getAuthenticationToken() - Method in class org.jbei.ice.storage.model.RemotePartner
getAuthorFirstName() - Method in class org.jbei.ice.lib.manuscript.Manuscript
getAuthorFirstName() - Method in class org.jbei.ice.storage.model.ManuscriptModel
getAuthorLastName() - Method in class org.jbei.ice.lib.manuscript.Manuscript
getAuthorLastName() - Method in class org.jbei.ice.storage.model.ManuscriptModel
getAutoAnnotations(long, boolean) - Method in class org.jbei.ice.services.rest.PartResource
getAutoCompleteForAvailableAccounts(String, int) - Method in class org.jbei.ice.services.rest.UserResource: Retrieves (up to specified limit), the list of users that match the value
getAutoCompleteForAvailableFolders(String, int) - Method in class org.jbei.ice.services.rest.FolderResource
getAvailable() - Method in class org.jbei.ice.lib.folder.CollectionCounts
getAvailableAccounts(String, int, int, boolean, String, String) - Method in class org.jbei.ice.lib.account.Accounts: Retrieves the user records available.
getAvailableEntries(ColumnField, boolean, int, int, String) - Method in class org.jbei.ice.lib.folder.collection.CollectionEntries: Retrieves entries available to user.
getAvailableFolders(String) - Method in class org.jbei.ice.lib.folder.FolderController: Retrieves folders that have been "promoted" by an administrator to imply that they are to be made available to everyone on the site
getAvailableFolders() - Method in class org.jbei.ice.lib.net.RemoteFolders
getBackbone() - Method in class org.jbei.ice.lib.dto.entry.PlasmidData
getBackbone() - Method in class org.jbei.ice.storage.model.Plasmid
getBasecalls() - Method in class org.jbei.ice.lib.parsers.abi.ABITrace: Returns an int[] array that represents the basecalls - each int in the array corresponds to an x-coordinate point in the graph that is a peak (a base location).
getBasePairCount() - Method in class org.jbei.ice.lib.dto.entry.PartData
getBioSafetyLevel() - Method in class org.jbei.ice.lib.dto.entry.PartData
getBioSafetyLevel() - Method in class org.jbei.ice.storage.model.Entry
getBioSafetyOption() - Method in class org.jbei.ice.lib.dto.search.SearchQuery
getBlastProgram() - Method in class org.jbei.ice.lib.dto.search.BlastQuery
getBlastQuery() - Method in class org.jbei.ice.lib.dto.search.SearchQuery
getBody() - Method in class org.jbei.ice.storage.model.Comment
getBuilder() - Method in class org.jbei.ice.storage.hibernate.HibernateRepository
getBulkImport(String, long, int, int) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController: Retrieves bulk import and entries associated with it that are referenced by the id in the parameter.
getBulkUpload() - Method in class org.jbei.ice.lib.folder.CollectionCounts
getBulkUploadDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getBulkUploadDrafts(String) - Method in class org.jbei.ice.lib.folder.FolderController
getBulkUploadFolder(long, int, int) - Method in class org.jbei.ice.lib.folder.collection.Collection: Retrieves bulk import and entries associated with it that are referenced by the id in the parameter.
getBulkUploadId() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadAutoUpdate
getByClientId(String) - Method in class org.jbei.ice.storage.hibernate.dao.ApiKeyDAO: Retrieves an api key by client id.
getByEmail(String) - Method in class org.jbei.ice.lib.account.AccountController: Retrieve Account by user id.
getByEmail(String) - Method in class org.jbei.ice.storage.hibernate.dao.AccountDAO: Retrieve an Account by the email field.
getByEntry(String, long) - Method in class org.jbei.ice.lib.entry.attachment.Attachments
getByEntry(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.AttachmentDAO: Retrieve all Attachments associated with the given Entry.
getByEntry(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceDAO: Retrieve the Sequence object associated with the given Entry object.
getByEntry(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.ShotgunSequenceDAO
getByEntry(Entry, int, int) - Method in class org.jbei.ice.storage.hibernate.dao.TraceSequenceDAO: Retrieve all TraceSequence objects associated with the given Entry object using the paging parameters, ordered by creation time in ascending order
getByFeature(Feature) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceFeatureDAO
getByFileId(String) - Method in class org.jbei.ice.storage.hibernate.dao.AttachmentDAO: Retrieves attachment referenced by a unique file identifier
getByFileId(String) - Method in class org.jbei.ice.storage.hibernate.dao.ShotgunSequenceDAO
getByFileId(String) - Method in class org.jbei.ice.storage.hibernate.dao.TraceSequenceDAO: Retrieve the TraceSequence object by its fileId.
getByFolder(Account, Folder) - Method in class org.jbei.ice.storage.hibernate.dao.RemoteAccessModelDAO
getByFolder(Folder) - Method in class org.jbei.ice.storage.hibernate.dao.RemoteShareModelDAO
getByName(String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO: Retrieve an Entry by it's name.
getByPartNumber(String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO: Retrieve an Entry by it's part number.
getByRecordId(String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO: Retrieve an Entry object in the database by recordId field.
getBytes() - Method in class org.jbei.ice.lib.entry.sequence.ByteArrayWrapper
getByUrl(String) - Method in class org.jbei.ice.storage.hibernate.dao.ExperimentDAO
getByUrl(String) - Method in class org.jbei.ice.storage.hibernate.dao.RemotePartnerDAO: Retrieves remote partners by url.
getByUUID(String) - Method in class org.jbei.ice.storage.hibernate.dao.GroupDAO: Retrieve Group object from the database by its uuid.
getByVisibility(String, Visibility, ColumnField, boolean, int, int, String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
getByVisibilityCount(String, Visibility, String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
getByVisibilityCount(Visibility) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
getCanEditFolders() - Method in class org.jbei.ice.lib.folder.Folders: Retrieves list of folders that specified user has write privileges on
getCanEditFolders(Account, Set<Group>) - Method in class org.jbei.ice.storage.hibernate.dao.FolderDAO: Retrieves folders that the specified account owns, or has write privileges on based on the permissions
getCanReadEntries(Account, List<Group>, List<Long>) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO: Filters the given list, removing those that the specified account does not have read privileges on // todo : this doesn't check permissions from folder (get list of all folders entries are in)
getChild() - Method in class org.jbei.ice.lib.dto.StorageLocation
getChildren() - Method in class org.jbei.ice.lib.dto.group.UserGroup
getChildren() - Method in class org.jbei.ice.lib.entry.EntryLinks: Retrieves the list of children this entry, that the user has read permissions
getChildren() - Method in class org.jbei.ice.storage.model.Storage: Make sure to get a copy from database before calling this method
getCircular() - Method in class org.jbei.ice.lib.dto.entry.PlasmidData
getCircular() - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter
getCircular() - Method in class org.jbei.ice.storage.model.Plasmid
getClasses() - Method in class org.jbei.ice.services.rest.multipart.IceApplication
getClient() - Method in class org.jbei.ice.storage.model.RemoteShareModel
getClientCount(Group) - Method in class org.jbei.ice.storage.hibernate.dao.RemoteClientModelDAO: Retrieves number of clients for the specified group
getClientId() - Method in class org.jbei.ice.lib.dto.access.AccessKey
getClientId() - Method in class org.jbei.ice.storage.model.ApiKey
getClientsForGroup(Group) - Method in class org.jbei.ice.storage.hibernate.dao.RemoteClientModelDAO: Retrieves clients belonging to specified group
getCollectionEntries(String, boolean, EntryType) - Method in class org.jbei.ice.lib.entry.Entries
getCollectionFolder(CollectionType, long) - Method in class org.jbei.ice.services.rest.CollectionResource: Retrieves the specified collection type's folder Since the folder is intended to be retrieved from a specified resource's context, this may not always return a result even the folder with the specified id exists
getCollectionStats() - Method in class org.jbei.ice.services.rest.CollectionResource: Retrieve the statistics (counts) of all the collections for the specified user
getCollectionSubFolders(CollectionType) - Method in class org.jbei.ice.services.rest.CollectionResource
getCommentCount() - Method in class org.jbei.ice.lib.dto.entry.PartStatistics
getCommentCount(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.CommentDAO
getCommentDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getCommentDate() - Method in class org.jbei.ice.lib.dto.comment.UserComment
getComments() - Method in class org.jbei.ice.lib.dto.sample.PartSample
getComments() - Method in class org.jbei.ice.lib.net.RemoteEntry
getComments(long) - Method in class org.jbei.ice.services.rest.PartResource
getComments() - Method in class org.jbei.ice.storage.model.Sample
getCommon(PartData, Entry) - Static method in class org.jbei.ice.storage.ModelToInfoFactory
getCommonFields() - Static method in class org.jbei.ice.lib.bulkupload.BulkCSVUploadHeaders
getCommonFields() - Static method in class org.jbei.ice.lib.entry.EntryFields
getCommonFields() - Static method in class org.jbei.ice.lib.search.filter.SearchFieldFactory
getCommonFieldValues(Entry, EntryField) - Static method in class org.jbei.ice.lib.entry.EntryUtil
getCommonFieldValues(PartData, EntryField) - Static method in class org.jbei.ice.lib.entry.PartDataUtil
getComponentUri() - Method in class org.jbei.ice.storage.model.Sequence
getConfig(String) - Method in class org.jbei.ice.services.rest.ConfigResource: Retrieves the value for the specified config key
getConfigurationDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getConfigValue(ConfigurationKey) - Static method in class org.jbei.ice.lib.utils.Utils
getContents(String, long, PageParameters) - Method in class org.jbei.ice.lib.folder.FolderContents: Retrieves the folder specified in the parameter and contents
getContents() - Method in class org.jbei.ice.storage.model.BulkUpload
getContents() - Method in class org.jbei.ice.storage.model.Folder
getContext() - Method in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication: Get unauthenticated ldap context.
getCount() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
getCount() - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
getCount() - Method in class org.jbei.ice.lib.dto.sample.UserSamples
getCount() - Method in class org.jbei.ice.lib.search.WebResult
getCount(Account) - Method in class org.jbei.ice.storage.hibernate.dao.RequestDAO
getCount(SampleRequestStatus, String) - Method in class org.jbei.ice.storage.hibernate.dao.RequestDAO
getCountByEntry(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.TraceSequenceDAO: Get number of trace sequences available for specified entry
getCreated() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
getCreated() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
getCreated() - Method in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
getCreated() - Method in class org.jbei.ice.lib.experiment.Study
getCreationTime() - Method in class org.jbei.ice.lib.dto.access.AccessKey
getCreationTime() - Method in class org.jbei.ice.lib.dto.entry.PartData
getCreationTime() - Method in class org.jbei.ice.lib.dto.group.UserGroup
getCreationTime() - Method in class org.jbei.ice.lib.dto.sample.PartSample
getCreationTime() - Method in class org.jbei.ice.lib.folder.AbstractFolder
getCreationTime() - Method in class org.jbei.ice.lib.manuscript.Manuscript
getCreationTime() - Method in class org.jbei.ice.storage.model.Account
getCreationTime() - Method in class org.jbei.ice.storage.model.ApiKey
getCreationTime() - Method in class org.jbei.ice.storage.model.BulkUpload
getCreationTime() - Method in class org.jbei.ice.storage.model.Comment
getCreationTime() - Method in class org.jbei.ice.storage.model.Entry
getCreationTime() - Method in class org.jbei.ice.storage.model.Experiment
getCreationTime() - Method in class org.jbei.ice.storage.model.Folder
getCreationTime() - Method in class org.jbei.ice.storage.model.Group
getCreationTime() - Method in class org.jbei.ice.storage.model.ManuscriptModel
getCreationTime() - Method in class org.jbei.ice.storage.model.Sample
getCreationTime() - Method in class org.jbei.ice.storage.model.ShotgunSequence
getCreationTime() - Method in class org.jbei.ice.storage.model.TraceSequence
getCreator() - Method in class org.jbei.ice.lib.dto.entry.PartData
getCreator() - Method in class org.jbei.ice.storage.model.Entry
getCreatorEmail() - Method in class org.jbei.ice.lib.dto.entry.PartData
getCreatorEmail() - Method in class org.jbei.ice.storage.model.Entry
getCreatorId() - Method in class org.jbei.ice.lib.dto.entry.PartData
getCSVHeaders(EntryField[]) - Method in class org.jbei.ice.lib.entry.EntriesAsCSV
getCSVHeaders(List<EntryField>) - Method in class org.jbei.ice.lib.net.RemoteEntriesAsCSV
getCSVTemplateBytes(EntryType, EntryType, boolean) - Static method in class org.jbei.ice.lib.bulkupload.FileBulkUpload: Creates a CSV template for download based on the the type of entries
getCuration() - Method in class org.jbei.ice.lib.dto.DNAFeature
getCuration() - Method in class org.jbei.ice.storage.model.Feature
getCustomFields() - Method in class org.jbei.ice.lib.dto.entry.PartData
getData() - Method in class org.jbei.ice.lib.dto.common.Results
getDateRead() - Method in class org.jbei.ice.storage.model.Message
getDateSent() - Method in class org.jbei.ice.storage.model.Message
getDcUri() - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
getDefaultFeatureSource() - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter: Return the default feature source for a Genbank file.
getDefaultPermissions() - Method in class org.jbei.ice.lib.account.AccountTransfer
getDefaultValue() - Method in enum org.jbei.ice.lib.dto.ConfigurationKey
getDeleted() - Method in class org.jbei.ice.lib.folder.CollectionCounts
getDeletedCount(String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
getDepositor() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
getDepositor() - Method in class org.jbei.ice.lib.dto.sample.PartSample
getDepositor() - Method in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
getDepositor() - Method in class org.jbei.ice.storage.model.Sample
getDepositor() - Method in class org.jbei.ice.storage.model.ShotgunSequence
getDepositor() - Method in class org.jbei.ice.storage.model.TraceSequence
getDescription() - Method in class org.jbei.ice.lib.account.AccountTransfer
getDescription() - Method in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
getDescription() - Method in class org.jbei.ice.lib.dto.entry.AttachmentInfo
getDescription() - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
getDescription() - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
getDescription() - Method in class org.jbei.ice.lib.dto.group.UserGroup
getDescription() - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter
getDescription() - Method in class org.jbei.ice.storage.model.Account
getDescription() - Method in class org.jbei.ice.storage.model.Attachment
getDescription() - Method in class org.jbei.ice.storage.model.Folder
getDescription() - Method in class org.jbei.ice.storage.model.Group
getDescription() - Method in class org.jbei.ice.storage.model.Storage
getDestination() - Method in class org.jbei.ice.lib.entry.EntrySelection
getDestinationAccounts() - Method in class org.jbei.ice.storage.model.Message
getDestinationGroups() - Method in class org.jbei.ice.storage.model.Message
getDisplay() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
getDisplay() - Method in enum org.jbei.ice.lib.dto.entry.EntryType
getDisplay() - Method in class org.jbei.ice.lib.dto.StorageLocation
getDisplayList() - Static method in enum org.jbei.ice.lib.shared.StatusType
getDisplayName() - Method in enum org.jbei.ice.lib.shared.StatusType
getDivision() - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter
getDnaComponent() - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.SBOLVisitor
getDone() - Method in class org.jbei.ice.lib.search.IndexBuildStatus
getEcotype() - Method in class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
getEcotype() - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
getEditMode() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadAutoUpdate
getEmail() - Method in class org.jbei.ice.lib.account.AccountTransfer
getEmail() - Method in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
getEmail() - Static method in class org.jbei.ice.lib.email.EmailFactory
getEmail() - Method in class org.jbei.ice.storage.model.Account
getEmail() - Method in class org.jbei.ice.storage.model.RemoteClientModel
getEnd() - Method in class org.jbei.ice.lib.dto.DNAFeatureLocation
getEnd() - Method in class org.jbei.ice.lib.parsers.genbank.GenbankLocation
getEnd() - Method in class org.jbei.ice.storage.model.AnnotationLocation
getEntries() - Method in class org.jbei.ice.lib.dto.DNAFeature
getEntries() - Method in class org.jbei.ice.lib.dto.web.PartnerEntries
getEntries() - Method in class org.jbei.ice.lib.entry.EntrySelection
getEntries(ColumnField, boolean, int, int, String) - Method in class org.jbei.ice.lib.entry.SharedEntries
getEntries(ColumnField, boolean, int, int, String) - Method in class org.jbei.ice.lib.entry.VisibleEntries
getEntries() - Method in class org.jbei.ice.lib.folder.AbstractFolder
getEntries(ColumnField, boolean, int, int) - Method in class org.jbei.ice.lib.folder.collection.CollectionEntries: Retrieves list of entries without filter text getEntries which this delegates to with null filter value
getEntries(ColumnField, boolean, int, int, String) - Method in class org.jbei.ice.lib.folder.collection.CollectionEntries: Retrieves parts (paged and sorted by the specified parameter values) based on the type of collection.
getEntries(int, int) - Method in class org.jbei.ice.lib.net.RemoteEntriesAsCSV
getEntries(String, boolean, int, int) - Method in class org.jbei.ice.lib.net.RemoteFolder
getEntriesByIdSet(List<Long>) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO: Retrieve Entry objects of the given list of ids.
getEntriesByVisibility(Visibility, ColumnField, boolean, int, int, String, String) - Method in class org.jbei.ice.lib.folder.collection.CollectionEntries: Retrieves entries by the specified visibility.
getEntriesFromSelectionContext(EntrySelection) - Method in class org.jbei.ice.lib.entry.Entries
getEntriesInFile(InputStream, FormDataContentDisposition) - Method in class org.jbei.ice.services.rest.FileResource
getEntry(String) - Method in class org.jbei.ice.lib.entry.HasEntry: Retrieve entry using a unique entry identifier
getEntry() - Method in class org.jbei.ice.storage.model.Attachment
getEntry() - Method in class org.jbei.ice.storage.model.Audit
getEntry() - Method in class org.jbei.ice.storage.model.Comment
getEntry() - Method in class org.jbei.ice.storage.model.Link
getEntry() - Method in class org.jbei.ice.storage.model.Parameter
getEntry() - Method in class org.jbei.ice.storage.model.Permission
getEntry() - Method in class org.jbei.ice.storage.model.Request
getEntry() - Method in class org.jbei.ice.storage.model.Sample
getEntry() - Method in class org.jbei.ice.storage.model.SelectionMarker
getEntry() - Method in class org.jbei.ice.storage.model.Sequence
getEntry() - Method in class org.jbei.ice.storage.model.ShotgunSequence
getEntry() - Method in class org.jbei.ice.storage.model.TraceSequence
getEntryAttachments(String, long, long) - Method in class org.jbei.ice.lib.net.RemoteEntries
getEntryByField(String, String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
getEntryCount(String) - Method in class org.jbei.ice.lib.entry.VisibleEntries: Retrieve the number of entries that is visible to a particular user
getEntryCount() - Method in class org.jbei.ice.lib.entry.VisibleEntries
getEntryDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getEntryDetails(String, long, long) - Method in class org.jbei.ice.lib.net.RemoteEntries
getEntryField() - Method in class org.jbei.ice.lib.bulkupload.EntryHeaderValue
getEntryFields() - Method in class org.jbei.ice.lib.entry.EntriesAsCSV
getEntryFields() - Method in class org.jbei.ice.lib.net.RemoteEntriesAsCSV
getEntryFolders(String) - Method in class org.jbei.ice.services.rest.PartResource: Returns the folders that an entry is contained in (filtered by permissions).
getEntryId() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadAutoUpdate
getEntryId() - Method in class org.jbei.ice.lib.dto.comment.UserComment
getEntryId() - Method in class org.jbei.ice.lib.dto.entry.PartStatistics
getEntryId() - Method in class org.jbei.ice.lib.dto.entry.SequenceInfo
getEntryIds(BulkUpload) - Method in class org.jbei.ice.storage.hibernate.dao.BulkUploadDAO
getEntryIds(Folder) - Method in class org.jbei.ice.storage.hibernate.dao.FolderDAO: Retrieve the list of ids of entries contained in a folder.
getEntryIdsByFeature(Feature) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceFeatureDAO
getEntryInfo() - Method in class org.jbei.ice.lib.dto.entry.HasEntryData
getEntryList() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
getEntryPermissions() - Method in class org.jbei.ice.lib.entry.EntryPermissions: Retrieves permissions associated with a part.
getEntryPermissions(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
getEntrySequenceFeatures(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceFeatureDAO
getEntrySummary(long) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
getEntryType() - Method in class org.jbei.ice.lib.entry.EntrySelection
getEntryTypes() - Method in class org.jbei.ice.lib.dto.search.SearchQuery
getErrors() - Method in class org.jbei.ice.lib.parsers.genbank.GenBankParser
geteValue() - Method in class org.jbei.ice.lib.dto.search.SearchResult
getExperimentalDataCount() - Method in class org.jbei.ice.lib.dto.entry.PartStatistics
getExperimentCount(long) - Method in class org.jbei.ice.storage.hibernate.dao.ExperimentDAO
getExperimentDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getExperimentList(long) - Method in class org.jbei.ice.storage.hibernate.dao.ExperimentDAO
getExpires() - Method in class org.jbei.ice.storage.model.ApiKey
getFailedFields() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadValidation
getFeature() - Method in class org.jbei.ice.storage.model.FeatureCurationModel
getFeature() - Method in class org.jbei.ice.storage.model.SequenceFeature
getFeatureCount() - Method in class org.jbei.ice.lib.dto.entry.PartData
getFeatureCount(String) - Method in class org.jbei.ice.storage.hibernate.dao.FeatureDAO
getFeatureCount(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceFeatureDAO
getFeatureCurationModelDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getFeatureDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getFeaturedDNASequence() - Method in class org.jbei.ice.lib.parsers.sbol.ICESBOLParserVisitor
getFeaturedSequence(Entry, boolean) - Method in class org.jbei.ice.lib.entry.sequence.PartSequence
getFeaturedSequence(Entry, boolean) - Method in class org.jbei.ice.lib.entry.sequence.SequenceController
getFeatures() - Method in class org.jbei.ice.lib.dto.DNAFeatures
getFeatures() - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
getFeatures() - Method in class org.jbei.ice.lib.parsers.genbank.FeaturesTag
getFeatures(int, int, String, boolean, String) - Method in class org.jbei.ice.services.rest.AnnotationResource: Retrieve list of annotations available.
getFeatures(int, int, String) - Method in class org.jbei.ice.storage.hibernate.dao.FeatureDAO
getFeaturesGroupBy(int, int) - Method in class org.jbei.ice.storage.hibernate.dao.FeatureDAO
getFeaturesGroupByCount() - Method in class org.jbei.ice.storage.hibernate.dao.FeatureDAO
getFeatureType(SequenceFeature) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter: Retrieve feature type from given SequenceFeature.
getFeatureType(String) - Static method in class org.jbei.ice.lib.entry.sequence.composers.formatters.IceSequenceOntology
getFetched() - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
getFetched() - Method in class org.jbei.ice.storage.model.RemotePartner
getField(String, long) - Method in class org.jbei.ice.lib.dto.entry.CustomFields
getField() - Method in class org.jbei.ice.lib.dto.search.FieldFilter
getField() - Method in enum org.jbei.ice.lib.dto.search.SearchBoostField
getFieldFilters() - Method in class org.jbei.ice.lib.dto.search.SearchQuery
getFieldsForPart(String, long) - Method in class org.jbei.ice.lib.dto.entry.CustomFields
getFile(TraceSequence) - Method in class org.jbei.ice.lib.entry.sequence.SequenceAnalysisController: Retrieve the File associated with the given TraceSequence.
getFile(String) - Method in class org.jbei.ice.storage.hibernate.dao.ShotgunSequenceDAO
getFileId() - Method in class org.jbei.ice.lib.dto.entry.AttachmentInfo
getFileId() - Method in class org.jbei.ice.lib.dto.entry.SequenceInfo
getFileId() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
getFileId() - Method in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
getFileId() - Method in class org.jbei.ice.storage.model.Attachment
getFileId() - Method in class org.jbei.ice.storage.model.ShotgunSequence
getFileId() - Method in class org.jbei.ice.storage.model.TraceSequence
getFilename() - Method in class org.jbei.ice.lib.dto.entry.AttachmentInfo
getFilename() - Method in class org.jbei.ice.lib.dto.entry.SequenceInfo
getFilename() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
getFilename() - Method in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
getFileName(String, String) - Method in class org.jbei.ice.lib.entry.attachment.Attachments: Retrieves the name of the file represented by the file identifer
getFileName() - Method in class org.jbei.ice.storage.model.Attachment
getFileName() - Method in class org.jbei.ice.storage.model.Sequence
getFilename() - Method in class org.jbei.ice.storage.model.ShotgunSequence
getFilename() - Method in class org.jbei.ice.storage.model.TraceSequence
getFilePath() - Method in class org.jbei.ice.lib.entry.EntriesAsCSV
getFilePath() - Method in class org.jbei.ice.lib.net.RemoteEntriesAsCSV
getFilter() - Method in class org.jbei.ice.lib.dto.common.PageParameters
getFilter() - Method in class org.jbei.ice.lib.dto.search.FieldFilter
getFilter() - Method in class org.jbei.ice.storage.hibernate.filter.EntryHasFilterFactory
getFilter() - Method in class org.jbei.ice.storage.hibernate.filter.EntrySecurityFilterFactory
getFirstName() - Method in class org.jbei.ice.lib.account.AccountTransfer
getFirstName() - Method in class org.jbei.ice.storage.model.Account
getFirstName() - Method in class org.jbei.ice.storage.model.Audit
getFolder(long, int, int) - Method in class org.jbei.ice.lib.folder.collection.Collection
getFolder(long) - Method in class org.jbei.ice.lib.folder.UserFolder
getFolder() - Method in class org.jbei.ice.lib.manuscript.Manuscript
getFolder(long) - Method in class org.jbei.ice.services.rest.FolderResource: Retrieve specified folder resource
getFolder() - Method in class org.jbei.ice.storage.model.ManuscriptModel
getFolder() - Method in class org.jbei.ice.storage.model.Permission
getFolderContentIds(long, EntryType, boolean) - Method in class org.jbei.ice.storage.hibernate.dao.FolderDAO: Retrieves the ids of any entries that are contained in the specified folder; optionally filtered by entry type
getFolderDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getFolderDetails() - Method in class org.jbei.ice.lib.dto.access.RemoteAccessPermission
getFolderEntries(long, boolean, EntryType) - Method in class org.jbei.ice.lib.entry.Entries
getFolderEntries(String, String, Map<String, Object>, String) - Method in class org.jbei.ice.lib.net.RemoteContact
getFolderId() - Method in class org.jbei.ice.lib.entry.EntrySelection
getFolderPermissions(long) - Method in class org.jbei.ice.services.rest.FolderResource: Retrieves list of permissions available for the specified folder.
getFolderPermissions(Folder) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
getFolders() - Method in class org.jbei.ice.lib.entry.EntryFolders
getFolders() - Method in class org.jbei.ice.services.rest.FolderResource
getFolders(Group) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
getFolders() - Method in class org.jbei.ice.storage.model.Entry
getFoldersByOwner(Account) - Method in class org.jbei.ice.storage.hibernate.dao.FolderDAO: Retrieve all Folders owned by given the Account.
getFoldersByType(FolderType) - Method in class org.jbei.ice.storage.hibernate.dao.FolderDAO
getFolderSize(long, String, boolean) - Method in class org.jbei.ice.storage.hibernate.dao.FolderDAO: Retrieves the count of the number of contents in the folder.
getFormat() - Method in class org.jbei.ice.lib.dto.entry.SequenceInfo
getFormat() - Method in class org.jbei.ice.storage.model.Sequence
getFrom() - Method in class org.jbei.ice.lib.dto.message.MessageInfo
getFromEmail() - Method in class org.jbei.ice.storage.model.Message
getFullName() - Method in class org.jbei.ice.lib.account.AccountTransfer
getFullName() - Method in class org.jbei.ice.storage.model.Account
getFundingSource() - Method in class org.jbei.ice.lib.dto.entry.PartData
getFundingSource() - Method in class org.jbei.ice.storage.model.Entry
getFwdHash() - Method in class org.jbei.ice.storage.model.Sequence
getGenbankStart() - Method in class org.jbei.ice.lib.dto.DNAFeatureLocation
getGenbankStart() - Method in class org.jbei.ice.lib.parsers.genbank.GenbankLocation
getGenbankStart() - Method in class org.jbei.ice.storage.model.AnnotationLocation
getGenbankType() - Method in class org.jbei.ice.storage.model.Feature
getGenbankType() - Method in class org.jbei.ice.storage.model.SequenceFeature
getGeneration() - Method in class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
getGeneration() - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
getGenotypePhenotype() - Method in class org.jbei.ice.lib.dto.entry.StrainData
getGenotypePhenotype() - Method in class org.jbei.ice.storage.model.Strain
getGivenName() - Method in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
getGroup() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
getGroup(long) - Method in class org.jbei.ice.services.rest.GroupResource: Retrieve specified group
getGroup() - Method in class org.jbei.ice.storage.model.Permission
getGroupById(String, long) - Method in class org.jbei.ice.lib.group.GroupController: Can access a group if you are an admin or the owner of that group
getGroupDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getGroupMembers(long) - Method in class org.jbei.ice.lib.group.Groups: Retrieves both local and remote members of the specified group if the user making the request has the appropriate permissions
getGroupMembers(long) - Method in class org.jbei.ice.services.rest.GroupResource
getGroups(String, int, int) - Method in class org.jbei.ice.services.rest.GroupResource
getGroups() - Method in class org.jbei.ice.storage.model.Account
getGroups() - Method in class org.jbei.ice.storage.model.RemoteClientModel
getGroupsBy(GroupType, boolean) - Method in class org.jbei.ice.storage.hibernate.dao.GroupDAO: Retrieves groups by type and autoJoin value
getGroupsByType(GroupType, int, int) - Method in class org.jbei.ice.storage.hibernate.dao.GroupDAO
getGroupsByTypeCount(GroupType) - Method in class org.jbei.ice.storage.hibernate.dao.GroupDAO
getGrowthTemperature() - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
getGrowthTemperature() - Method in class org.jbei.ice.storage.model.Request
getHarvestDate() - Method in class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
getHarvestDate() - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
getHasAttachment() - Method in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
getHash() - Method in class org.jbei.ice.storage.model.Feature
getHashedToken() - Method in class org.jbei.ice.storage.model.ApiKey
getHasSample() - Method in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
getHasSequence() - Method in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
getHeaders() - Method in class org.jbei.ice.lib.bulkupload.ProcessedBulkUpload
getHeadersForType(EntryType) - Static method in class org.jbei.ice.lib.bulkupload.BulkCSVUploadHeaders
getHexString(byte[]) - Static method in class org.jbei.ice.lib.utils.Utils: Convert byte array to Hex notation.
getHistory(long, int, int, boolean, String) - Method in class org.jbei.ice.services.rest.PartResource
getHistoryCount() - Method in class org.jbei.ice.lib.dto.entry.PartStatistics
getHomozygosity() - Method in class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
getHomozygosity() - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
getHost() - Method in class org.jbei.ice.lib.dto.entry.StrainData
getHost() - Method in class org.jbei.ice.storage.model.Strain
getId() - Method in class org.jbei.ice.lib.account.AccountTransfer
getId() - Method in class org.jbei.ice.lib.dto.access.AccessKey
getId() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
getId() - Method in class org.jbei.ice.lib.dto.comment.UserComment
getId() - Method in class org.jbei.ice.lib.dto.DNAFeature
getId() - Method in class org.jbei.ice.lib.dto.entry.AttachmentInfo
getId() - Method in class org.jbei.ice.lib.dto.entry.CustomField
getId() - Method in class org.jbei.ice.lib.dto.entry.PartData
getId() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
getId() - Method in class org.jbei.ice.lib.dto.group.UserGroup
getId() - Method in class org.jbei.ice.lib.dto.History
getId() - Method in class org.jbei.ice.lib.dto.message.MessageInfo
getId() - Method in class org.jbei.ice.lib.dto.sample.PartSample
getId() - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
getId() - Method in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
getId() - Method in class org.jbei.ice.lib.dto.StorageLocation
getId() - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
getId() - Method in class org.jbei.ice.lib.experiment.Study
getId() - Method in class org.jbei.ice.lib.folder.AbstractFolder
getId() - Method in class org.jbei.ice.lib.manuscript.Manuscript
getId() - Method in interface org.jbei.ice.storage.DataModel
getId() - Method in class org.jbei.ice.storage.model.Account
getId() - Method in class org.jbei.ice.storage.model.AccountPreferences
getId() - Method in class org.jbei.ice.storage.model.AnnotationLocation
getId() - Method in class org.jbei.ice.storage.model.ApiKey
getId() - Method in class org.jbei.ice.storage.model.Attachment
getId() - Method in class org.jbei.ice.storage.model.Audit
getId() - Method in class org.jbei.ice.storage.model.BulkUpload
getId() - Method in class org.jbei.ice.storage.model.Comment
getId() - Method in class org.jbei.ice.storage.model.Configuration
getId() - Method in class org.jbei.ice.storage.model.Entry
getId() - Method in class org.jbei.ice.storage.model.Experiment
getId() - Method in class org.jbei.ice.storage.model.Feature
getId() - Method in class org.jbei.ice.storage.model.FeatureCurationModel
getId() - Method in class org.jbei.ice.storage.model.Folder
getId() - Method in class org.jbei.ice.storage.model.Group
getId() - Method in class org.jbei.ice.storage.model.Link
getId() - Method in class org.jbei.ice.storage.model.ManuscriptModel
getId() - Method in class org.jbei.ice.storage.model.Message
getId() - Method in class org.jbei.ice.storage.model.Parameter
getId() - Method in class org.jbei.ice.storage.model.Permission
getId() - Method in class org.jbei.ice.storage.model.Preference
getId() - Method in class org.jbei.ice.storage.model.RemoteAccessModel
getId() - Method in class org.jbei.ice.storage.model.RemoteClientModel
getId() - Method in class org.jbei.ice.storage.model.RemotePartner
getId() - Method in class org.jbei.ice.storage.model.RemoteShareModel
getId() - Method in class org.jbei.ice.storage.model.Request
getId() - Method in class org.jbei.ice.storage.model.Sample
getId() - Method in class org.jbei.ice.storage.model.SelectionMarker
getId() - Method in class org.jbei.ice.storage.model.Sequence
getId() - Method in class org.jbei.ice.storage.model.SequenceFeature
getId() - Method in class org.jbei.ice.storage.model.SequenceFeatureAttribute
getId() - Method in class org.jbei.ice.storage.model.ShotgunSequence
getId() - Method in class org.jbei.ice.storage.model.Storage
getId() - Method in class org.jbei.ice.storage.model.TraceSequence
getId() - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
getIdentification() - Method in class org.jbei.ice.storage.model.Feature
getIdentifier() - Method in class org.jbei.ice.lib.dto.DNAFeature
getIdentifier() - Method in class org.jbei.ice.lib.dto.entry.ParsedEntryId
getIdentifier() - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
getIdentifier() - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter
getIdentifier() - Method in class org.jbei.ice.storage.model.RemoteAccessModel
getIdentifier() - Method in class org.jbei.ice.storage.model.Sequence
getImage(int, int) - Method in class org.jbei.ice.lib.parsers.abi.ABITrace: Returns a BufferedImage that represents the entire trace.
getImportType() - Method in class org.jbei.ice.storage.model.BulkUpload
getIndex() - Method in class org.jbei.ice.lib.dto.entry.PartData
getIndex() - Method in class org.jbei.ice.storage.model.Storage
getIndexStatus(IndexType) - Method in class org.jbei.ice.lib.search.SearchController
getIndexStatus(String) - Method in class org.jbei.ice.services.rest.SearchResource
getInfo(Entry) - Static method in class org.jbei.ice.storage.ModelToInfoFactory
getInitials() - Method in class org.jbei.ice.lib.account.AccountTransfer
getInitials() - Method in class org.jbei.ice.storage.model.Account
getInstance() - Static method in class org.jbei.ice.lib.executor.IceExecutorService
getInstance() - Static method in class org.jbei.ice.lib.parsers.GeneralParser
getInstance() - Static method in class org.jbei.ice.lib.search.IndexerProgressMonitor
getInstance() - Static method in class org.jbei.ice.services.rest.IceRestClient
getInstance() - Static method in class org.jbei.ice.storage.hibernate.search.HibernateSearch: Retrieve the singleton instance of this class.
getInstitution() - Method in class org.jbei.ice.lib.account.AccountTransfer
getInstitution() - Method in class org.jbei.ice.storage.model.Account
getInstitution() - Method in class org.jbei.ice.storage.model.Audit
getIntellectualProperty() - Method in class org.jbei.ice.lib.dto.entry.PartData
getIntellectualProperty() - Method in class org.jbei.ice.storage.model.Entry
getIntValue() - Method in enum org.jbei.ice.lib.shared.BioSafetyOption
getIp() - Method in class org.jbei.ice.storage.model.Account
getIsCircular() - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
getKey(String) - Method in interface org.jbei.auth.KeyTable
getKey(String) - Method in class org.jbei.auth.MemoryKeyTable
getKey() - Method in class org.jbei.ice.lib.dto.bulkupload.PreferenceInfo
getKey() - Method in class org.jbei.ice.lib.dto.Setting
getKey() - Method in class org.jbei.ice.lib.parsers.genbank.Tag
getKey() - Method in class org.jbei.ice.storage.model.Configuration
getKey() - Method in class org.jbei.ice.storage.model.Parameter
getKey() - Method in class org.jbei.ice.storage.model.Preference
getKey() - Method in class org.jbei.ice.storage.model.SequenceFeatureAttribute
getKeys(int, int, String, boolean, boolean) - Method in class org.jbei.ice.lib.account.UserApiKeys: Retrieves either list of available keys for current user or all keys.
getKeyValue() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadAutoUpdate
getKeywords() - Method in class org.jbei.ice.lib.dto.entry.PartData
getKeywords() - Method in class org.jbei.ice.storage.model.Entry
getLabel() - Method in class org.jbei.ice.lib.dto.DNAFeatures
getLabel() - Method in enum org.jbei.ice.lib.dto.entry.EntryField
getLabel() - Method in class org.jbei.ice.lib.dto.group.UserGroup
getLabel() - Method in class org.jbei.ice.lib.dto.sample.PartSample
getLabel() - Method in class org.jbei.ice.lib.experiment.Study
getLabel() - Method in class org.jbei.ice.storage.model.Experiment
getLabel() - Method in class org.jbei.ice.storage.model.Group
getLabel() - Method in class org.jbei.ice.storage.model.Sample
getLastContact() - Method in class org.jbei.ice.storage.model.RemotePartner
getLastContactTime() - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
getLastLogin() - Method in class org.jbei.ice.lib.account.AccountTransfer
getLastLoginTime() - Method in class org.jbei.ice.storage.model.Account
getLastName() - Method in class org.jbei.ice.lib.account.AccountTransfer
getLastName() - Method in class org.jbei.ice.storage.model.Account
getLastName() - Method in class org.jbei.ice.storage.model.Audit
getLastUpdate() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadAutoUpdate
getLastUpdate() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
getLastUpdateTime() - Method in class org.jbei.ice.storage.model.BulkUpload
getLength() - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
getLimit() - Method in class org.jbei.ice.lib.dto.common.PageParameters
getLink() - Method in class org.jbei.ice.storage.model.Link
getLinkedEntries() - Method in class org.jbei.ice.storage.model.Entry
getLinkedParts() - Method in class org.jbei.ice.lib.dto.entry.PartData
getLinkedParts(String, LinkType) - Method in class org.jbei.ice.services.rest.PartResource: Get linked parts
getLinks() - Method in class org.jbei.ice.lib.dto.entry.PartData
getLinks() - Method in class org.jbei.ice.storage.model.Entry
getLinksAsString(Set<Link>) - Static method in class org.jbei.ice.lib.entry.EntryUtil: String representation of Links.
getList(int, int, String, boolean, String) - Method in class org.jbei.ice.services.rest.ManuscriptResource
getLocation() - Method in class org.jbei.ice.lib.dto.sample.PartSample
getLocation() - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
getLocations() - Method in class org.jbei.ice.lib.dto.DNAFeature
getLongDescription() - Method in class org.jbei.ice.lib.dto.entry.PartData
getLongDescription() - Method in class org.jbei.ice.storage.model.Entry
getLongDescriptionType() - Method in class org.jbei.ice.storage.model.Entry
getManuscriptModelDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getMatchDetails() - Method in class org.jbei.ice.lib.dto.search.SearchResult
getMatchingAccounts(String, int) - Method in class org.jbei.ice.storage.hibernate.dao.AccountDAO: Retrieves accounts whose firstName, lastName, or email fields match the specified token up to the specified limit.
getMatchingEntryPartNumbers(String, int, Set<String>) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
getMatchingGroups(String, String, int) - Method in class org.jbei.ice.lib.group.GroupController
getMatchingGroups(String, int) - Method in class org.jbei.ice.lib.group.Groups
getMatchingGroups(Account, String, int) - Method in class org.jbei.ice.storage.hibernate.dao.GroupDAO
getMatchingPartNumbersForLinks(EntryType, String, int) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController: Retrieves part numbers that match the token passed in the parameter, that are compatible with the type in the parameter.
getMatchingPlasmidField(AutoCompleteField, String, int) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
getMatchingSelectionMarkers(String, int) - Method in class org.jbei.ice.storage.hibernate.dao.SelectionMarkerDAO
getMatchingValues(String, int) - Method in class org.jbei.ice.lib.dto.entry.AutoCompleteFieldValues: Retrieves list of values that match the user specified token up to the specified limit
getMaxScore() - Method in class org.jbei.ice.lib.dto.search.SearchResult
getMemberCount() - Method in class org.jbei.ice.lib.dto.group.UserGroup
getMemberCount(String) - Method in class org.jbei.ice.storage.hibernate.dao.GroupDAO
getMemberGroupUUIDs(Account) - Method in class org.jbei.ice.storage.hibernate.dao.GroupDAO: Retrieves all UUIDs that the specified account either owns or is a member of
getMembers() - Method in class org.jbei.ice.lib.dto.group.UserGroup
getMembers() - Method in class org.jbei.ice.storage.model.Group
getMessage() - Method in class org.jbei.ice.lib.dto.comment.UserComment
getMessage() - Method in class org.jbei.ice.lib.dto.message.MessageInfo
getMessage() - Method in class org.jbei.ice.services.rest.ErrorResponse
getMessage() - Method in class org.jbei.ice.storage.model.Message
getMessageDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getMimeType(String) - Static method in class org.jbei.ice.services.rest.ExtensionToMimeType: Determines the appropriate mime type (from list of hardcoded values) using the provided extension.
getModel(String, RemotePartner) - Method in class org.jbei.ice.storage.hibernate.dao.RemoteClientModelDAO
getModificationTime() - Method in class org.jbei.ice.lib.dto.entry.PartData
getModificationTime() - Method in class org.jbei.ice.storage.model.Account
getModificationTime() - Method in class org.jbei.ice.storage.model.Comment
getModificationTime() - Method in class org.jbei.ice.storage.model.Entry
getModificationTime() - Method in class org.jbei.ice.storage.model.Folder
getModificationTime() - Method in class org.jbei.ice.storage.model.Group
getModificationTime() - Method in class org.jbei.ice.storage.model.Sample
getModificationTime() - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
getModified() - Method in class org.jbei.ice.lib.dto.comment.UserComment
getName() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
getName() - Method in class org.jbei.ice.lib.dto.DNAFeature
getName() - Method in class org.jbei.ice.lib.dto.DNAFeatureNote
getName() - Method in class org.jbei.ice.lib.dto.entry.CustomField
getName() - Method in enum org.jbei.ice.lib.dto.entry.EntryType
getName() - Method in class org.jbei.ice.lib.dto.entry.PartData
getName() - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
getName() - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
getName() - Method in enum org.jbei.ice.lib.dto.search.BlastProgram
getName() - Method in class org.jbei.ice.lib.dto.StorageLocation
getName() - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
getName() - Method in class org.jbei.ice.lib.entry.sequence.ByteArrayWrapper
getName() - Method in class org.jbei.ice.storage.model.BulkUpload
getName() - Method in class org.jbei.ice.storage.model.Entry
getName() - Method in class org.jbei.ice.storage.model.Feature
getName() - Method in class org.jbei.ice.storage.model.Folder
getName() - Method in class org.jbei.ice.storage.model.RemotePartner
getName() - Method in class org.jbei.ice.storage.model.SelectionMarker
getName() - Method in class org.jbei.ice.storage.model.SequenceFeature
getName() - Method in class org.jbei.ice.storage.model.Storage
getNamespace() - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.AbstractFormatter
getNewMessageCount() - Method in class org.jbei.ice.lib.account.AccountTransfer
getNewMessageCount(Account) - Method in class org.jbei.ice.lib.message.Messages
getNident() - Method in class org.jbei.ice.lib.dto.search.SearchResult
getNotes() - Method in class org.jbei.ice.lib.dto.DNAFeature
getNotes() - Method in class org.jbei.ice.storage.model.Sample
getNumberOfEntries(String) - Method in class org.jbei.ice.lib.entry.SharedEntries
getNumberOfOwnerEntries(Account, String) - Method in class org.jbei.ice.lib.account.Accounts
getNumberOfOwnerEntries() - Method in class org.jbei.ice.lib.entry.OwnerEntries
getObjectById(long) - Method in class org.jbei.ice.lib.access.Authorization
getOffset() - Method in class org.jbei.ice.lib.dto.common.PageParameters
getOrCreateRemoteClient(String, RemotePartner) - Method in class org.jbei.ice.lib.access.RemoteAccess: Checks if there is an existing client for the specified userId and remote partner.
getOrCreateRemoteClient(String, RemotePartner) - Method in class org.jbei.ice.lib.folder.FolderPermissions: Checks if there is an existing client for the specified userId and remote partner.
getOrganization() - Method in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
getOrientation() - Method in class org.jbei.ice.lib.parsers.bl2seq.Bl2SeqResult
getOriginOfReplication() - Method in class org.jbei.ice.lib.dto.entry.PlasmidData
getOriginOfReplication() - Method in class org.jbei.ice.storage.model.Plasmid
getOwner(T) - Method in class org.jbei.ice.lib.access.Authorization
getOwner() - Method in class org.jbei.ice.lib.dto.entry.PartData
getOwner(Folder) - Method in class org.jbei.ice.lib.dto.folder.FolderAuthorization
getOwner() - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
getOwner(Entry) - Method in class org.jbei.ice.lib.entry.EntryAuthorization
getOwner(Sample) - Method in class org.jbei.ice.lib.entry.sample.SampleAuthorization
getOwner() - Method in class org.jbei.ice.storage.model.Entry
getOwner() - Method in class org.jbei.ice.storage.model.Group
getOwnerEmail() - Method in class org.jbei.ice.lib.dto.entry.PartData
getOwnerEmail() - Method in class org.jbei.ice.lib.dto.group.UserGroup
getOwnerEmail() - Method in class org.jbei.ice.lib.experiment.Study
getOwnerEmail() - Method in class org.jbei.ice.storage.model.ApiKey
getOwnerEmail() - Method in class org.jbei.ice.storage.model.Entry
getOwnerEmail() - Method in class org.jbei.ice.storage.model.Experiment
getOwnerEmail() - Method in class org.jbei.ice.storage.model.Folder
getOwnerEmail() - Method in class org.jbei.ice.storage.model.Storage
getOwnerEntryIds(String, EntryType) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO: Retrieves list of entry ids whose owner email column matches the specified ownerEmail parameter, with a visibility of
getOwnerId() - Method in class org.jbei.ice.lib.dto.entry.PartData
getParagonUrl() - Method in class org.jbei.ice.lib.manuscript.Manuscript
getParagonUrl() - Method in class org.jbei.ice.storage.model.ManuscriptModel
getParameterDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getParameters() - Method in class org.jbei.ice.lib.dto.search.SearchQuery
getParameters() - Method in class org.jbei.ice.storage.model.Entry
getParent() - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
getParent() - Method in class org.jbei.ice.storage.model.Folder
getParent() - Method in class org.jbei.ice.storage.model.Storage
getParentId() - Method in class org.jbei.ice.lib.dto.group.UserGroup
getParents() - Method in class org.jbei.ice.lib.dto.entry.PartData
getParents() - Method in class org.jbei.ice.lib.entry.EntryLinks: Retrieves list of this entry's parents that user has read access to
getParents(long) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO: links are stored in a join table in the form [entry_id, linked_entry_id] which is used to represent a parent child reln.
getParents() - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
getPart(String) - Method in class org.jbei.ice.lib.dto.web.WebEntries: Checks the local database for the entry with id recordId If it exists locally and is public, it returns it.
getPartByCustomFields(UriInfo) - Method in class org.jbei.ice.services.rest.CustomFieldResource
getPartData() - Method in class org.jbei.ice.lib.bulkupload.PartWithSample
getPartData() - Method in class org.jbei.ice.lib.dto.entry.ParsedEntryId
getPartData() - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
getPartExperiments(String) - Method in class org.jbei.ice.services.rest.PartResource
getPartId() - Method in class org.jbei.ice.lib.dto.entry.CustomField
getPartId() - Method in class org.jbei.ice.lib.dto.entry.PartData
getPartId() - Method in class org.jbei.ice.lib.dto.sample.PartSample
getPartId() - Method in class org.jbei.ice.lib.experiment.Study
getPartName() - Method in class org.jbei.ice.lib.dto.sample.PartSample
getPartner() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
getPartner() - Method in class org.jbei.ice.lib.dto.History
getPartner() - Method in class org.jbei.ice.lib.dto.search.SearchResult
getPartner() - Method in class org.jbei.ice.lib.dto.web.PartnerEntries
getPartner() - Method in class org.jbei.ice.lib.dto.web.RemoteUser
getPartner() - Method in class org.jbei.ice.lib.search.WebResult
getPartner() - Method in class org.jbei.ice.lib.search.WebSearch.SearchTask
getPartners() - Method in class org.jbei.ice.lib.dto.web.WebOfRegistries
getPartners(String, String) - Method in class org.jbei.ice.lib.net.RemoteContact
getPartners() - Method in class org.jbei.ice.lib.net.WebPartners: Retrieves list of partners for this instance
getPartnerStatus() - Method in class org.jbei.ice.storage.model.RemotePartner
getPartNumber() - Method in class org.jbei.ice.storage.model.Entry
getPartNumberPrefix() - Static method in class org.jbei.ice.lib.entry.EntryUtil
getPartNumbersForUpload(EntryType, String, int) - Method in class org.jbei.ice.services.rest.BulkUploadResource: Retrieves matching part numbers to be linked to entries in a bulk upload
getPartSample() - Method in class org.jbei.ice.lib.bulkupload.PartWithSample
getPartsByFields(String, List<CustomField>) - Method in class org.jbei.ice.lib.dto.entry.CustomFields
getPartsForTransfer(List<Long>) - Method in class org.jbei.ice.lib.net.RemoteTransfer: Using the list of entry Ids, populates a list of PartData objects that maintains the hierarchical relationships
getPartStudies() - Method in class org.jbei.ice.lib.experiment.Experiments: Retrieves experiment data associated with a specific entry
getPassword() - Method in class org.jbei.ice.lib.account.AccountTransfer
getPassword() - Method in class org.jbei.ice.storage.model.Account
getPending() - Method in class org.jbei.ice.lib.folder.CollectionCounts
getPendingBulkUploads(String) - Method in class org.jbei.ice.lib.folder.FolderController: Retrieves information about submitted bulk uploads that have status "PENDING".
getPendingImports(String) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController: Retrieves list of bulk imports that are owned by the system.
getPendingUploads(String) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController
getPendingUploads() - Method in class org.jbei.ice.services.rest.BulkUploadResource
getPermission() - Method in class org.jbei.ice.storage.model.RemoteAccessModel
getPermission() - Method in class org.jbei.ice.storage.model.RemoteShareModel
getPermissionDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getPermissions() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
getPermissions(String) - Method in class org.jbei.ice.services.rest.PartResource
getPermissions() - Method in class org.jbei.ice.storage.model.BulkUpload
getPermissions() - Method in class org.jbei.ice.storage.model.Entry
getPersonal() - Method in class org.jbei.ice.lib.folder.CollectionCounts
getPersonalEntries(ColumnField, boolean, int, int, String) - Method in class org.jbei.ice.lib.folder.collection.CollectionEntries: Retrieves entries owned by user
getPlantType() - Method in class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
getPlantType() - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
getPlasmidData() - Method in class org.jbei.ice.lib.dto.entry.PartData
getPlasmidFieldValues(Plasmid, EntryField) - Static method in class org.jbei.ice.lib.entry.EntryUtil
getPlasmidFieldValues(PlasmidData, EntryField) - Static method in class org.jbei.ice.lib.entry.PartDataUtil
getPlateDescription() - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
getPlateDescription() - Method in class org.jbei.ice.storage.model.Request
getPreference(Account, String) - Method in class org.jbei.ice.storage.hibernate.dao.PreferencesDAO
getPreferences() - Method in class org.jbei.ice.lib.dto.user.UserPreferences
getPreferences() - Method in class org.jbei.ice.storage.model.AccountPreferences
getPreferencesDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getPreferenceValue(String, String) - Method in class org.jbei.ice.lib.account.PreferencesController
getPrincipalInvestigator() - Method in class org.jbei.ice.lib.dto.entry.PartData
getPrincipalInvestigator() - Method in class org.jbei.ice.storage.model.Entry
getPrincipalInvestigatorEmail() - Method in class org.jbei.ice.lib.dto.entry.PartData
getPrincipalInvestigatorEmail() - Method in class org.jbei.ice.storage.model.Entry
getPrincipalInvestigatorId() - Method in class org.jbei.ice.lib.dto.entry.PartData
getProfileEntries(long, int, int, String, boolean, String) - Method in class org.jbei.ice.services.rest.UserResource
getProfileGroups(long) - Method in class org.jbei.ice.services.rest.UserResource
getPromoters() - Method in class org.jbei.ice.lib.dto.entry.PlasmidData
getPromoters() - Method in class org.jbei.ice.storage.model.Plasmid
getPropertyValue(ConfigurationKey) - Method in class org.jbei.ice.lib.config.ConfigurationController
getPropertyValue(String) - Method in class org.jbei.ice.lib.config.ConfigurationController
getPublicAttachment(String, long, String) - Method in class org.jbei.ice.lib.net.RemoteEntries
getPublicEntries(ColumnField, int, int, boolean) - Method in class org.jbei.ice.lib.folder.FolderController: Retrieves entries that are made available publicly
getPublicEntries(long, int, int, String, boolean) - Method in class org.jbei.ice.lib.net.RemoteEntries
getPublicEntry(String, String, String) - Method in class org.jbei.ice.lib.net.RemoteContact
getPublicEntry(String, long, long) - Method in class org.jbei.ice.lib.net.RemoteEntries
getPublicEntrySequence(String, String, String) - Method in class org.jbei.ice.lib.net.RemoteContact
getPublicEntrySequence(long, String) - Method in class org.jbei.ice.lib.net.RemoteEntries
getPublicEntryStatistics(String, long, String) - Method in class org.jbei.ice.lib.net.RemoteContact
getPublicEntryStatistics(String, long, long) - Method in class org.jbei.ice.lib.net.RemoteEntries
getPublicEntryTooltip(String, long, long) - Method in class org.jbei.ice.lib.net.RemoteEntries
getPublicFolderEntries(long, long, int, int, String, boolean) - Method in class org.jbei.ice.services.rest.PartnerResource
getPublicFolders() - Method in class org.jbei.ice.lib.folder.FolderController: Retrieves folders that are shared shared publicly.
getPublicFolders() - Method in class org.jbei.ice.services.rest.FolderResource
getPublicTooltipDetails(String, long, String) - Method in class org.jbei.ice.lib.net.RemoteContact
getQuery() - Method in class org.jbei.ice.lib.dto.search.SearchResults
getQuery() - Method in class org.jbei.ice.lib.search.WebSearchResults
getQueryAlignment() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
getQueryAlignment() - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
getQueryEnd() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
getQueryEnd() - Method in class org.jbei.ice.lib.parsers.bl2seq.Bl2SeqResult
getQueryEnd() - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
getQueryLength() - Method in class org.jbei.ice.lib.dto.search.SearchResult
getQuerySequence() - Method in class org.jbei.ice.lib.parsers.bl2seq.Bl2SeqResult
getQueryStart() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
getQueryStart() - Method in class org.jbei.ice.lib.parsers.bl2seq.Bl2SeqResult
getQueryStart() - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
getQueryString() - Method in class org.jbei.ice.lib.dto.search.SearchQuery
getQuoted() - Method in class org.jbei.ice.storage.model.SequenceFeatureAttribute
getRawBody() - Method in class org.jbei.ice.lib.parsers.genbank.Tag
getRecordId() - Method in class org.jbei.ice.lib.dto.entry.PartData
getRecordId() - Method in class org.jbei.ice.storage.model.Entry
getRecordType() - Method in class org.jbei.ice.storage.model.Entry
getRecordTypes(List<Long>) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
getReferences() - Method in class org.jbei.ice.lib.dto.entry.PartData
getReferences() - Method in class org.jbei.ice.lib.parsers.genbank.ReferenceTag
getReferences() - Method in class org.jbei.ice.storage.model.Entry
getRegisterDate() - Method in class org.jbei.ice.lib.account.AccountTransfer
getRegistryPartners(boolean) - Method in class org.jbei.ice.lib.net.WoRController
getRegistryPartners() - Method in class org.jbei.ice.storage.hibernate.dao.RemotePartnerDAO
getRemoteAccessModelDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getRemoteAttachment(long, String, String) - Method in class org.jbei.ice.services.rest.FileResource
getRemoteClientModel() - Method in class org.jbei.ice.storage.model.Audit
getRemoteClientModel() - Method in class org.jbei.ice.storage.model.RemoteAccessModel
getRemoteClientModelDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getRemoteContents(String, Folder, PageParameters) - Method in class org.jbei.ice.lib.folder.FolderContents: Retrieves contents of a folder that has been shared remotely with this instance
getRemoteContents(String, String, long, String, PageParameters, String) - Method in class org.jbei.ice.lib.net.RemoteContact
getRemoteEntries() - Method in class org.jbei.ice.lib.entry.EntrySelection
getRemoteEntry(String, String, long, long, String, String) - Method in class org.jbei.ice.lib.net.RemoteContact
getRemotelySharedContents(String, String, RegistryPartner, long, PageParameters) - Method in class org.jbei.ice.lib.folder.FolderContents
getRemoteMembers() - Method in class org.jbei.ice.lib.dto.group.UserGroup
getRemotePartComments(long, long) - Method in class org.jbei.ice.services.rest.PartnerResource
getRemotePartner() - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
getRemotePartner() - Method in class org.jbei.ice.storage.model.RemoteClientModel
getRemotePartnerDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getRemotePartSamples(long, long) - Method in class org.jbei.ice.services.rest.PartnerResource
getRemoteSequence() - Method in class org.jbei.ice.lib.net.RemoteSequence
getRemoteShare() - Method in class org.jbei.ice.storage.model.Permission
getRemoteShareModelDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getRemoteUser(long, String) - Method in class org.jbei.ice.lib.access.RemoteAccess
getRemoteUser(long, String) - Method in class org.jbei.ice.services.rest.PartnerResource
getReplicatesIn() - Method in class org.jbei.ice.lib.dto.entry.PlasmidData
getReplicatesIn() - Method in class org.jbei.ice.storage.model.Plasmid
getRequestDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getRequested() - Method in class org.jbei.ice.storage.model.Request
getRequestedEntry(String, String, String, long, RegistryPartner) - Method in class org.jbei.ice.lib.entry.EntryController
getRequestedSamples(long, int, int, String, boolean, long, SampleRequestStatus) - Method in class org.jbei.ice.services.rest.UserResource
getRequestedSequence(RegistryPartner, String, String, String, long) - Method in class org.jbei.ice.lib.entry.sequence.SequenceController
getRequester() - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
getRequestFile(String, ArrayList<Long>) - Method in class org.jbei.ice.services.rest.SampleResource
getRequests() - Method in class org.jbei.ice.lib.dto.sample.UserSamples
getRequests(String, int, int, String, boolean, SampleRequestStatus, String) - Method in class org.jbei.ice.lib.entry.sample.RequestRetriever
getRequests(int, int, String, boolean, String, SampleRequestStatus) - Method in class org.jbei.ice.services.rest.SampleResource
getRequestTime() - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
getRequestType() - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
getRestrictionEnzymes() - Method in class org.jbei.ice.storage.model.AccountPreferences
getResultCount() - Method in class org.jbei.ice.lib.dto.AccountResults
getResultCount() - Method in class org.jbei.ice.lib.dto.common.Results
getResultCount() - Method in class org.jbei.ice.lib.dto.search.SearchResults
getResults() - Method in class org.jbei.ice.lib.dto.AccountResults
getResults() - Method in class org.jbei.ice.lib.dto.search.SearchResults
getResults() - Method in class org.jbei.ice.lib.search.WebResult
getResults() - Method in class org.jbei.ice.lib.search.WebSearch.SearchTask
getResults() - Method in class org.jbei.ice.lib.search.WebSearchResults
getRetrieveCount() - Method in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
getRevHash() - Method in class org.jbei.ice.storage.model.Sequence
getSalt() - Method in class org.jbei.ice.storage.model.Account
getSalt() - Method in class org.jbei.ice.storage.model.RemotePartner
getSampleByToken(String) - Method in class org.jbei.ice.services.rest.SampleResource
getSampleCount() - Method in class org.jbei.ice.lib.dto.entry.PartStatistics
getSampleCount(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.SampleDAO
getSampleDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getSampleField() - Method in class org.jbei.ice.lib.bulkupload.SampleHeaderValue
getSampleRequestByStatus(Account, Entry, SampleRequestStatus) - Method in class org.jbei.ice.storage.hibernate.dao.RequestDAO
getSampleRequestInCart(Account, Entry) - Method in class org.jbei.ice.storage.hibernate.dao.RequestDAO
getSamples() - Method in class org.jbei.ice.lib.dto.comment.UserComment
getSamples() - Method in class org.jbei.ice.lib.net.RemoteEntry
getSamples(String) - Method in class org.jbei.ice.services.rest.PartResource
getSamples() - Method in class org.jbei.ice.storage.model.Comment
getSamples() - Method in class org.jbei.ice.storage.model.Entry
getSamplesByBarcode(String, String) - Method in class org.jbei.ice.lib.entry.sample.SampleService
getSamplesByEntry(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.SampleDAO
getSamplesByStorage(Storage) - Method in class org.jbei.ice.storage.hibernate.dao.SampleDAO: Retrieve Sample objects associated with the given Storage object.
getSBOLVisual(String) - Method in class org.jbei.ice.services.rest.FileResource
getScore() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
getScore() - Method in class org.jbei.ice.lib.dto.search.SearchResult
getScore() - Method in class org.jbei.ice.lib.parsers.bl2seq.Bl2SeqResult
getScore() - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
getSearchQuery() - Method in class org.jbei.ice.lib.entry.EntrySelection
getSearchResults(SearchQuery) - Method in class org.jbei.ice.lib.entry.Entries
getSecret() - Method in class org.jbei.ice.lib.dto.access.AccessKey
getSecret() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
getSecret() - Method in class org.jbei.ice.storage.model.ApiKey
getSecret() - Method in class org.jbei.ice.storage.model.RemoteShareModel
getSeedFieldValues(ArabidopsisSeed, EntryField) - Static method in class org.jbei.ice.lib.entry.EntryUtil
getSeedFieldValues(ArabidopsisSeedData, EntryField) - Static method in class org.jbei.ice.lib.entry.PartDataUtil
getSeedParents() - Method in class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
getSelectionMarkerDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getSelectionMarkers() - Method in class org.jbei.ice.lib.dto.entry.PartData
getSelectionMarkers() - Method in class org.jbei.ice.storage.model.Entry
getSelectionMarkersAsList(Set<SelectionMarker>) - Static method in class org.jbei.ice.lib.entry.EntryUtil
getSelectionMarkersAsString() - Method in class org.jbei.ice.storage.model.Entry
getSelectionType() - Method in class org.jbei.ice.lib.entry.EntrySelection
getSent() - Method in class org.jbei.ice.lib.dto.message.MessageInfo
getSent() - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
getSent() - Method in class org.jbei.ice.storage.model.RemotePartner
getSequence() - Method in class org.jbei.ice.lib.dto.DNAFeature
getSequence() - Method in class org.jbei.ice.lib.dto.DNASequence
getSequence() - Method in class org.jbei.ice.lib.dto.entry.SequenceInfo
getSequence() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
getSequence() - Method in class org.jbei.ice.lib.dto.search.BlastQuery
getSequence(String) - Method in class org.jbei.ice.lib.dto.web.WebEntries
getSequence(String, String, String, long, String, String) - Method in class org.jbei.ice.lib.net.RemoteContact
getSequence(String, long, String) - Method in class org.jbei.ice.lib.net.RemoteEntries
getSequence() - Method in class org.jbei.ice.lib.parsers.abi.ABITrace: Returns the original programatically determined (unedited) sequence as a SymbolList.
getSequence() - Method in class org.jbei.ice.lib.parsers.genbank.OriginTag
getSequence(long, long) - Method in class org.jbei.ice.services.rest.PartnerResource
getSequence(String, boolean, String, String, long) - Method in class org.jbei.ice.services.rest.PartResource
getSequence(int) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceDAO: Enables retrieving sequences in the database without loading everything in memory
Expected usage is long count = getSequenceCount(); int offset = 0; while( offset < count ) { Sequence sequence = dao.getSequence(offset); // do something with sequence }
getSequence() - Method in class org.jbei.ice.storage.model.Entry
getSequence() - Method in class org.jbei.ice.storage.model.Feature
getSequence() - Method in class org.jbei.ice.storage.model.Sequence
getSequence() - Method in class org.jbei.ice.storage.model.SequenceFeature
getSequence() - Method in class org.jbei.ice.storage.model.TraceSequence
getSequenceCount() - Method in class org.jbei.ice.lib.dto.entry.PartStatistics
getSequenceCount() - Method in class org.jbei.ice.storage.hibernate.dao.SequenceDAO
getSequenceDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getSequenceDocument(SBOLRootObject) - Method in class org.jbei.ice.lib.bulkupload.BulkFileSBOLUpload
getSequenceFeature() - Method in class org.jbei.ice.storage.model.AnnotationLocation
getSequenceFeature() - Method in class org.jbei.ice.storage.model.SequenceFeatureAttribute
getSequenceFeatureAttributes() - Method in class org.jbei.ice.storage.model.SequenceFeature
getSequenceFeatureDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getSequenceFeatures(String, List<Group>, String, int, int) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceFeatureDAO
getSequenceFeatures() - Method in class org.jbei.ice.storage.model.Sequence
getSequenceFeaturesCount(String, List<Group>, String) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceFeatureDAO
getSequenceFile(String, long, SequenceFormat) - Method in class org.jbei.ice.lib.entry.sequence.SequenceController
getSequenceFileName() - Method in class org.jbei.ice.lib.dto.entry.PartData
getSequenceFilename(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceDAO
getSequenceHash() - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
getSequenceLength() - Method in class org.jbei.ice.lib.parsers.abi.ABITrace: Returns the length of the sequence (number of bases) in this trace.
getSequenceString(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceDAO
getSequenceTraces(long, long) - Method in class org.jbei.ice.services.rest.PartnerResource
getSequenceUser() - Method in class org.jbei.ice.storage.model.Sequence
getSessionFactory() - Static method in class org.jbei.ice.storage.hibernate.HibernateUtil: Retrieve the SessionFactory.
getSessionId() - Method in class org.jbei.ice.lib.account.AccountTransfer
getShared() - Method in class org.jbei.ice.lib.folder.CollectionCounts
getSharedEntries(ColumnField, boolean, int, int, String) - Method in class org.jbei.ice.lib.folder.collection.CollectionEntries: Retrieves entries shared with user.
getSharedUserFolders(String) - Method in class org.jbei.ice.lib.folder.FolderController: Retrieves folders that have been shared with specified user as an individual or as part of a group.
getSharer() - Method in class org.jbei.ice.storage.model.RemoteShareModel
getShortDescription() - Method in class org.jbei.ice.lib.dto.entry.PartData
getShortDescription() - Method in class org.jbei.ice.storage.model.Entry
getShotgunSequenceCount(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.ShotgunSequenceDAO
getShotgunSequenceDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getShotgunSequenceFile(String) - Method in class org.jbei.ice.services.rest.FileResource
getShotgunSequences(UriInfo, long, int, int) - Method in class org.jbei.ice.services.rest.PartResource
getSirName() - Method in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
getSiteSettings() - Method in class org.jbei.ice.lib.config.ConfigurationController
getSiteSettings() - Method in class org.jbei.ice.services.rest.ConfigResource
getSize(ArrayList<IDataTransferModel>, Class<?>, Type, Annotation[], MediaType) - Method in class org.jbei.ice.services.rest.ArrayDataJSONHandler
getSize(IDataTransferModel, Class<?>, Type, Annotation[], MediaType) - Method in class org.jbei.ice.services.rest.PartDataJSONHandler
getSort(boolean, ColumnField) - Method in class org.jbei.ice.storage.hibernate.search.HibernateSearch
getSortField() - Method in class org.jbei.ice.lib.dto.common.PageParameters
getSortField() - Method in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
getStart() - Method in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
getStatistics(long) - Method in class org.jbei.ice.services.rest.PartResource
getStatistics(long, long) - Method in class org.jbei.ice.services.rest.WebResource
getStatus() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
getStatus() - Method in class org.jbei.ice.lib.dto.entry.PartData
getStatus() - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
getStatus() - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
getStatus() - Method in class org.jbei.ice.lib.executor.Task
getStatus() - Method in class org.jbei.ice.lib.manuscript.Manuscript
getStatus() - Static method in class org.jbei.ice.lib.search.blast.BlastPlus
getStatus() - Method in class org.jbei.ice.lib.search.IndexerProgressMonitor
getStatus() - Method in class org.jbei.ice.storage.model.ApiKey
getStatus() - Method in class org.jbei.ice.storage.model.BulkUpload
getStatus() - Method in class org.jbei.ice.storage.model.Entry
getStatus() - Method in class org.jbei.ice.storage.model.ManuscriptModel
getStatus() - Method in class org.jbei.ice.storage.model.Message
getStatus() - Method in class org.jbei.ice.storage.model.Request
getStorage() - Method in class org.jbei.ice.storage.model.Sample
getStorageDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getStorageType() - Method in class org.jbei.ice.storage.model.Storage
getStrainData() - Method in class org.jbei.ice.lib.dto.entry.PartData
getStrainFieldValues(Strain, EntryField) - Static method in class org.jbei.ice.lib.entry.EntryUtil
getStrainFieldValues(StrainData, EntryField) - Static method in class org.jbei.ice.lib.entry.PartDataUtil
getStrand() - Method in class org.jbei.ice.lib.dto.DNAFeature
getStrand() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
getStrand(SequenceFeature) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter: Get the strand of the SequenceFeature feature.
getStrand() - Method in class org.jbei.ice.storage.model.SequenceFeature
getStrand() - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
getString(InputStream) - Static method in class org.jbei.ice.lib.utils.Utils
getSubFolders(CollectionType) - Method in class org.jbei.ice.lib.folder.collection.Collections: Retrieves the sub folders for the specified collection type
getSubjectAlignment() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
getSubjectAlignment() - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
getSubjectEnd() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
getSubjectEnd() - Method in class org.jbei.ice.lib.parsers.bl2seq.Bl2SeqResult
getSubjectEnd() - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
getSubjects() - Method in class org.jbei.ice.storage.model.Experiment
getSubjectSequence() - Method in class org.jbei.ice.lib.parsers.bl2seq.Bl2SeqResult
getSubjectStart() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
getSubjectStart() - Method in class org.jbei.ice.lib.parsers.bl2seq.Bl2SeqResult
getSubjectStart() - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
getSystemVersion(String) - Method in class org.jbei.ice.lib.config.ConfigurationController
getThisInstanceWithNewApiKey() - Method in class org.jbei.ice.lib.net.WebPartners: Generates a new partner object representing this ICE instance with a new API key
getThisServer(boolean) - Method in class org.jbei.ice.services.rest.RestResource
getThisUri() - Method in class org.jbei.ice.lib.net.WebPartners
getTime() - Method in class org.jbei.ice.lib.dto.History
getTime() - Method in class org.jbei.ice.storage.model.Audit
getTitle() - Method in class org.jbei.ice.lib.dto.message.MessageInfo
getTitle() - Method in class org.jbei.ice.lib.manuscript.Manuscript
getTitle() - Method in class org.jbei.ice.storage.model.ManuscriptModel
getTitle() - Method in class org.jbei.ice.storage.model.Message
getTmpFile(String, String) - Method in class org.jbei.ice.services.rest.FileResource: Retrieves a temp file by fileId
getToken() - Method in class org.jbei.ice.lib.dto.access.AccessKey
getToken() - Method in class org.jbei.ice.storage.model.RemoteAccessModel
getToolTipDetails(String, String, long, String, String) - Method in class org.jbei.ice.lib.net.RemoteContact
getTooltipDetails(String, boolean, long) - Method in class org.jbei.ice.services.rest.PartResource: Retrieves either a remote or local tooltip
getTotal() - Method in class org.jbei.ice.lib.search.IndexBuildStatus
getTotalCount() - Method in class org.jbei.ice.lib.search.WebSearchResults
getTotalCount(String) - Method in class org.jbei.ice.storage.hibernate.dao.ManuscriptModelDAO
getTrace(AtomicSymbol) - Method in class org.jbei.ice.lib.parsers.abi.ABITrace: Returns one of the four traces - all of the y-coordinate values, each of which correspond to a single x-coordinate relative to the position in the array, so that if element 4 in the array is 972, then x is 4 and y is 972 for that point.
getTraceLength() - Method in class org.jbei.ice.lib.parsers.abi.ABITrace: Returns the length of the trace (number of x-coordinate points in the graph).
getTraces(int, int) - Method in class org.jbei.ice.lib.entry.sequence.TraceSequences
getTraces() - Method in class org.jbei.ice.lib.net.RemoteEntry
getTraces(long, int, int) - Method in class org.jbei.ice.services.rest.PartResource
getTraceSequence() - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
getTraceSequenceAlignment() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
getTraceSequenceAlignment() - Method in class org.jbei.ice.storage.model.TraceSequence
getTraceSequenceByFileId(String) - Method in class org.jbei.ice.lib.entry.sequence.SequenceAnalysisController
getTraceSequenceDAO() - Static method in class org.jbei.ice.storage.DAOFactory
getTraceSequenceFile(String, String) - Method in class org.jbei.ice.services.rest.FileResource
getTraceSequences(Entry) - Method in class org.jbei.ice.lib.entry.sequence.SequenceAnalysisController: Retrieve the TraceSequence associated with the given Entry entry.
getTransferred() - Method in class org.jbei.ice.lib.folder.CollectionCounts
getTransferredFolders(String) - Method in class org.jbei.ice.lib.folder.FolderController
getType() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadAutoUpdate
getType() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
getType() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
getType() - Method in class org.jbei.ice.lib.dto.DNAFeature
getType() - Method in class org.jbei.ice.lib.dto.entry.PartData
getType() - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
getType() - Method in class org.jbei.ice.lib.dto.group.UserGroup
getType() - Method in class org.jbei.ice.lib.dto.StorageLocation
getType() - Method in class org.jbei.ice.lib.parsers.genbank.Tag
getType() - Method in class org.jbei.ice.storage.model.Account
getType() - Method in class org.jbei.ice.storage.model.Folder
getType() - Method in class org.jbei.ice.storage.model.Group
getType() - Method in class org.jbei.ice.storage.model.Request
getTypeId() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
getUIAsset(String) - Method in class org.jbei.ice.lib.config.ConfigurationController
getUniqueEnd() - Method in class org.jbei.ice.storage.model.SequenceFeature
getUniqueGenbankStart() - Method in class org.jbei.ice.storage.model.SequenceFeature
getUpdate() - Method in class org.jbei.ice.lib.parsers.sbol.ICESBOLParserVisitor
getUpdated() - Method in class org.jbei.ice.storage.model.Request
getUpdateTime() - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
getUpload() - Method in class org.jbei.ice.storage.model.Permission
getUploadCSV(String, String) - Method in class org.jbei.ice.services.rest.FileResource
getUploadInfo() - Method in class org.jbei.ice.lib.bulkupload.ProcessedBulkUpload
getUploadPermissions(String, long) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController
getUploadPermissions(long) - Method in class org.jbei.ice.services.rest.BulkUploadResource: Retrieves permissions associated with an upload
getUri() - Method in class org.jbei.ice.lib.dto.DNAFeature
getUri() - Method in class org.jbei.ice.lib.dto.DNAFeatureLocation
getUri() - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
getURI(String) - Static method in class org.jbei.ice.lib.entry.sequence.composers.formatters.IceSequenceOntology
getUri() - Method in class org.jbei.ice.storage.model.Feature
getUri() - Method in class org.jbei.ice.storage.model.Sequence
getUri() - Method in class org.jbei.ice.storage.model.SequenceFeature
getUrl() - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
getUrl() - Method in class org.jbei.ice.lib.experiment.Study
getUrl() - Method in class org.jbei.ice.storage.model.Experiment
getUrl() - Method in class org.jbei.ice.storage.model.Link
getUrl() - Method in class org.jbei.ice.storage.model.RemotePartner
getUrlToken(String) - Static method in class org.jbei.ice.lib.access.AccessTokens
getUser() - Method in class org.jbei.ice.lib.dto.web.RemoteUser
getUser(String, String, String) - Method in class org.jbei.ice.lib.net.RemoteContact
getUserAccount(String, String) - Static method in class org.jbei.ice.lib.account.UserSessions: Retrieves the account object associated with the session identifier.
getUserEntryCount() - Method in class org.jbei.ice.lib.account.AccountTransfer
getUserFolders(String) - Method in class org.jbei.ice.lib.folder.FolderController
getUserGroups() - Method in class org.jbei.ice.lib.dto.message.MessageInfo
getUserId() - Method in interface org.jbei.auth.Authorization
getUserId() - Method in class org.jbei.auth.hmac.DefaultHmacSignature
getUserId() - Method in interface org.jbei.auth.hmac.HmacSignature
getUserId() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
getUserId() - Method in class org.jbei.ice.lib.dto.History
getUserId() - Method in class org.jbei.ice.lib.dto.user.UserPreferences
getUserId() - Method in class org.jbei.ice.services.rest.RestResource: Extract the User ID from header values in the resource request.
getUserId(String) - Method in class org.jbei.ice.services.rest.RestResource: Extract the User ID from a query parameter value or header values in the resource request.
getUserId() - Method in class org.jbei.ice.storage.model.Audit
getUserIdBySession(String) - Static method in class org.jbei.ice.lib.account.UserSessions
getUserMessage() - Method in class org.jbei.ice.lib.bulkupload.ProcessedBulkUpload
getUserPreferences(String, long) - Method in class org.jbei.ice.lib.account.PreferencesController
getUserPreferences(long) - Method in class org.jbei.ice.services.rest.UserResource
getUserRequests(int, int, String, boolean, long, SampleRequestStatus) - Method in class org.jbei.ice.services.rest.SampleResource
getUserSamples(String, SampleRequestStatus, int, int, String, boolean) - Method in class org.jbei.ice.lib.entry.sample.RequestRetriever
getUuid() - Method in class org.jbei.ice.lib.dto.group.UserGroup
getUuid() - Method in class org.jbei.ice.storage.model.Group
getUuid() - Method in class org.jbei.ice.storage.model.Sample
getUuid() - Method in class org.jbei.ice.storage.model.Storage
getValue() - Method in class org.jbei.ice.lib.dto.bulkupload.PreferenceInfo
getValue() - Method in class org.jbei.ice.lib.dto.DNAFeatureNote
getValue() - Method in class org.jbei.ice.lib.dto.entry.CustomField
getValue() - Method in enum org.jbei.ice.lib.dto.entry.Visibility
getValue() - Method in class org.jbei.ice.lib.dto.Setting
getValue() - Method in class org.jbei.ice.lib.parsers.genbank.Tag
getValue() - Method in enum org.jbei.ice.lib.shared.BioSafetyOption
getValue() - Method in class org.jbei.ice.storage.model.Configuration
getValue() - Method in class org.jbei.ice.storage.model.Parameter
getValue() - Method in class org.jbei.ice.storage.model.Preference
getValue() - Method in class org.jbei.ice.storage.model.SequenceFeatureAttribute
getVersion() - Method in class org.jbei.ice.lib.config.SiteSettings
getVersion(UriInfo) - Method in class org.jbei.ice.services.rest.ConfigResource
getVersionId() - Method in class org.jbei.ice.storage.model.Entry
getViewCount() - Method in class org.jbei.ice.lib.dto.entry.PartData
getVisibility() - Method in class org.jbei.ice.lib.dto.entry.PartData
getVisibility() - Method in class org.jbei.ice.storage.model.Entry
getVisibleEntryCount() - Method in class org.jbei.ice.lib.account.AccountTransfer
getVisibleEntryIds(boolean, Group) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
getWebEntries(long, int, int, String, boolean) - Method in class org.jbei.ice.services.rest.PartnerResource: Retrieves entries for specified partner using the specified paging parameters
getWebEntries(boolean, int, int) - Method in class org.jbei.ice.services.rest.WebResource
getWebEntry(long, long) - Method in class org.jbei.ice.services.rest.WebResource
getWebEntry(String) - Method in class org.jbei.ice.services.rest.WebResource
getWebEntrySequence(long, String) - Method in class org.jbei.ice.services.rest.WebResource
getWebEntryTooltip(long, long) - Method in class org.jbei.ice.services.rest.PartnerResource
getWebEntryTooltip(long, long) - Method in class org.jbei.ice.services.rest.WebResource
getWebPartner(String) - Method in class org.jbei.ice.services.rest.AccessTokenResource: Validates web of registries access token (api key)
getWebPartner(String) - Method in class org.jbei.ice.services.rest.PartnerResource: Retrieve details about a specific partner
getWebPartner() - Method in class org.jbei.ice.services.rest.RestResource
getWebPartners() - Method in class org.jbei.ice.services.rest.PartnerResource: Retrieves list of available web partners requested by user or an ICE instance
getWor(String, String, Class<T>, Map<String, Object>, String) - Method in class org.jbei.ice.services.rest.IceRestClient
getZipFileName() - Method in class org.jbei.ice.lib.manuscript.Manuscript
givenName - Variable in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
GMail - Class in org.jbei.ice.lib.email: Utility Methods for using gmail to email.
GMail() - Constructor for class org.jbei.ice.lib.email.GMail
Group - Class in org.jbei.ice.storage.model: Aggregate users into groups.
Group() - Constructor for class org.jbei.ice.storage.model.Group
GroupController - Class in org.jbei.ice.lib.group
GroupController() - Constructor for class org.jbei.ice.lib.group.GroupController
groupDAO - Variable in class org.jbei.ice.lib.access.Permissions
GroupDAO - Class in org.jbei.ice.storage.hibernate.dao: Data Accessor object to manipulate Group objects.
GroupDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.GroupDAO
groupHasReadPermission(List<Group>, Set<Folder>) - Method in class org.jbei.ice.lib.access.PermissionsController
groupHasWritePermission(List<Group>, Set<Folder>) - Method in class org.jbei.ice.lib.access.PermissionsController
GroupResource - Class in org.jbei.ice.services.rest: REST resource for groups
GroupResource() - Constructor for class org.jbei.ice.services.rest.GroupResource
Groups - Class in org.jbei.ice.lib.group: Groups of users with methods for manipulation (and access)
Groups(String) - Constructor for class org.jbei.ice.lib.group.Groups
GroupType - Enum in org.jbei.ice.lib.dto.group: Different types of groups that the system supports

H

handleRemoteAddRequest(RegistryPartner) - Method in class org.jbei.ice.lib.net.WebPartners: Handles requests from remote ice instances that will like to be in a WoR config with this instance Serves the dual purpose of: please add me as a partner to your list with token add accepted; use this as the authorization token
handleRemoteRemoveRequest(String, String) - Method in class org.jbei.ice.lib.net.RemoteContact
hasAttachment(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.AttachmentDAO
hasBlastQuery() - Method in class org.jbei.ice.lib.dto.search.SearchQuery
HasEntry - Class in org.jbei.ice.lib.entry: Parent class for all objects that have an entry, or need to retrieve one Provides a means to retrieve an entry using an id that can either be the database identifier for the entry object or any one of the other unique entry fields.
HasEntry() - Constructor for class org.jbei.ice.lib.entry.HasEntry
HasEntryData - Class in org.jbei.ice.lib.dto.entry
HasEntryData() - Constructor for class org.jbei.ice.lib.dto.entry.HasEntryData
hasFilter() - Method in class org.jbei.ice.lib.dto.search.SearchQuery
hashCode() - Method in class org.jbei.ice.storage.model.Account
hashCode() - Method in class org.jbei.ice.storage.model.Entry
hasOriginalSequence(long) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceDAO: Determines if the user uploaded a sequence file and associated it with an entry
hasPermission(Entry, Folder, BulkUpload, Account, Group, boolean, boolean) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
hasPermissionMulti(Entry, Set<Folder>, Account, List<Group>, boolean, boolean) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
hasSample(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.SampleDAO
hasSequence(long) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceDAO
hasSetWriteFolderPermission(Folder, Account) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
hasWritePermission(String, Folder) - Method in class org.jbei.ice.lib.access.PermissionsController
headerFields - Variable in class org.jbei.ice.lib.bulkupload.BulkCSVUpload
Headers - Class in org.jbei.ice.services.rest: Rest Header constants
Headers() - Constructor for class org.jbei.ice.services.rest.Headers
HeaderValue - Interface in org.jbei.ice.lib.bulkupload: Value of header
HibernateRepository<T extends DataModel> - Class in org.jbei.ice.storage.hibernate: Parent abstract class for Hibernate Persistence
HibernateRepository() - Constructor for class org.jbei.ice.storage.hibernate.HibernateRepository
HibernateSearch - Class in org.jbei.ice.storage.hibernate.search: Apache Lucene full text library functionality in Hibernate.
HibernateUtil - Class in org.jbei.ice.storage.hibernate: Helper class to Initialize Hibernate, and obtain new sessions.
History - Class in org.jbei.ice.lib.dto
History() - Constructor for class org.jbei.ice.lib.dto.History
HMAC_SIGNATURE - Static variable in class org.jbei.ice.services.rest.AuthenticationInterceptor: Property/Attribute name for mapping the HmacSignature object for the request.
HmacAuthorizor - Class in org.jbei.auth.hmac: Creates Authorization objects based on HMAC values in HTTP Authorization headers.
HmacAuthorizor(KeyTable) - Constructor for class org.jbei.auth.hmac.HmacAuthorizor
hmacHeader - Variable in class org.jbei.ice.services.rest.RestResource
HmacInputStream - Class in org.jbei.auth.hmac: Decorates an InputStream to pass all read bytes to a Mac.
HmacInputStream(InputStream, Mac) - Constructor for class org.jbei.auth.hmac.HmacInputStream
HmacOutputStream - Class in org.jbei.auth.hmac: Decorates an OutputStream to pass all written bytes through a Mac.
HmacOutputStream(OutputStream, Mac) - Constructor for class org.jbei.auth.hmac.HmacOutputStream
HmacSignature - Interface in org.jbei.auth.hmac: Utility class to handle generating HMAC signatures in REST requests.
HmacSignatureFactory - Class in org.jbei.auth.hmac: Generates HmacSignature objects for use in authenticating requests to a REST service.
HmacSignatureFactory(KeyTable) - Constructor for class org.jbei.auth.hmac.HmacSignatureFactory: Constructor initializes factory with the secret used to sign requests.

I

IAuthentication - Interface in org.jbei.ice.lib.account.authentication: Interface for different authentication types.
IceApplication - Class in org.jbei.ice.services.rest.multipart
IceApplication() - Constructor for class org.jbei.ice.services.rest.multipart.IceApplication
ICEExceptionMapper - Class in org.jbei.ice.services.rest
ICEExceptionMapper() - Constructor for class org.jbei.ice.services.rest.ICEExceptionMapper
IceExecutorService - Class in org.jbei.ice.lib.executor
IceFilter - Class in org.jbei.ice.servlet.filter
IceFilter() - Constructor for class org.jbei.ice.servlet.filter.IceFilter
IceRequestFilter - Class in org.jbei.ice.services.rest: Request filter which begins transaction for request.
IceRequestFilter() - Constructor for class org.jbei.ice.services.rest.IceRequestFilter
IceResponseFilter - Class in org.jbei.ice.services.rest: Rolls back the transaction if http status is 500 otherwise commits transaction if started
IceResponseFilter() - Constructor for class org.jbei.ice.services.rest.IceResponseFilter
IceRestClient - Class in org.jbei.ice.services.rest: ICE REST client
IceRestClient() - Constructor for class org.jbei.ice.services.rest.IceRestClient
ICESBOLParserVisitor - Class in org.jbei.ice.lib.parsers.sbol: Implementation of the ICESBOLParserVisitor
ICESBOLParserVisitor() - Constructor for class org.jbei.ice.lib.parsers.sbol.ICESBOLParserVisitor
ICESBOLParserVisitor(EntryType) - Constructor for class org.jbei.ice.lib.parsers.sbol.ICESBOLParserVisitor
IceSequenceOntology - Class in org.jbei.ice.lib.entry.sequence.composers.formatters
IceSequenceOntology() - Constructor for class org.jbei.ice.lib.entry.sequence.composers.formatters.IceSequenceOntology
IceServletContextListener - Class in org.jbei.ice.servlet: Ice servlet context listener for running initializing and pre-shutdown instructions
IceServletContextListener() - Constructor for class org.jbei.ice.servlet.IceServletContextListener
id - Variable in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
id - Variable in class org.jbei.ice.storage.model.Group
IDataTransferModel - Interface in org.jbei.ice.storage: Interface for data transfer objects
IFormatter - Interface in org.jbei.ice.lib.entry.sequence.composers.formatters: Interface for Formatters.
importTraceSequence(String, String, InputStream) - Method in class org.jbei.ice.lib.entry.sequence.TraceSequences: Create a new TraceSequence record and associated with the Entry entry.
IndexBuildStatus - Class in org.jbei.ice.lib.search
IndexBuildStatus(long, long) - Constructor for class org.jbei.ice.lib.search.IndexBuildStatus
IndexerProgressMonitor - Class in org.jbei.ice.lib.search
indexingCompleted() - Method in class org.jbei.ice.lib.search.IndexerProgressMonitor
indexingInterrupted() - Method in class org.jbei.ice.lib.search.IndexerProgressMonitor
IndexType - Enum in org.jbei.ice.lib.dto.search: Represents the different kinds of indexes available
info(String) - Static method in class org.jbei.ice.lib.common.logging.Logger
infoToEntry(PartData) - Static method in class org.jbei.ice.servlet.InfoToModelFactory
infoToEntryForField(Entry, Entry, String, EntryField) - Static method in class org.jbei.ice.servlet.InfoToModelFactory: Updates the entry based on the field that is specified.
InfoToModelFactory - Class in org.jbei.ice.servlet: Factory object for converting data transfer objects to model objects
InfoToModelFactory() - Constructor for class org.jbei.ice.servlet.InfoToModelFactory
init(FilterConfig) - Method in class org.jbei.ice.servlet.filter.IceFilter
init() - Method in class org.jbei.ice.servlet.IceServletContextListener
initialized - Variable in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
initializeMock() - Static method in class org.jbei.ice.storage.hibernate.HibernateUtil: Initialize a in-memory mock database for testing.
initPropertyValues() - Method in class org.jbei.ice.lib.config.ConfigurationController: Initializes the database on new install
initSignature(String, String, String, String, Map<String, ? extends Iterable<String>>) - Method in class org.jbei.auth.hmac.HmacAuthorizor: Creates an initial signature object based on the request and Authorization header value.
intValue(String) - Static method in enum org.jbei.ice.lib.shared.BioSafetyOption
INVALID - Static variable in interface org.jbei.auth.Authorization: Pre-made invalid authorization object.
invalidate(String) - Method in class org.jbei.ice.lib.account.AccountController: De-authenticate the given sessionKey.
invalidateSession(String) - Static method in class org.jbei.ice.lib.account.UserSessions: Invalidates the session id for the specified user by removing the stored session id
InvalidCredentialsException - Exception in org.jbei.ice.lib.account.authentication: Exception for Invalid Credentials.
InvalidCredentialsException(String) - Constructor for exception org.jbei.ice.lib.account.authentication.InvalidCredentialsException: Create new InvalidCredentialsException with a message.
InvalidCredentialsException(Throwable) - Constructor for exception org.jbei.ice.lib.account.authentication.InvalidCredentialsException: Create a new InvalidCredentialsException with a Throwable.
invalidFields - Variable in class org.jbei.ice.lib.bulkupload.BulkCSVUpload
InvalidFormatParserException - Exception in org.jbei.ice.lib.parsers: Exception class for parsers.
InvalidFormatParserException() - Constructor for exception org.jbei.ice.lib.parsers.InvalidFormatParserException
InvalidFormatParserException(String, Throwable) - Constructor for exception org.jbei.ice.lib.parsers.InvalidFormatParserException
InvalidFormatParserException(String) - Constructor for exception org.jbei.ice.lib.parsers.InvalidFormatParserException
InvalidFormatParserException(Throwable) - Constructor for exception org.jbei.ice.lib.parsers.InvalidFormatParserException
IRepository<T extends DataModel> - Interface in org.jbei.ice.storage: Interface for the persistent layer
isAdd() - Method in class org.jbei.ice.lib.dto.bulkupload.PreferenceInfo
isAdmin(String) - Method in class org.jbei.ice.lib.access.Authorization
isAdmin() - Method in class org.jbei.ice.lib.account.AccountTransfer
isAdministrator(String) - Method in class org.jbei.ice.lib.account.AccountController: Check in the database if an account is a moderator.
isAdministrator(Account) - Method in class org.jbei.ice.lib.account.Accounts
isAdministrator() - Method in class org.jbei.ice.lib.entry.sequence.annotation.Annotations
isAll() - Method in class org.jbei.ice.lib.entry.EntrySelection
isAscending() - Method in class org.jbei.ice.lib.dto.common.PageParameters
isAuthenticated() - Method in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
isAutoJoin() - Method in class org.jbei.ice.lib.dto.group.UserGroup
isAutoJoin() - Method in class org.jbei.ice.storage.model.Group
isCanEdit() - Method in class org.jbei.ice.lib.dto.entry.PartData
isCanEdit() - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
isCanEdit() - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
isCanEdit() - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
isCanEdit() - Method in class org.jbei.ice.lib.dto.sample.PartSample
isCanEdit() - Method in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
isCanRead() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
isCanRead() - Method in class org.jbei.ice.storage.model.Permission
isCanWrite() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
isCanWrite() - Method in class org.jbei.ice.storage.model.Permission
isDebugEnabled() - Static method in class org.jbei.ice.lib.common.logging.Logger
isEntry() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
isExclude() - Method in class org.jbei.ice.lib.dto.Curation
isExclude() - Method in class org.jbei.ice.storage.model.FeatureCurationModel
isFolder() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
isHasAttachment() - Method in class org.jbei.ice.lib.dto.entry.PartData
isHasFooter() - Method in class org.jbei.ice.lib.config.SiteSettings
isHasLoginMessage() - Method in class org.jbei.ice.lib.config.SiteSettings
isHasLogo() - Method in class org.jbei.ice.lib.config.SiteSettings
isHasOriginalSequence() - Method in class org.jbei.ice.lib.dto.entry.PartData
isHasSample() - Method in class org.jbei.ice.lib.dto.entry.PartData
isHasSequence() - Method in class org.jbei.ice.lib.dto.entry.PartData
isInbetween() - Method in class org.jbei.ice.lib.parsers.genbank.GenbankLocation
isInbetween() - Method in class org.jbei.ice.storage.model.AnnotationLocation
isInCart() - Method in class org.jbei.ice.lib.dto.sample.PartSample
isInWebOfRegistries() - Method in class org.jbei.ice.lib.net.WebPartners: Checks if the web of registries admin config value has been set to enable this ICE instance to join the web of registries configuration
isOwner(String, T) - Method in class org.jbei.ice.lib.access.Authorization
isPropagatePermission() - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
isPropagatePermissions() - Method in class org.jbei.ice.storage.model.Folder
isPubliclyVisible(Entry) - Method in class org.jbei.ice.lib.access.PermissionsController: Determines whether an entry has assigned public privileges either directly or by virtue of being in a folder that has public privileges assigned
isPublicRead() - Method in class org.jbei.ice.lib.dto.entry.PartData
isPublicReadAccess() - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
isPublicVisible(Folder) - Method in class org.jbei.ice.lib.access.PermissionsController
isQuoted() - Method in class org.jbei.ice.lib.dto.DNAFeatureNote
isRead() - Method in class org.jbei.ice.lib.dto.message.MessageInfo
isRead() - Method in class org.jbei.ice.storage.model.Message
isReadable(Class<?>, Type, Annotation[], MediaType) - Method in class org.jbei.ice.services.rest.ArrayDataJSONHandler
isReadable(Class<?>, Type, Annotation[], MediaType) - Method in class org.jbei.ice.services.rest.PartDataJSONHandler
isRequired() - Method in enum org.jbei.ice.lib.dto.entry.EntryField
isSampleField() - Method in class org.jbei.ice.lib.bulkupload.EntryHeaderValue
isSampleField() - Method in interface org.jbei.ice.lib.bulkupload.HeaderValue
isSampleField() - Method in class org.jbei.ice.lib.bulkupload.SampleHeaderValue
isSentToAbrc() - Method in class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
isSentToABRC() - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
isSingleResidue() - Method in class org.jbei.ice.lib.parsers.genbank.GenbankLocation
isSingleResidue() - Method in class org.jbei.ice.storage.model.AnnotationLocation
isSortAscending() - Method in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
isSubType() - Method in class org.jbei.ice.lib.bulkupload.EntryHeaderValue
isSuccess() - Method in class org.jbei.ice.lib.bulkupload.ProcessedBulkUpload
isTopLevel() - Method in enum org.jbei.ice.lib.dto.sample.SampleType
isUpload() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
isValid() - Method in interface org.jbei.auth.Authorization
isValid() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadValidation: Validates the bulk upload entries Note This retrieves the entries for the upload at the time of validation
isValidOption(Integer) - Static method in enum org.jbei.ice.lib.shared.BioSafetyOption
isValidPassword(Account, String) - Method in class org.jbei.ice.lib.account.authentication.LocalAuthentication: Check if the given password is valid for the account.
isValidUrl(String) - Method in class org.jbei.ice.lib.net.WebPartners: Validates the url by pre-pending "https://" as the scheme
isWebEnabled() - Method in class org.jbei.ice.lib.dto.web.WebOfRegistries
isWebEnabled() - Method in class org.jbei.ice.lib.net.WoRController
isWikiUser(String) - Method in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication: Check if the user is in the settings file specified ldap group before authenticating.
isWriteable(Class<?>, Type, Annotation[], MediaType) - Method in class org.jbei.ice.services.rest.ArrayDataJSONHandler
isWriteable(Class<?>, Type, Annotation[], MediaType) - Method in class org.jbei.ice.services.rest.PartDataJSONHandler

J

join(Collection<?>) - Static method in class org.jbei.ice.lib.entry.PartDataUtil: Concatenate a Collection of Strings using the given delimiter.
join(Part, Part) - Method in class org.jbei.ice.lib.utils.PackageAssembler: Join two standardized Parts.
join(String, Collection<?>) - Static method in class org.jbei.ice.lib.utils.Utils: Concatenate a Collection of Strings using the given delimiter.

K

KeyTable - Interface in org.jbei.auth
KEYWORDS_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser

L

label - Variable in class org.jbei.ice.storage.model.Group
LblLdapAuthentication - Class in org.jbei.ice.lib.account.authentication: Authentication for LBL's LDAP system.
LblLdapAuthentication() - Constructor for class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
Link - Class in org.jbei.ice.storage.model: Store url link information.
Link() - Constructor for class org.jbei.ice.storage.model.Link
linkedHeaders - Variable in class org.jbei.ice.lib.bulkupload.BulkCSVUpload
LinkType - Enum in org.jbei.ice.lib.entry: Represents the type of hierarchical relationship between two entries
list(long) - Method in class org.jbei.ice.services.rest.CustomFieldResource
list(String, boolean, int, int, String) - Method in class org.jbei.ice.storage.hibernate.dao.ManuscriptModelDAO
LocalAuthentication - Class in org.jbei.ice.lib.account.authentication: Default ICE authentication scheme
LocalAuthentication() - Constructor for class org.jbei.ice.lib.account.authentication.LocalAuthentication
LOCUS_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
log(String, String) - Method in class org.jbei.ice.services.rest.RestResource: Used to log user actions
Logger - Class in org.jbei.ice.lib.common.logging: Logger for ICE.
Logger() - Constructor for class org.jbei.ice.lib.common.logging.Logger

M

Manuscript - Class in org.jbei.ice.lib.manuscript
Manuscript() - Constructor for class org.jbei.ice.lib.manuscript.Manuscript
ManuscriptModel - Class in org.jbei.ice.storage.model
ManuscriptModel() - Constructor for class org.jbei.ice.storage.model.ManuscriptModel
ManuscriptModelDAO - Class in org.jbei.ice.storage.hibernate.dao
ManuscriptModelDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.ManuscriptModelDAO
ManuscriptResource - Class in org.jbei.ice.services.rest
ManuscriptResource() - Constructor for class org.jbei.ice.services.rest.ManuscriptResource
Manuscripts - Class in org.jbei.ice.lib.manuscript
Manuscripts(String) - Constructor for class org.jbei.ice.lib.manuscript.Manuscripts
ManuscriptStatus - Enum in org.jbei.ice.lib.manuscript
markMessageAsRead(long) - Method in class org.jbei.ice.lib.message.Messages: Marks a message as read and returns the number of unread messages
matchGroupNames(String, int) - Method in class org.jbei.ice.services.rest.GroupResource
MemoryKeyTable - Class in org.jbei.auth: Simple KeyTable stores mapping of KeyID => Key in memory.
MemoryKeyTable() - Constructor for class org.jbei.auth.MemoryKeyTable: Calls super HashMap constructor.
MemoryKeyTable(int, float) - Constructor for class org.jbei.auth.MemoryKeyTable: Calls super HashMap constructor.
MemoryKeyTable(int) - Constructor for class org.jbei.auth.MemoryKeyTable: Calls super HashMap constructor.
MemoryKeyTable(Map<? extends String, ? extends Key>) - Constructor for class org.jbei.auth.MemoryKeyTable: Calls super HashMap constructor.
Message - Class in org.jbei.ice.storage.model: Encapsulates system and user messages which can be sent to groups or individuals.
Message() - Constructor for class org.jbei.ice.storage.model.Message
MessageDAO - Class in org.jbei.ice.storage.hibernate.dao: Hibernate DAO for Message
MessageDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.MessageDAO
MessageInfo - Class in org.jbei.ice.lib.dto.message: DTO for message object
MessageInfo() - Constructor for class org.jbei.ice.lib.dto.message.MessageInfo
MessageResource - Class in org.jbei.ice.services.rest: Rest resource for handling messages in ICE
MessageResource() - Constructor for class org.jbei.ice.services.rest.MessageResource
Messages - Class in org.jbei.ice.lib.message
Messages(String) - Constructor for class org.jbei.ice.lib.message.Messages
MessageStatus - Enum in org.jbei.ice.lib.message: Used to set the status of a message.
ModelToInfoFactory - Class in org.jbei.ice.storage: Factory for converting Entrys to a PartData data transfer objects
ModelToInfoFactory() - Constructor for class org.jbei.ice.storage.ModelToInfoFactory
modifyFolderEntries(long, boolean, EntrySelection) - Method in class org.jbei.ice.services.rest.FolderResource: Modifies the contents of a folder either by removing or moving entries as determined by the move parameter
moveEntriesToTrash(String, ArrayList<PartData>) - Method in class org.jbei.ice.lib.entry.EntryController: Moves the specified list of entries to the deleted folder.
moveToTrash(ArrayList<PartData>) - Method in class org.jbei.ice.services.rest.PartResource

N

nameToType(String) - Static method in enum org.jbei.ice.lib.dto.entry.EntryType
newSession() - Static method in class org.jbei.ice.storage.hibernate.HibernateUtil: Open a new Session from the sessionFactory.
NID_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser

O

org.jbei.auth - package org.jbei.auth
org.jbei.auth.hmac - package org.jbei.auth.hmac
org.jbei.ice - package org.jbei.ice
org.jbei.ice.lib.access - package org.jbei.ice.lib.access: Permissions related classes.
org.jbei.ice.lib.account - package org.jbei.ice.lib.account
org.jbei.ice.lib.account.authentication - package org.jbei.ice.lib.account.authentication: Authentication classes.
org.jbei.ice.lib.bulkupload - package org.jbei.ice.lib.bulkupload
org.jbei.ice.lib.common.logging - package org.jbei.ice.lib.common.logging: Logging facilities.
org.jbei.ice.lib.config - package org.jbei.ice.lib.config
org.jbei.ice.lib.dto - package org.jbei.ice.lib.dto: Value Objects classes.
org.jbei.ice.lib.dto.access - package org.jbei.ice.lib.dto.access
org.jbei.ice.lib.dto.bulkupload - package org.jbei.ice.lib.dto.bulkupload
org.jbei.ice.lib.dto.comment - package org.jbei.ice.lib.dto.comment
org.jbei.ice.lib.dto.common - package org.jbei.ice.lib.dto.common
org.jbei.ice.lib.dto.entry - package org.jbei.ice.lib.dto.entry
org.jbei.ice.lib.dto.folder - package org.jbei.ice.lib.dto.folder
org.jbei.ice.lib.dto.group - package org.jbei.ice.lib.dto.group
org.jbei.ice.lib.dto.message - package org.jbei.ice.lib.dto.message
org.jbei.ice.lib.dto.sample - package org.jbei.ice.lib.dto.sample
org.jbei.ice.lib.dto.search - package org.jbei.ice.lib.dto.search
org.jbei.ice.lib.dto.user - package org.jbei.ice.lib.dto.user
org.jbei.ice.lib.dto.web - package org.jbei.ice.lib.dto.web
org.jbei.ice.lib.email - package org.jbei.ice.lib.email
org.jbei.ice.lib.entry - package org.jbei.ice.lib.entry
org.jbei.ice.lib.entry.attachment - package org.jbei.ice.lib.entry.attachment
org.jbei.ice.lib.entry.sample - package org.jbei.ice.lib.entry.sample
org.jbei.ice.lib.entry.sequence - package org.jbei.ice.lib.entry.sequence
org.jbei.ice.lib.entry.sequence.annotation - package org.jbei.ice.lib.entry.sequence.annotation
org.jbei.ice.lib.entry.sequence.composers - package org.jbei.ice.lib.entry.sequence.composers: Wrapper classes for formatted sequence generators.
org.jbei.ice.lib.entry.sequence.composers.formatters - package org.jbei.ice.lib.entry.sequence.composers.formatters: Formatters for various sequence file formats.
org.jbei.ice.lib.entry.sequence.composers.pigeon - package org.jbei.ice.lib.entry.sequence.composers.pigeon
org.jbei.ice.lib.executor - package org.jbei.ice.lib.executor
org.jbei.ice.lib.experiment - package org.jbei.ice.lib.experiment
org.jbei.ice.lib.folder - package org.jbei.ice.lib.folder
org.jbei.ice.lib.folder.collection - package org.jbei.ice.lib.folder.collection
org.jbei.ice.lib.group - package org.jbei.ice.lib.group
org.jbei.ice.lib.manuscript - package org.jbei.ice.lib.manuscript
org.jbei.ice.lib.message - package org.jbei.ice.lib.message
org.jbei.ice.lib.net - package org.jbei.ice.lib.net
org.jbei.ice.lib.parsers - package org.jbei.ice.lib.parsers: Parsers for different file formats.
org.jbei.ice.lib.parsers.abi - package org.jbei.ice.lib.parsers.abi
org.jbei.ice.lib.parsers.bl2seq - package org.jbei.ice.lib.parsers.bl2seq: Parser for bl2seq.
org.jbei.ice.lib.parsers.fasta - package org.jbei.ice.lib.parsers.fasta: Parser for fasta.
org.jbei.ice.lib.parsers.genbank - package org.jbei.ice.lib.parsers.genbank
org.jbei.ice.lib.parsers.sbol - package org.jbei.ice.lib.parsers.sbol
org.jbei.ice.lib.search - package org.jbei.ice.lib.search
org.jbei.ice.lib.search.blast - package org.jbei.ice.lib.search.blast: BLAST search classes.
org.jbei.ice.lib.search.filter - package org.jbei.ice.lib.search.filter
org.jbei.ice.lib.shared - package org.jbei.ice.lib.shared
org.jbei.ice.lib.utils - package org.jbei.ice.lib.utils: Non-web related utility classes.
org.jbei.ice.services.rest - package org.jbei.ice.services.rest
org.jbei.ice.services.rest.multipart - package org.jbei.ice.services.rest.multipart
org.jbei.ice.servlet - package org.jbei.ice.servlet
org.jbei.ice.servlet.filter - package org.jbei.ice.servlet.filter
org.jbei.ice.storage - package org.jbei.ice.storage: Database access classes.
org.jbei.ice.storage.hibernate - package org.jbei.ice.storage.hibernate
org.jbei.ice.storage.hibernate.bridge - package org.jbei.ice.storage.hibernate.bridge
org.jbei.ice.storage.hibernate.dao - package org.jbei.ice.storage.hibernate.dao
org.jbei.ice.storage.hibernate.filter - package org.jbei.ice.storage.hibernate.filter
org.jbei.ice.storage.hibernate.search - package org.jbei.ice.storage.hibernate.search
org.jbei.ice.storage.model - package org.jbei.ice.storage.model: Data models for ice objects.
ORGANISM_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
organization - Variable in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
ORIGIN_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
OriginTag - Class in org.jbei.ice.lib.parsers.genbank
OriginTag() - Constructor for class org.jbei.ice.lib.parsers.genbank.OriginTag
OwnerEntries - Class in org.jbei.ice.lib.entry: Entries for specified owner
OwnerEntries(String, long) - Constructor for class org.jbei.ice.lib.entry.OwnerEntries
OwnerEntries(String, String) - Constructor for class org.jbei.ice.lib.entry.OwnerEntries
ownerEntryCount(String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
ownerEntryCount(Account, String, Set<Group>) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO

P

PackageAssembler - Class in org.jbei.ice.lib.utils: Abstract class for assembling standardized format DNA.
PackageAssembler() - Constructor for class org.jbei.ice.lib.utils.PackageAssembler
PageParameters - Class in org.jbei.ice.lib.dto.common: POJO for specifying parameters for a page of results
PageParameters() - Constructor for class org.jbei.ice.lib.dto.common.PageParameters
PageParameters(int, int, ColumnField, boolean, String) - Constructor for class org.jbei.ice.lib.dto.common.PageParameters
Parameter - Class in org.jbei.ice.storage.model: Stores key-value information for Entry.
Parameter() - Constructor for class org.jbei.ice.storage.model.Parameter
ParameterDAO - Class in org.jbei.ice.storage.hibernate.dao: Data accessor object for handling Parameters
ParameterDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.ParameterDAO
Parameters() - Constructor for class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
parse(byte[]) - Method in class org.jbei.ice.lib.parsers.ABIParser
parse(String) - Method in class org.jbei.ice.lib.parsers.AbstractParser
parse(String) - Method in class org.jbei.ice.lib.parsers.fasta.FastaParser
parse(String) - Method in class org.jbei.ice.lib.parsers.genbank.GenBankParser
parse(String) - Method in class org.jbei.ice.lib.parsers.GeneralParser
parse(byte[]) - Method in class org.jbei.ice.lib.parsers.GeneralParser
parse(String) - Method in class org.jbei.ice.lib.parsers.PlainParser
ParsedEntryId - Class in org.jbei.ice.lib.dto.entry: The results of an entry identifier that was parsed in order to retrieve it.
ParsedEntryId(String, PartData) - Constructor for class org.jbei.ice.lib.dto.entry.ParsedEntryId
parseFeaturesTag(Tag) - Method in class org.jbei.ice.lib.parsers.genbank.GenBankParser
parseSequenceFile(InputStream, String, boolean) - Method in class org.jbei.ice.lib.entry.sequence.PartSequence: Parses a sequence in a file and associates it with the current entry
parseToEntry(String, String) - Method in class org.jbei.ice.lib.parsers.sbol.SBOLParser
parseToGenBank(SBOLDocument, String, Entry, String) - Method in class org.jbei.ice.lib.parsers.sbol.SBOLParser: Parse the SBOL document to genbank format, save and associate with entry
Part - Class in org.jbei.ice.storage.model: Store Part specific fields.
Part() - Constructor for class org.jbei.ice.storage.model.Part
Part.AssemblyStandard - Enum in org.jbei.ice.storage.model
PartData - Class in org.jbei.ice.lib.dto.entry: Data transfer object for parts and associated meta-data
PartData(EntryType) - Constructor for class org.jbei.ice.lib.dto.entry.PartData
partData - Variable in class org.jbei.ice.lib.parsers.AbstractParser
PartDataJSONHandler - Class in org.jbei.ice.services.rest: Custom Writer and Reader for classes that extend IDataTransferModel using GSON for JSON conversion
PartDataJSONHandler() - Constructor for class org.jbei.ice.services.rest.PartDataJSONHandler
PartDataUtil - Class in org.jbei.ice.lib.entry
PartDataUtil() - Constructor for class org.jbei.ice.lib.entry.PartDataUtil
PartDefaults - Class in org.jbei.ice.lib.entry: Defaults for a specified biological part type
PartDefaults(String) - Constructor for class org.jbei.ice.lib.entry.PartDefaults
PartInformation - Class in org.jbei.ice.lib.dto.entry: General information for part data
PartInformation() - Constructor for class org.jbei.ice.lib.dto.entry.PartInformation
PartnerEntries - Class in org.jbei.ice.lib.dto.web
PartnerEntries(RegistryPartner, Results<PartData>) - Constructor for class org.jbei.ice.lib.dto.web.PartnerEntries
PartnerResource - Class in org.jbei.ice.services.rest: Resource for interacting with partners in the web of registries configuration with this instance
PartnerResource() - Constructor for class org.jbei.ice.services.rest.PartnerResource
PartResource - Class in org.jbei.ice.services.rest: Rest resource for interacting representations of biological parts on ICE
PartResource() - Constructor for class org.jbei.ice.services.rest.PartResource
PartSample - Class in org.jbei.ice.lib.dto.sample: Parent class for the different types of samples
PartSample() - Constructor for class org.jbei.ice.lib.dto.sample.PartSample
PartSequence - Class in org.jbei.ice.lib.entry.sequence: Biological part with associated sequence information
PartSequence(String, EntryType) - Constructor for class org.jbei.ice.lib.entry.sequence.PartSequence: Constructor for creating a new part to associate a sequence with
PartSequence(String, String) - Constructor for class org.jbei.ice.lib.entry.sequence.PartSequence
PartStatistics - Class in org.jbei.ice.lib.dto.entry
PartStatistics() - Constructor for class org.jbei.ice.lib.dto.entry.PartStatistics
PartWithSample - Class in org.jbei.ice.lib.bulkupload: Wrapper around PartData and Part Sample objects that belong together.
PartWithSample(PartSample, PartData) - Constructor for class org.jbei.ice.lib.bulkupload.PartWithSample
performTransfer(RemotePartner, PartData) - Method in class org.jbei.ice.lib.net.RemoteTransfer: Transfers the sequence file for the part and any parts that are linked to it.
Permission - Class in org.jbei.ice.storage.model: Permission object for storing permissions related to either folders or entries on an account or group basis
Permission() - Constructor for class org.jbei.ice.storage.model.Permission
permissionDAO - Variable in class org.jbei.ice.lib.access.Permissions
PermissionDAO - Class in org.jbei.ice.storage.hibernate.dao: Permission data accessor Object
PermissionDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.PermissionDAO
PermissionEntryBridge - Class in org.jbei.ice.lib.access: Permission bridge that indexes the fields needed by the EntrySecurityFilterFactory
PermissionEntryBridge() - Constructor for class org.jbei.ice.lib.access.PermissionEntryBridge
PermissionException - Exception in org.jbei.ice.lib.access: Exception thrown when user is authorized to access the application but does not have the required permission or role to access requested elements
PermissionException(String) - Constructor for exception org.jbei.ice.lib.access.PermissionException
PermissionException() - Constructor for exception org.jbei.ice.lib.access.PermissionException
PermissionException(String, Throwable) - Constructor for exception org.jbei.ice.lib.access.PermissionException
PermissionResource - Class in org.jbei.ice.services.rest: Resource for interacting with permissions.
PermissionResource() - Constructor for class org.jbei.ice.services.rest.PermissionResource
Permissions - Class in org.jbei.ice.lib.access
Permissions() - Constructor for class org.jbei.ice.lib.access.Permissions
PermissionsController - Class in org.jbei.ice.lib.access: Controller for permissions
PermissionsController() - Constructor for class org.jbei.ice.lib.access.PermissionsController
PigeonSBOLv - Class in org.jbei.ice.lib.entry.sequence.composers.pigeon: Sends post request to pigeon to generate SBOLv
PigeonSBOLv() - Constructor for class org.jbei.ice.lib.entry.sequence.composers.pigeon.PigeonSBOLv
placeSampleInCart(String, SampleRequest) - Method in class org.jbei.ice.lib.entry.sample.RequestRetriever: Creates a new sample request for the specified user and specified entry.
PlainParser - Class in org.jbei.ice.lib.parsers: Parser to handle file with simply nucleotide sequences.
PlainParser() - Constructor for class org.jbei.ice.lib.parsers.PlainParser
PlantType - Enum in org.jbei.ice.lib.dto.entry: Arabidopsis seed plant type
Plasmid - Class in org.jbei.ice.storage.model: Store Plasmid specific fields.
Plasmid() - Constructor for class org.jbei.ice.storage.model.Plasmid
PlasmidData - Class in org.jbei.ice.lib.dto.entry
PlasmidData() - Constructor for class org.jbei.ice.lib.dto.entry.PlasmidData
post(InputStream, String, FormDataContentDisposition) - Method in class org.jbei.ice.services.rest.BulkUploadResource
post(InputStream, FormDataContentDisposition) - Method in class org.jbei.ice.services.rest.FileResource
post(String, String, Object, Class<T>, Map<String, Object>) - Method in class org.jbei.ice.services.rest.IceRestClient
post(String, String, Object, Class<T>, Map<String, Object>) - Method in class org.jbei.ice.services.rest.RestClient
postSequenceFile(String, String, EntryType, String) - Method in class org.jbei.ice.services.rest.IceRestClient
postToPigeon(String) - Static method in class org.jbei.ice.lib.entry.sequence.composers.pigeon.PigeonSBOLv
postWor(String, String, Object, Class<T>, Map<String, Object>, String) - Method in class org.jbei.ice.services.rest.IceRestClient
Preference - Class in org.jbei.ice.storage.model: Entity for storing user preferences.
Preference() - Constructor for class org.jbei.ice.storage.model.Preference
Preference(Account, String, String) - Constructor for class org.jbei.ice.storage.model.Preference
PreferenceInfo - Class in org.jbei.ice.lib.dto.bulkupload: DTO for preferences
PreferenceInfo() - Constructor for class org.jbei.ice.lib.dto.bulkupload.PreferenceInfo
PreferenceKey - Enum in org.jbei.ice.lib.dto.user: Preset key for user preferences.
PreferencesController - Class in org.jbei.ice.lib.account: Controller for managing user preferences.
PreferencesController() - Constructor for class org.jbei.ice.lib.account.PreferencesController
PreferencesDAO - Class in org.jbei.ice.storage.hibernate.dao: Data accessor for working with preference objects
PreferencesDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.PreferencesDAO
process() - Method in class org.jbei.ice.lib.bulkupload.FileBulkUpload: Process bulk file upload.
ProcessedBulkUpload - Class in org.jbei.ice.lib.bulkupload: Represents the results of a processed upload.
ProcessedBulkUpload() - Constructor for class org.jbei.ice.lib.bulkupload.ProcessedBulkUpload
processFeaturesBlastOutput(String) - Static method in class org.jbei.ice.lib.search.blast.BlastPlus: Process the output of the blast run for features into a list of feature objects
Expected format for the output (per line) is feature_id, label, type, qstart, qend, sstart, send, sstrand Therefore line[0] is feature_id, line[1] is label etc
Since we are only interested in features that have a full match (covers entire feature) some matches are manually eliminated.
processRemoteWebPartnerAdd(RegistryPartner) - Method in class org.jbei.ice.lib.net.WebPartners: Process a web partner add request from a remote instance
processUpload() - Method in class org.jbei.ice.lib.bulkupload.BulkCSVUpload: Processes the csv upload
processUpload() - Method in class org.jbei.ice.lib.bulkupload.BulkFileSBOLUpload
processUpload() - Method in class org.jbei.ice.lib.bulkupload.BulkZipUpload: Process the zip file.
ProgramTookTooLongException - Exception in org.jbei.ice.lib.search.blast: Program Took Too Long exception
ProgramTookTooLongException() - Constructor for exception org.jbei.ice.lib.search.blast.ProgramTookTooLongException
ProgramTookTooLongException(String, Throwable) - Constructor for exception org.jbei.ice.lib.search.blast.ProgramTookTooLongException
ProgramTookTooLongException(String) - Constructor for exception org.jbei.ice.lib.search.blast.ProgramTookTooLongException
ProgramTookTooLongException(Throwable) - Constructor for exception org.jbei.ice.lib.search.blast.ProgramTookTooLongException
PROJECT_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
promoteFolder(String, Folder) - Method in class org.jbei.ice.lib.folder.FolderController: "Promote"s a collection into a featured collection.
propagateFolderPermissions(String, Folder, boolean) - Method in class org.jbei.ice.lib.access.PermissionsController: Propagates the permissions for the folder to the contained entries
PUBLIC_GROUP_DESCRIPTION - Static variable in class org.jbei.ice.lib.group.GroupController
PUBLIC_GROUP_NAME - Static variable in class org.jbei.ice.lib.group.GroupController
PUBLIC_GROUP_UUID - Static variable in class org.jbei.ice.lib.group.GroupController
put(String, String, Object, Class<T>) - Method in class org.jbei.ice.services.rest.IceRestClient
put(String, String, Object) - Method in class org.jbei.ice.services.rest.IceRestClient
putSession(String, String) - Static method in class org.jbei.ice.lib.account.UserSessions
putWor(String, String, Object, Class<T>, Map<String, Object>, String) - Method in class org.jbei.ice.services.rest.IceRestClient
putZipEntry(ByteArrayWrapper, ZipOutputStream) - Method in class org.jbei.ice.lib.entry.EntriesAsCSV
putZipEntry(ByteArrayWrapper, ZipOutputStream) - Method in class org.jbei.ice.lib.net.RemoteEntriesAsCSV

Q

query() - Method in class org.jbei.ice.services.rest.BulkUploadResource
query(boolean) - Method in class org.jbei.ice.services.rest.WebResource: Retrieves information on other ice instances that is in a web of registries configuration with this instance; also know as registry partners
querySessionId - Variable in class org.jbei.ice.services.rest.RestResource
QueryType - Enum in org.jbei.ice.lib.search

R

read() - Method in class org.jbei.auth.hmac.HmacInputStream
read(byte[], int, int) - Method in class org.jbei.auth.hmac.HmacInputStream
read(long, int, int) - Method in class org.jbei.ice.services.rest.BulkUploadResource: Retrieves specified bulk upload resource including
read(String, int, int, String, boolean, String, List<String>) - Method in class org.jbei.ice.services.rest.CollectionResource: Retrieve entries by collection type using paging parameters, including a filter
read(String, int, int, String, boolean, String, String, String, List<String>) - Method in class org.jbei.ice.services.rest.FolderResource: Retrieves the entries for specified folder.
read(String, boolean, String, String, long) - Method in class org.jbei.ice.services.rest.PartResource: Retrieves a part using any of the unique identifiers.
read(String) - Method in class org.jbei.ice.services.rest.UserResource
readFrom(Class<ArrayList<IDataTransferModel>>, Type, Annotation[], MediaType, MultivaluedMap<String, String>, InputStream) - Method in class org.jbei.ice.services.rest.ArrayDataJSONHandler
readFrom(Class<IDataTransferModel>, Type, Annotation[], MediaType, MultivaluedMap<String, String>, InputStream) - Method in class org.jbei.ice.services.rest.PartDataJSONHandler
readRemoteUser(long) - Method in class org.jbei.ice.services.rest.PartnerResource: Retrieves available folders from the specified remote ice partner
rebuild() - Method in class org.jbei.ice.lib.entry.sequence.annotation.Annotations: Rebuild the annotations blast database
rebuildAllAlignments(Entry) - Method in class org.jbei.ice.lib.entry.sequence.SequenceAnalysisController: Calculate sequence alignments between the sequence associated with an Entry entry with all the TraceSequences associated with that entry.
rebuildAnnotations() - Method in class org.jbei.ice.services.rest.AnnotationResource
RebuildBlastIndexTask - Class in org.jbei.ice.lib.search.blast: Task to rebuild the blast index
RebuildBlastIndexTask(boolean) - Constructor for class org.jbei.ice.lib.search.blast.RebuildBlastIndexTask
rebuildDatabase(boolean) - Static method in class org.jbei.ice.lib.search.blast.BlastPlus: Re-builds the blast database, using a lock file to prevent concurrent rebuilds.
rebuildFeaturesBlastDatabase(String) - Static method in class org.jbei.ice.lib.search.blast.BlastPlus
rebuildIndexes(String, IndexType) - Method in class org.jbei.ice.lib.search.SearchController: Rebuilds the search indices.
RebuildLuceneIndexTask - Class in org.jbei.ice.lib.search: Task to rebuild lucene index
RebuildLuceneIndexTask() - Constructor for class org.jbei.ice.lib.search.RebuildLuceneIndexTask
receiveTransferredEntry(PartData) - Method in class org.jbei.ice.lib.net.TransferredParts
REFERENCE_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
ReferenceTag - Class in org.jbei.ice.lib.parsers.genbank
ReferenceTag() - Constructor for class org.jbei.ice.lib.parsers.genbank.ReferenceTag
refreshPartnerKey(RegistryPartner, String, String) - Method in class org.jbei.ice.lib.net.RemoteContact
RegistryPartner - Class in org.jbei.ice.lib.dto.web: Data transfer model for RemotePartner
RegistryPartner() - Constructor for class org.jbei.ice.lib.dto.web.RegistryPartner
REMOTE_USER_ID - Static variable in class org.jbei.ice.services.rest.Headers
REMOTE_USER_ID - Variable in class org.jbei.ice.services.rest.RestResource
REMOTE_USER_TOKEN - Static variable in class org.jbei.ice.services.rest.Headers
REMOTE_USER_TOKEN - Variable in class org.jbei.ice.services.rest.RestResource
RemoteAccess - Class in org.jbei.ice.lib.access: Access privileges for remote resources
RemoteAccess() - Constructor for class org.jbei.ice.lib.access.RemoteAccess
RemoteAccessModel - Class in org.jbei.ice.storage.model: Stores access information for remote shares
RemoteAccessModel() - Constructor for class org.jbei.ice.storage.model.RemoteAccessModel
RemoteAccessModelDAO - Class in org.jbei.ice.storage.hibernate.dao
RemoteAccessModelDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.RemoteAccessModelDAO
RemoteAccessPermission - Class in org.jbei.ice.lib.dto.access: Access permission for remote access.
RemoteAccessPermission() - Constructor for class org.jbei.ice.lib.dto.access.RemoteAccessPermission
RemoteClientModel - Class in org.jbei.ice.storage.model: Abstract notion of a client.
RemoteClientModel() - Constructor for class org.jbei.ice.storage.model.RemoteClientModel
RemoteClientModelDAO - Class in org.jbei.ice.storage.hibernate.dao
RemoteClientModelDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.RemoteClientModelDAO
RemoteContact - Class in org.jbei.ice.lib.net: Remote communications with other ice instances Any method calls to this class will likely be slow since it requires remote access
RemoteContact() - Constructor for class org.jbei.ice.lib.net.RemoteContact
RemoteEntries - Class in org.jbei.ice.lib.net: Entries that are on other registry instances other than this instance.
RemoteEntries() - Constructor for class org.jbei.ice.lib.net.RemoteEntries
RemoteEntriesAsCSV - Class in org.jbei.ice.lib.net: Represents remote entries from web partners in csv form
RemoteEntriesAsCSV(boolean) - Constructor for class org.jbei.ice.lib.net.RemoteEntriesAsCSV
RemoteEntry - Class in org.jbei.ice.lib.net
RemoteEntry(long, long) - Constructor for class org.jbei.ice.lib.net.RemoteEntry
RemoteFolder - Class in org.jbei.ice.lib.net
RemoteFolder(long, long) - Constructor for class org.jbei.ice.lib.net.RemoteFolder
RemoteFolders - Class in org.jbei.ice.lib.net
RemoteFolders(long) - Constructor for class org.jbei.ice.lib.net.RemoteFolders
remotelyAddEntrySelection(String, long, String, EntrySelection, RegistryPartner) - Method in class org.jbei.ice.lib.folder.FolderContents
RemotePartner - Class in org.jbei.ice.storage.model: Represents a remote entity that this ice instance knows about and could potentially communicate with or allow communications from
Field Descriptions: NAME: Name of the remote instance for display purposes. URL: Unique resource locator for the partner.
RemotePartner() - Constructor for class org.jbei.ice.storage.model.RemotePartner
RemotePartnerDAO - Class in org.jbei.ice.storage.hibernate.dao: Data Accessor Object for managing RemotePartner Objects
RemotePartnerDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.RemotePartnerDAO
RemotePartnerStatus - Enum in org.jbei.ice.lib.dto.web: Status for remote partners
RemoteSequence - Class in org.jbei.ice.lib.net: Sequence that is available remotely
RemoteSequence(long, long) - Constructor for class org.jbei.ice.lib.net.RemoteSequence
RemoteShareModel - Class in org.jbei.ice.storage.model: Stores shares for entries or folders.
RemoteShareModel() - Constructor for class org.jbei.ice.storage.model.RemoteShareModel
RemoteShareModelDAO - Class in org.jbei.ice.storage.hibernate.dao
RemoteShareModelDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.RemoteShareModelDAO
RemoteTransfer - Class in org.jbei.ice.lib.net
RemoteTransfer() - Constructor for class org.jbei.ice.lib.net.RemoteTransfer
RemoteUser - Class in org.jbei.ice.lib.dto.web
RemoteUser() - Constructor for class org.jbei.ice.lib.dto.web.RemoteUser
remoteUserId - Variable in class org.jbei.ice.services.rest.RestResource
RemoteUsers - Class in org.jbei.ice.lib.dto.web
RemoteUsers() - Constructor for class org.jbei.ice.lib.dto.web.RemoteUsers
remoteUserToken - Variable in class org.jbei.ice.services.rest.RestResource
remoteWebPartnerRemoveRequest(String, String) - Method in class org.jbei.ice.services.rest.WebResource
remove(long) - Method in class org.jbei.ice.lib.folder.FolderPermissions
remove(String, long) - Method in class org.jbei.ice.lib.net.WebPartners
removeFolderContents(String, long, EntrySelection, boolean) - Method in class org.jbei.ice.lib.folder.FolderContents: Removes the specified contents of a folder, optionally adding them to another folder
removeFolderEntries(Folder, List<Long>) - Method in class org.jbei.ice.storage.hibernate.dao.FolderDAO: Removes, from the list of entries in the specified folder, those whose ids match the ids passed in the parameter
removeLink(long, LinkType) - Method in class org.jbei.ice.lib.entry.EntryLinks: Removes link specified entry id based on the specified type
removeMemberFromGroup(long, String) - Method in class org.jbei.ice.lib.account.AccountController
removePermission(String, AccessPermission) - Method in class org.jbei.ice.lib.access.PermissionsController
removePermission(long) - Method in class org.jbei.ice.lib.entry.EntryPermissions
removePermission(long, long) - Method in class org.jbei.ice.services.rest.BulkUploadResource
removePermission(long, long) - Method in class org.jbei.ice.services.rest.FolderResource
removePermission(String, long) - Method in class org.jbei.ice.services.rest.PartResource
removePermission(Entry, Folder, BulkUpload, Account, Group, boolean, boolean) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
removePermissions(Entry) - Method in class org.jbei.ice.lib.entry.EntryPermissionTask
removeRemotePartner(long, String) - Method in class org.jbei.ice.lib.net.WebPartners: Delete the partner information specified by the url in the param
removeSampleFromCart(String, long) - Method in class org.jbei.ice.lib.entry.sample.RequestRetriever
removeShotgunSequence(ShotgunSequence) - Method in class org.jbei.ice.lib.entry.sequence.SequenceAnalysisController
removeToken(String) - Static method in class org.jbei.ice.lib.access.AccessTokens
removeTraceSequence(TraceSequence) - Method in class org.jbei.ice.lib.entry.sequence.SequenceAnalysisController: Remove a TraceSequence from the database and disk.
removeWebPartner(String, String) - Method in class org.jbei.ice.lib.net.WoRController: Removes the web partner uniquely identified by the url
removeWebPartner(String) - Method in class org.jbei.ice.services.rest.PartnerResource
removeWebPartner(String) - Method in class org.jbei.ice.services.rest.WebResource
renameBulkUpload(String, long, String) - Method in class org.jbei.ice.lib.bulkupload.BulkEntryCreator: Renames the bulk upload referenced by the id in the parameter
request - Variable in class org.jbei.ice.services.rest.RestResource
Request - Class in org.jbei.ice.storage.model: Storage data model for sample requests
Request() - Constructor for class org.jbei.ice.storage.model.Request
RequestDAO - Class in org.jbei.ice.storage.hibernate.dao: Data accessor object for Sample Request objects
RequestDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.RequestDAO
requestKey(String) - Method in class org.jbei.ice.lib.account.UserApiKeys: Generates an access key using the client identifier
RequestRetriever - Class in org.jbei.ice.lib.entry.sample: Handler for sample requests
RequestRetriever() - Constructor for class org.jbei.ice.lib.entry.sample.RequestRetriever
requiredFields - Variable in class org.jbei.ice.lib.bulkupload.BulkCSVUpload
requireUserId() - Method in class org.jbei.ice.services.rest.RestResource: Attempts to retrieve the identifier for the specific user
requireUserIdOrWebPartner(String) - Method in class org.jbei.ice.services.rest.RestResource: Requires either a valid user request or request from a web partner
requireWebPartner() - Method in class org.jbei.ice.services.rest.RestResource
resetPassword(String) - Method in class org.jbei.ice.lib.account.AccountController: Reset a user's password
resetPassword(AccountTransfer) - Method in class org.jbei.ice.services.rest.UserResource
respond(Response.Status, Object) - Method in class org.jbei.ice.services.rest.RestResource: Create a Response object from an entity object.
respond(Object) - Method in class org.jbei.ice.services.rest.RestResource: Create a Response object from an entity object.
respond(Response.Status) - Method in class org.jbei.ice.services.rest.RestResource: Create an empty Response object.
respond(boolean) - Method in class org.jbei.ice.services.rest.RestResource: Create an empty Response object.
RestClient - Class in org.jbei.ice.services.rest: Parent Rest Client class
RestClient() - Constructor for class org.jbei.ice.services.rest.RestClient
RestResource - Class in org.jbei.ice.services.rest: Parent class for all rest resource objects.
RestResource() - Constructor for class org.jbei.ice.services.rest.RestResource
Results<T extends IDataTransferModel> - Class in org.jbei.ice.lib.dto.common: Wrapper around a list of data transfer models in response to a paging request
Results() - Constructor for class org.jbei.ice.lib.dto.common.Results
retrieveAccountGroupUUIDs(String) - Method in class org.jbei.ice.lib.group.GroupController
retrieveAccountPermissions(Folder, boolean, boolean) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
retrieveAccountPreferences(Account, ArrayList<PreferenceKey>) - Method in class org.jbei.ice.lib.account.PreferencesController
retrieveAllEntries(ColumnField, boolean, int, int, String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
retrieveByAccount(Account) - Method in class org.jbei.ice.storage.hibernate.dao.BulkUploadDAO
retrieveByStatus(BulkUploadStatus) - Method in class org.jbei.ice.storage.hibernate.dao.BulkUploadDAO
retrieveByUser(String, String) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController: Retrieves list of user saved bulk imports.
retrieveComments(Entry) - Method in class org.jbei.ice.storage.hibernate.dao.CommentDAO
retrieveDraftEntries(long, int, int) - Method in class org.jbei.ice.storage.hibernate.dao.BulkUploadDAO
retrieveEntryComments(String, long) - Method in class org.jbei.ice.lib.entry.EntryController
retrieveEntryDetails(String, String) - Method in class org.jbei.ice.lib.entry.EntryController
retrieveEntryDetails(String, Entry) - Method in class org.jbei.ice.lib.entry.EntryController
retrieveEntrySamples(String, String) - Method in class org.jbei.ice.lib.entry.sample.SampleService
retrieveEntryStatistics(String, long) - Method in class org.jbei.ice.lib.entry.EntryController
retrieveEntryTipDetails(String) - Method in class org.jbei.ice.lib.entry.EntryController
retrieveFolderContents(long, PageParameters, boolean) - Method in class org.jbei.ice.storage.hibernate.dao.FolderDAO: Retrieves list of entries that conforms to the parameters
retrieveFolderPermissions(Account, Set<Group>) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
retrieveGroupPermissions(Folder, boolean, boolean) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
retrieveMemberGroups(Account) - Method in class org.jbei.ice.storage.hibernate.dao.GroupDAO
retrieveMessage(long) - Method in class org.jbei.ice.storage.hibernate.dao.MessageDAO
retrieveMessageCount(Account, List<Group>) - Method in class org.jbei.ice.storage.hibernate.dao.MessageDAO
retrieveMessages(Account, List<Group>, int, int) - Method in class org.jbei.ice.storage.hibernate.dao.MessageDAO
retrieveNewMessageCount(Account) - Method in class org.jbei.ice.storage.hibernate.dao.MessageDAO
retrieveOwnerEntries(ColumnField, boolean, int, int, String) - Method in class org.jbei.ice.lib.entry.OwnerEntries
retrieveOwnerEntries(String, ColumnField, boolean, int, int, String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO: Retrieves entries owned by account with specified email and with visibility of "pending" or "ok"
retrievePartSequence(String, String) - Method in class org.jbei.ice.lib.entry.sequence.SequenceController
retrievePermission(Entry, Folder, BulkUpload, Account, Group, boolean, boolean) - Method in class org.jbei.ice.storage.hibernate.dao.PermissionDAO
retrievePreferenceValues(Account, HashSet<String>) - Method in class org.jbei.ice.storage.hibernate.dao.PreferencesDAO
retrieveRemoteToolTip(String, long, long) - Method in class org.jbei.ice.lib.net.RemoteEntries
retrieveSavedDraftCount(long) - Method in class org.jbei.ice.storage.hibernate.dao.BulkUploadDAO
retrieveSetFolderPermission(Folder, boolean) - Method in class org.jbei.ice.lib.access.PermissionsController: Retrieves permissions that have been explicitly set for the folders with the exception of the public read permission if specified in the parameter.
retrieveStorageByIndex(String, SampleType) - Method in class org.jbei.ice.storage.hibernate.dao.StorageDAO: Retrieve a Storage object by its index and SampleType fields.
retrieveStorageTube(String) - Method in class org.jbei.ice.storage.hibernate.dao.StorageDAO: Retrieves Storage object representing a tube.
retrieveSystemSettings(String) - Method in class org.jbei.ice.lib.config.ConfigurationController
retrieveUserEntries(Account, String, Set<Group>, ColumnField, boolean, int, int, String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO: Retrieves the entries for the specified owner, that the requester has read access to
retrieveUserPreferenceList(Account, List<SearchBoostField>) - Method in class org.jbei.ice.lib.account.PreferencesController
retrieveVisibleEntries(Account, Set<Group>, ColumnField, boolean, int, int, String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO: Retrieve Entries visible to everyone.
reverseComplement(String) - Static method in class org.jbei.ice.lib.utils.SequenceUtils: Calculate the reverse complement of the given DNA sequence.
revertSubmitted(Account, long) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController
rollbackTransaction() - Static method in class org.jbei.ice.storage.hibernate.HibernateUtil
run(SearchQuery, boolean) - Method in class org.jbei.ice.lib.search.WebSearch: Searches all registries in the web of registries configuration with this registry.
runBlast(BlastQuery) - Static method in class org.jbei.ice.lib.search.blast.BlastPlus: Run a blast query using the following output format options stitle - subject title qstart - query match start index qend - query match end index sstart - subject match start index send sstrand evalue bitscore length - alignment length nident - number of identical matches
runBlast2Seq(String, String) - Static method in class org.jbei.ice.lib.search.blast.BlastPlus: Run the bl2seq program on multiple subjects.
runCheckFeatures(BlastQuery) - Static method in class org.jbei.ice.lib.search.blast.BlastPlus: Run a blast query against the sequence features blast database.
runSearch(String, SearchQuery) - Method in class org.jbei.ice.lib.search.SearchController: Executes search using parameters specified in the query.
runSearchThread(RemotePartner, SearchQuery) - Method in class org.jbei.ice.lib.search.WebSearch
runTask(Task) - Method in class org.jbei.ice.lib.executor.IceExecutorService

S

Sample - Class in org.jbei.ice.storage.model: Store Sample information.
Sample() - Constructor for class org.jbei.ice.storage.model.Sample
SampleAuthorization - Class in org.jbei.ice.lib.entry.sample
SampleAuthorization() - Constructor for class org.jbei.ice.lib.entry.sample.SampleAuthorization
SampleCreator - Class in org.jbei.ice.lib.entry.sample: Handles creation of sample and associated actions
SampleCreator() - Constructor for class org.jbei.ice.lib.entry.sample.SampleCreator
SampleDAO - Class in org.jbei.ice.storage.hibernate.dao
SampleDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.SampleDAO
SampleField - Enum in org.jbei.ice.lib.dto.bulkupload: Complete list of storage location fields for samples
SampleHeaderValue - Class in org.jbei.ice.lib.bulkupload
SampleHeaderValue(SampleField) - Constructor for class org.jbei.ice.lib.bulkupload.SampleHeaderValue
SampleRequest - Class in org.jbei.ice.lib.dto.sample: Data transfer object for sample requests
SampleRequest() - Constructor for class org.jbei.ice.lib.dto.sample.SampleRequest
SampleRequestStatus - Enum in org.jbei.ice.lib.dto.sample: Request status for user sample request
SampleRequestType - Enum in org.jbei.ice.lib.dto.sample: Available forms that the samples can be requested in
SampleResource - Class in org.jbei.ice.services.rest: REST Resource for samples
SampleResource() - Constructor for class org.jbei.ice.services.rest.SampleResource
SampleService - Class in org.jbei.ice.lib.entry.sample: Service for dealing with Samples
SampleService() - Constructor for class org.jbei.ice.lib.entry.sample.SampleService
SampleType - Enum in org.jbei.ice.lib.dto.sample: // todo : this needs to be split into locationtype and sampletype to differentiate between the two // with sample types being top level objects only
save(Account) - Method in class org.jbei.ice.lib.account.AccountController: Store Account into the database.
save(String, Attachment, InputStream) - Method in class org.jbei.ice.lib.entry.attachment.Attachments: Save attachment to the database and the disk.
save(DNASequence, String, String) - Method in class org.jbei.ice.lib.entry.sequence.PartSequence
save(String, Sequence) - Method in class org.jbei.ice.lib.entry.sequence.SequenceController: Save the given Sequence into the database, with the option to rebuild the search index.
save(Group) - Method in class org.jbei.ice.lib.group.GroupController
save(DNASequence, String) - Method in class org.jbei.ice.lib.parsers.AbstractParser
save(TraceSequence) - Method in class org.jbei.ice.storage.hibernate.dao.TraceSequenceDAO: Save the given TraceSequence object in the database.
saveFiles(PartData, Entry, HashMap<String, InputStream>) - Method in class org.jbei.ice.lib.bulkupload.BulkEntryCreator
saveSequence(Sequence) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceDAO: Save the given Sequence object in the database.
SBOL2Formatter - Class in org.jbei.ice.lib.entry.sequence.composers.formatters
SBOL2Formatter() - Constructor for class org.jbei.ice.lib.entry.sequence.composers.formatters.SBOL2Formatter
SBOL2Visitor - Class in org.jbei.ice.lib.entry.sequence.composers.formatters
SBOL2Visitor(SBOLDocument) - Constructor for class org.jbei.ice.lib.entry.sequence.composers.formatters.SBOL2Visitor
SBOLFormatter - Class in org.jbei.ice.lib.entry.sequence.composers.formatters: Format to SBOL using libSBOLj
SBOLFormatter() - Constructor for class org.jbei.ice.lib.entry.sequence.composers.formatters.SBOLFormatter
SBOLParser - Class in org.jbei.ice.lib.parsers.sbol: Parse SBOL files that are imported by the user.
SBOLParser(String, String, boolean) - Constructor for class org.jbei.ice.lib.parsers.sbol.SBOLParser
SBOLVisitor - Class in org.jbei.ice.lib.entry.sequence.composers.formatters
SBOLVisitor() - Constructor for class org.jbei.ice.lib.entry.sequence.composers.formatters.SBOLVisitor
SBOLVisualDownloadServlet - Class in org.jbei.ice.servlet: Servlet for serving the SBOL visual icon in ICE.
SBOLVisualDownloadServlet() - Constructor for class org.jbei.ice.servlet.SBOLVisualDownloadServlet
scheduleBlastIndexRebuildTask(boolean) - Static method in class org.jbei.ice.lib.search.blast.BlastPlus: Schedule task to rebuild the blast index
score - Variable in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
search(boolean, SearchQuery) - Method in class org.jbei.ice.services.rest.SearchResource: Advanced Search.
search(String, boolean, int, int, String, boolean) - Method in class org.jbei.ice.services.rest.SearchResource: Keyword search
SearchBoostField - Enum in org.jbei.ice.lib.dto.search: Search fields that have user boost support (shown in the user preference section)
SearchController - Class in org.jbei.ice.lib.search: Controller for running searches on the ice platform
SearchController() - Constructor for class org.jbei.ice.lib.search.SearchController
SearchFieldFactory - Class in org.jbei.ice.lib.search.filter: Maintains information about the particular fields for the entry types (not exactly a factory in that regard) and also the class types for hibernate search
SearchFieldFactory() - Constructor for class org.jbei.ice.lib.search.filter.SearchFieldFactory
searchFieldForEntryField(EntryField) - Static method in class org.jbei.ice.lib.search.filter.SearchFieldFactory: Determines the search field for the specified entry field
searchPartFields(String, String, int) - Method in class org.jbei.ice.services.rest.SearchResource: Search entries by using filters on the values
SearchQuery - Class in org.jbei.ice.lib.dto.search
SearchQuery() - Constructor for class org.jbei.ice.lib.dto.search.SearchQuery: set the query default values
SearchQuery.Parameters - Class in org.jbei.ice.lib.dto.search
SearchResource - Class in org.jbei.ice.services.rest: REST resource for searching.
SearchResource() - Constructor for class org.jbei.ice.services.rest.SearchResource
SearchResult - Class in org.jbei.ice.lib.dto.search: DTO for searches
SearchResult() - Constructor for class org.jbei.ice.lib.dto.search.SearchResult
SearchResults - Class in org.jbei.ice.lib.dto.search: Wrapper around a list of search results which also contains information about the search.
SearchResults() - Constructor for class org.jbei.ice.lib.dto.search.SearchResults
SearchTask(RemotePartner, SearchQuery) - Constructor for class org.jbei.ice.lib.search.WebSearch.SearchTask
searchURL - Variable in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
searchWebEntries(SearchQuery, boolean) - Method in class org.jbei.ice.services.rest.WebResource
SEGMENT_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
SelectionMarker - Class in org.jbei.ice.storage.model: Represents a selection marker for entry.
SelectionMarker() - Constructor for class org.jbei.ice.storage.model.SelectionMarker
SelectionMarker(String, Entry) - Constructor for class org.jbei.ice.storage.model.SelectionMarker
SelectionMarkerDAO - Class in org.jbei.ice.storage.hibernate.dao
SelectionMarkerDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.SelectionMarkerDAO
send(String, String, String, String) - Method in class org.jbei.ice.lib.email.CustomEmail: Sends an email to the specified recipient with a carbon copy send to the specified ccEmail.
send(String, String, String) - Method in class org.jbei.ice.lib.email.CustomEmail: Send an email, and cc to the administrator.
send(String, String, String) - Method in class org.jbei.ice.lib.email.Email
send(String, String, String, String) - Method in class org.jbei.ice.lib.email.GMail: Sends an email to the specified recipient with a carbon copy send to the specified ccEmail.
send(String, String, String) - Method in class org.jbei.ice.lib.email.GMail: Send an email, and cc to the administrator.
send(MessageInfo) - Method in class org.jbei.ice.lib.message.Messages: Sends message contained in the MessageInfo to the specified recipients.
sendError(String, String) - Method in class org.jbei.ice.lib.email.CustomEmail: Send an email to the administrator.
sendError(String, String) - Method in class org.jbei.ice.lib.email.Email
sendError(String, String) - Method in class org.jbei.ice.lib.email.GMail: Send an email to the administrator.
sendMessage(MessageInfo) - Method in class org.jbei.ice.services.rest.MessageResource
sendToken(AccessPermission, RemotePartner) - Method in class org.jbei.ice.lib.folder.FolderPermissions: Send access permission to a remote partner with a "secret"
Sequence - Class in org.jbei.ice.storage.model: Stores the unique sequence for an Entry object.
Sequence() - Constructor for class org.jbei.ice.storage.model.Sequence
Sequence(String, String, String, String, Entry) - Constructor for class org.jbei.ice.storage.model.Sequence
SequenceAnalysisController - Class in org.jbei.ice.lib.entry.sequence: ABI to manipulate DNA sequence trace analysis
SequenceAnalysisController() - Constructor for class org.jbei.ice.lib.entry.sequence.SequenceAnalysisController
SequenceController - Class in org.jbei.ice.lib.entry.sequence: ABI to manipulate Sequences.
SequenceController() - Constructor for class org.jbei.ice.lib.entry.sequence.SequenceController
SequenceDAO - Class in org.jbei.ice.storage.hibernate.dao: Manipulate Sequence and associated objects in the database.
SequenceDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.SequenceDAO
SequenceFeature - Class in org.jbei.ice.storage.model: Stores the sequence annotation information, and associates Feature objects to a Sequence object.
SequenceFeature() - Constructor for class org.jbei.ice.storage.model.SequenceFeature
SequenceFeature(Sequence, Feature, int, String, String, SequenceFeature.AnnotationType) - Constructor for class org.jbei.ice.storage.model.SequenceFeature
SequenceFeature.AnnotationType - Enum in org.jbei.ice.storage.model: Annotation type for "parts".
SequenceFeatureAttribute - Class in org.jbei.ice.storage.model: Store genbank style attributes.
SequenceFeatureAttribute() - Constructor for class org.jbei.ice.storage.model.SequenceFeatureAttribute
SequenceFeatureComparator - Class in org.jbei.ice.lib.entry.sequence.composers.formatters: Comparator for the sequence feature
SequenceFeatureComparator() - Constructor for class org.jbei.ice.lib.entry.sequence.composers.formatters.SequenceFeatureComparator
SequenceFeatureDAO - Class in org.jbei.ice.storage.hibernate.dao: Hibernate Data accessor object for SequenceFeatures
SequenceFeatureDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.SequenceFeatureDAO
SequenceFormat - Enum in org.jbei.ice.lib.entry.sequence: Different sequence formats supported by ICE
SequenceInfo - Class in org.jbei.ice.lib.dto.entry: Data transfer object for sequence
SequenceInfo() - Constructor for class org.jbei.ice.lib.dto.entry.SequenceInfo
sequenceToDNASequence(Sequence) - Method in class org.jbei.ice.lib.entry.sequence.PartSequence
sequenceToDNASequence(Sequence) - Method in class org.jbei.ice.lib.entry.sequence.SequenceController: Generate a FeaturedDNASequence from a given Sequence object.
SequenceUtils - Class in org.jbei.ice.lib.utils: Utility methods for sequences.
SequenceUtils() - Constructor for class org.jbei.ice.lib.utils.SequenceUtils
serialVersionUID - Static variable in class org.jbei.ice.lib.dto.search.BlastQuery
serialVersionUID - Static variable in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
serialVersionUID - Static variable in class org.jbei.ice.lib.dto.search.SearchQuery
serialVersionUID - Static variable in class org.jbei.ice.lib.dto.search.SearchResult
sessionId - Variable in class org.jbei.ice.services.rest.RestResource
set(String, Object, Document, LuceneOptions) - Method in class org.jbei.ice.lib.access.PermissionEntryBridge
set(String, Object, Document, LuceneOptions) - Method in class org.jbei.ice.storage.hibernate.bridge.EntryBooleanPropertiesBridge
setAccessPermissions(ArrayList<AccessPermission>) - Method in class org.jbei.ice.lib.dto.entry.PartData
setAccessPermissions(List<AccessPermission>) - Method in class org.jbei.ice.lib.folder.AbstractFolder
setAccount(AccountTransfer) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
setAccount(AccountTransfer) - Method in class org.jbei.ice.lib.dto.access.AccessKey
setAccount(AccountTransfer) - Method in class org.jbei.ice.lib.dto.access.AccessPermission
setAccount(AccountTransfer) - Method in class org.jbei.ice.lib.dto.History
setAccount(String) - Method in class org.jbei.ice.storage.hibernate.filter.EntrySecurityFilterFactory
setAccount(Account) - Method in class org.jbei.ice.storage.model.AccountPreferences
setAccount(Account) - Method in class org.jbei.ice.storage.model.BulkUpload
setAccount(Account) - Method in class org.jbei.ice.storage.model.Comment
setAccount(Account) - Method in class org.jbei.ice.storage.model.Permission
setAccount(Account) - Method in class org.jbei.ice.storage.model.Preference
setAccount(Account) - Method in class org.jbei.ice.storage.model.Request
setAccountInfo(PartSample, String) - Method in class org.jbei.ice.lib.entry.sample.SampleService
setAccountTransfer(AccountTransfer) - Method in class org.jbei.ice.lib.dto.comment.UserComment
setAccountType(AccountType) - Method in class org.jbei.ice.lib.account.AccountTransfer
setAction(String) - Method in class org.jbei.ice.lib.dto.History
setAction(String) - Method in class org.jbei.ice.storage.model.Audit
setAdd(boolean) - Method in class org.jbei.ice.lib.dto.bulkupload.PreferenceInfo
setAdded(Date) - Method in class org.jbei.ice.storage.model.RemotePartner
setAddTime(long) - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
setAdmin(boolean) - Method in class org.jbei.ice.lib.account.AccountTransfer
setAlias(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setAlias(String) - Method in class org.jbei.ice.storage.model.Entry
setAlignment(String) - Method in class org.jbei.ice.lib.dto.search.SearchResult
setAll(boolean) - Method in class org.jbei.ice.lib.entry.EntrySelection
setAnnotationType(String) - Method in class org.jbei.ice.lib.dto.DNAFeature
setApiKey(String) - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
setApiKey(String) - Method in class org.jbei.ice.storage.model.RemotePartner
setArabidopsisSeedData(ArabidopsisSeedData) - Method in class org.jbei.ice.lib.dto.entry.PartData
setArticle(AccessPermission.Article) - Method in class org.jbei.ice.lib.dto.access.AccessPermission
setArticleId(long) - Method in class org.jbei.ice.lib.dto.access.AccessPermission
setAscending(boolean) - Method in class org.jbei.ice.lib.dto.common.PageParameters
setAssetName(String) - Method in class org.jbei.ice.lib.config.SiteSettings
setAttachments(ArrayList<AttachmentInfo>) - Method in class org.jbei.ice.lib.dto.entry.PartData
setAuthenticationToken(String) - Method in class org.jbei.ice.storage.model.RemotePartner
setAuthorFirstName(String) - Method in class org.jbei.ice.lib.manuscript.Manuscript
setAuthorFirstName(String) - Method in class org.jbei.ice.storage.model.ManuscriptModel
setAuthorLastName(String) - Method in class org.jbei.ice.lib.manuscript.Manuscript
setAuthorLastName(String) - Method in class org.jbei.ice.storage.model.ManuscriptModel
setAutoJoin(boolean) - Method in class org.jbei.ice.lib.dto.group.UserGroup
setAutoJoin(boolean) - Method in class org.jbei.ice.storage.model.Group
setAvailable(long) - Method in class org.jbei.ice.lib.folder.CollectionCounts
setBackbone(String) - Method in class org.jbei.ice.lib.dto.entry.PlasmidData
setBackbone(String) - Method in class org.jbei.ice.storage.model.Plasmid
setBasePairCount(long) - Method in class org.jbei.ice.lib.dto.entry.PartData
setBioSafetyLevel(Integer) - Method in class org.jbei.ice.lib.dto.entry.PartData
setBioSafetyLevel(Integer) - Method in class org.jbei.ice.storage.model.Entry
setBioSafetyOption(BioSafetyOption) - Method in class org.jbei.ice.lib.dto.search.SearchQuery
setBlastProgram(BlastProgram) - Method in class org.jbei.ice.lib.dto.search.BlastQuery
setBlastQuery(BlastQuery) - Method in class org.jbei.ice.lib.dto.search.SearchQuery
setBody(String) - Method in class org.jbei.ice.storage.model.Comment
setBulkUploadId(long) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadAutoUpdate
setCanEdit(boolean) - Method in class org.jbei.ice.lib.dto.entry.PartData
setCanEdit(boolean) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
setCanEdit(boolean) - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
setCanEdit(boolean) - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
setCanEdit(boolean) - Method in class org.jbei.ice.lib.dto.sample.PartSample
setCanEdit(boolean) - Method in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
setCanRead(boolean) - Method in class org.jbei.ice.storage.model.Permission
setCanWrite(boolean) - Method in class org.jbei.ice.storage.model.Permission
setChild(StorageLocation) - Method in class org.jbei.ice.lib.dto.StorageLocation
setCircular(Boolean) - Method in class org.jbei.ice.lib.dto.entry.PlasmidData
setCircular(boolean) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter
setCircular(Boolean) - Method in class org.jbei.ice.storage.model.Plasmid
setClient(RemoteClientModel) - Method in class org.jbei.ice.storage.model.RemoteShareModel
setClientId(String) - Method in class org.jbei.ice.lib.dto.access.AccessKey
setClientId(String) - Method in class org.jbei.ice.storage.model.ApiKey
setCommentCount(int) - Method in class org.jbei.ice.lib.dto.entry.PartStatistics
setCommentDate(long) - Method in class org.jbei.ice.lib.dto.comment.UserComment
setComponentUri(String) - Method in class org.jbei.ice.storage.model.Sequence
setContents(List<Entry>) - Method in class org.jbei.ice.storage.model.BulkUpload
setCount(int) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
setCount(long) - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
setCount(int) - Method in class org.jbei.ice.lib.dto.sample.UserSamples
setCount(long) - Method in class org.jbei.ice.lib.search.WebResult
setCreated(Date) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
setCreated(Date) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
setCreated(long) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
setCreated(Date) - Method in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
setCreated(long) - Method in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
setCreated(long) - Method in class org.jbei.ice.lib.experiment.Study
setCreationTime(long) - Method in class org.jbei.ice.lib.dto.access.AccessKey
setCreationTime(long) - Method in class org.jbei.ice.lib.dto.entry.PartData
setCreationTime(long) - Method in class org.jbei.ice.lib.dto.group.UserGroup
setCreationTime(long) - Method in class org.jbei.ice.lib.dto.sample.PartSample
setCreationTime(long) - Method in class org.jbei.ice.lib.folder.AbstractFolder
setCreationTime(long) - Method in class org.jbei.ice.lib.manuscript.Manuscript
setCreationTime(Date) - Method in class org.jbei.ice.storage.model.Account
setCreationTime(Date) - Method in class org.jbei.ice.storage.model.ApiKey
setCreationTime(Date) - Method in class org.jbei.ice.storage.model.BulkUpload
setCreationTime(Date) - Method in class org.jbei.ice.storage.model.Comment
setCreationTime(Date) - Method in class org.jbei.ice.storage.model.Entry
setCreationTime(Date) - Method in class org.jbei.ice.storage.model.Experiment
setCreationTime(Date) - Method in class org.jbei.ice.storage.model.Folder
setCreationTime(Date) - Method in class org.jbei.ice.storage.model.Group
setCreationTime(Date) - Method in class org.jbei.ice.storage.model.ManuscriptModel
setCreationTime(Date) - Method in class org.jbei.ice.storage.model.Sample
setCreationTime(Date) - Method in class org.jbei.ice.storage.model.ShotgunSequence
setCreationTime(Date) - Method in class org.jbei.ice.storage.model.TraceSequence
setCreator(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setCreator(String) - Method in class org.jbei.ice.storage.model.Entry
setCreatorEmail(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setCreatorEmail(String) - Method in class org.jbei.ice.storage.model.Entry
setCreatorId(long) - Method in class org.jbei.ice.lib.dto.entry.PartData
setCuration(Curation) - Method in class org.jbei.ice.lib.dto.DNAFeature
setCuration(FeatureCurationModel) - Method in class org.jbei.ice.storage.model.Feature
setCustomFields(ArrayList<CustomField>) - Method in class org.jbei.ice.lib.dto.entry.PartData
setData(List<T>) - Method in class org.jbei.ice.lib.dto.common.Results
setDateRead(Date) - Method in class org.jbei.ice.storage.model.Message
setDateSent(Date) - Method in class org.jbei.ice.storage.model.Message
setDcUri(String) - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
setDeleted(long) - Method in class org.jbei.ice.lib.folder.CollectionCounts
setDepositor(AccountTransfer) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
setDepositor(AccountTransfer) - Method in class org.jbei.ice.lib.dto.sample.PartSample
setDepositor(AccountTransfer) - Method in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
setDepositor(String) - Method in class org.jbei.ice.storage.model.Sample
setDepositor(String) - Method in class org.jbei.ice.storage.model.ShotgunSequence
setDepositor(String) - Method in class org.jbei.ice.storage.model.TraceSequence
setDescription(String) - Method in class org.jbei.ice.lib.account.AccountTransfer
setDescription(String) - Method in class org.jbei.ice.lib.dto.entry.AttachmentInfo
setDescription(String) - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
setDescription(String) - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
setDescription(String) - Method in class org.jbei.ice.lib.dto.group.UserGroup
setDescription(String) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter
setDescription(String) - Method in class org.jbei.ice.storage.model.Account
setDescription(String) - Method in class org.jbei.ice.storage.model.Attachment
setDescription(String) - Method in class org.jbei.ice.storage.model.Folder
setDescription(String) - Method in class org.jbei.ice.storage.model.Group
setDescription(String) - Method in class org.jbei.ice.storage.model.Storage
setDestination(ArrayList<FolderDetails>) - Method in class org.jbei.ice.lib.entry.EntrySelection
setDestinationAccounts(HashSet<Account>) - Method in class org.jbei.ice.storage.model.Message
setDestinationGroups(HashSet<Group>) - Method in class org.jbei.ice.storage.model.Message
setDisplay(String) - Method in class org.jbei.ice.lib.dto.access.AccessPermission
setDisplay(String) - Method in class org.jbei.ice.lib.dto.StorageLocation
setDivision(String) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter
setDrafts(long) - Method in class org.jbei.ice.lib.folder.CollectionCounts
setEcotype(String) - Method in class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
setEcotype(String) - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
setEmail(String) - Method in class org.jbei.ice.lib.account.AccountTransfer
setEmail(String) - Method in class org.jbei.ice.storage.model.Account
setEmail(String) - Method in class org.jbei.ice.storage.model.RemoteClientModel
setEnable(String, boolean, String) - Method in class org.jbei.ice.lib.net.WoRController: Runs the web of registries task for contacting the appropriate partners to enable or disable web of registries functionality
setEnd(int) - Method in class org.jbei.ice.lib.dto.DNAFeatureLocation
setEnd(int) - Method in class org.jbei.ice.lib.parsers.genbank.GenbankLocation
setEnd(int) - Method in class org.jbei.ice.storage.model.AnnotationLocation
setEntries(Results<PartData>) - Method in class org.jbei.ice.lib.dto.web.PartnerEntries
setEntries(List<Long>, EntryField...) - Method in class org.jbei.ice.lib.entry.EntriesAsCSV: Directly set the list of entries whose fields and (optionally) sequences are to be extracted
setEntries(ArrayList<Long>) - Method in class org.jbei.ice.lib.entry.EntrySelection
setEntries(List<PartData>) - Method in class org.jbei.ice.lib.folder.AbstractFolder
setEntry(Entry) - Method in class org.jbei.ice.storage.model.Attachment
setEntry(Entry) - Method in class org.jbei.ice.storage.model.Audit
setEntry(Entry) - Method in class org.jbei.ice.storage.model.Comment
setEntry(Entry) - Method in class org.jbei.ice.storage.model.Link
setEntry(Entry) - Method in class org.jbei.ice.storage.model.Parameter
setEntry(Entry) - Method in class org.jbei.ice.storage.model.Permission
setEntry(Entry) - Method in class org.jbei.ice.storage.model.Request
setEntry(Entry) - Method in class org.jbei.ice.storage.model.Sample
setEntry(Entry) - Method in class org.jbei.ice.storage.model.SelectionMarker
setEntry(Entry) - Method in class org.jbei.ice.storage.model.Sequence
setEntry(Entry) - Method in class org.jbei.ice.storage.model.ShotgunSequence
setEntry(Entry) - Method in class org.jbei.ice.storage.model.TraceSequence
setEntryId(long) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadAutoUpdate
setEntryId(long) - Method in class org.jbei.ice.lib.dto.comment.UserComment
setEntryId(long) - Method in class org.jbei.ice.lib.dto.entry.PartStatistics
setEntryId(long) - Method in class org.jbei.ice.lib.dto.entry.SequenceInfo
setEntryInfo(PartData) - Method in class org.jbei.ice.lib.dto.entry.HasEntryData
setEntryStatus(BulkUpload, Visibility) - Method in class org.jbei.ice.storage.hibernate.dao.BulkUploadDAO
setEntryType(EntryType) - Method in class org.jbei.ice.lib.entry.EntrySelection
setEntryTypes(List<EntryType>) - Method in class org.jbei.ice.lib.dto.search.SearchQuery
setEntryVisibility(List<Long>, Visibility) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
seteValue(String) - Method in class org.jbei.ice.lib.dto.search.SearchResult
setExclude(boolean) - Method in class org.jbei.ice.lib.dto.Curation
setExclude(boolean) - Method in class org.jbei.ice.storage.model.FeatureCurationModel
setExperimentalDataCount(int) - Method in class org.jbei.ice.lib.dto.entry.PartStatistics
setExpires(Date) - Method in class org.jbei.ice.storage.model.ApiKey
setFeature(Feature) - Method in class org.jbei.ice.storage.model.FeatureCurationModel
setFeature(Feature) - Method in class org.jbei.ice.storage.model.SequenceFeature
setFeatureCount(long) - Method in class org.jbei.ice.lib.dto.entry.PartData
setFeatures(List<DNAFeature>) - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
setFeatures(List<DNAFeature>) - Method in class org.jbei.ice.lib.parsers.genbank.FeaturesTag
setFetched(long) - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
setFetched(long) - Method in class org.jbei.ice.storage.model.RemotePartner
setField(EntryField) - Method in class org.jbei.ice.lib.dto.search.FieldFilter
setField(ArrayList<String>) - Method in class org.jbei.ice.storage.hibernate.filter.EntryHasFilterFactory
setFieldFilters(ArrayList<FieldFilter>) - Method in class org.jbei.ice.lib.dto.search.SearchQuery
setFileData(String, Entry, PartData) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadController
setFileData(String, Entry, PartData) - Method in class org.jbei.ice.lib.folder.collection.Collection
setFileId(String) - Method in class org.jbei.ice.lib.dto.entry.AttachmentInfo
setFileId(String) - Method in class org.jbei.ice.lib.dto.entry.SequenceInfo
setFileId(String) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
setFileId(String) - Method in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
setFileId(String) - Method in class org.jbei.ice.storage.model.Attachment
setFileId(String) - Method in class org.jbei.ice.storage.model.ShotgunSequence
setFileId(String) - Method in class org.jbei.ice.storage.model.TraceSequence
setFilename(String) - Method in class org.jbei.ice.lib.dto.entry.AttachmentInfo
setFilename(String) - Method in class org.jbei.ice.lib.dto.entry.SequenceInfo
setFilename(String) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
setFilename(String) - Method in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
setFileName(String) - Method in class org.jbei.ice.storage.model.Attachment
setFileName(String) - Method in class org.jbei.ice.storage.model.Sequence
setFilename(String) - Method in class org.jbei.ice.storage.model.ShotgunSequence
setFilename(String) - Method in class org.jbei.ice.storage.model.TraceSequence
setFilter(String) - Method in class org.jbei.ice.lib.dto.common.PageParameters
setFilter(String) - Method in class org.jbei.ice.lib.dto.search.FieldFilter
setFirstName(String) - Method in class org.jbei.ice.lib.account.AccountTransfer
setFirstName(String) - Method in class org.jbei.ice.storage.model.Account
setFirstName(String) - Method in class org.jbei.ice.storage.model.Audit
setFolder(FolderDetails) - Method in class org.jbei.ice.lib.manuscript.Manuscript
setFolder(Folder) - Method in class org.jbei.ice.storage.model.ManuscriptModel
setFolder(Folder) - Method in class org.jbei.ice.storage.model.Permission
setFolderDetails(FolderDetails) - Method in class org.jbei.ice.lib.dto.access.RemoteAccessPermission
setFolderId(String) - Method in class org.jbei.ice.lib.entry.EntrySelection
setFolderPermissions(String, long, List<AccessPermission>) - Method in class org.jbei.ice.lib.access.PermissionsController
setFolderType(Folder, FolderType) - Method in class org.jbei.ice.lib.manuscript.Manuscripts
setFormat(SequenceFormat) - Method in class org.jbei.ice.lib.dto.entry.SequenceInfo
setFormat(SequenceFormat) - Method in class org.jbei.ice.storage.model.Sequence
setFrom(String) - Method in class org.jbei.ice.lib.dto.message.MessageInfo
setFromEmail(String) - Method in class org.jbei.ice.storage.model.Message
setFundingSource(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setFundingSource(String) - Method in class org.jbei.ice.storage.model.Entry
setFwdHash(String) - Method in class org.jbei.ice.storage.model.Sequence
setGenbankStart(int) - Method in class org.jbei.ice.lib.dto.DNAFeatureLocation
setGenbankStart(int) - Method in class org.jbei.ice.lib.parsers.genbank.GenbankLocation
setGenbankStart(int) - Method in class org.jbei.ice.storage.model.AnnotationLocation
setGenbankType(String) - Method in class org.jbei.ice.storage.model.Feature
setGeneration(Generation) - Method in class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
setGeneration(Generation) - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
setGenotypePhenotype(String) - Method in class org.jbei.ice.lib.dto.entry.StrainData
setGenotypePhenotype(String) - Method in class org.jbei.ice.storage.model.Strain
setGroup(UserGroup) - Method in class org.jbei.ice.lib.dto.access.AccessPermission
setGroup(Group) - Method in class org.jbei.ice.storage.model.Permission
setGroupMembers(Group, List<AccountTransfer>, List<RemoteUser>) - Method in class org.jbei.ice.lib.group.Groups
setGroupUUids(HashSet<String>) - Method in class org.jbei.ice.storage.hibernate.filter.EntrySecurityFilterFactory
setGrowthTemperature(int) - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
setGrowthTemperature(int) - Method in class org.jbei.ice.storage.model.Request
setHarvestDate(String) - Method in class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
setHarvestDate(Date) - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
setHasAttachment(boolean) - Method in class org.jbei.ice.lib.dto.entry.PartData
setHasAttachment(boolean) - Method in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
setHasFooter(boolean) - Method in class org.jbei.ice.lib.config.SiteSettings
setHash(String) - Method in class org.jbei.ice.storage.model.Feature
setHashedToken(String) - Method in class org.jbei.ice.storage.model.ApiKey
setHasLoginMessage(boolean) - Method in class org.jbei.ice.lib.config.SiteSettings
setHasLogo(boolean) - Method in class org.jbei.ice.lib.config.SiteSettings
setHasOriginalSequence(boolean) - Method in class org.jbei.ice.lib.dto.entry.PartData
setHasSample(boolean) - Method in class org.jbei.ice.lib.dto.entry.PartData
setHasSample(boolean) - Method in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
setHasSequence(boolean) - Method in class org.jbei.ice.lib.dto.entry.PartData
setHasSequence(boolean) - Method in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
setHeaders(List<HeaderValue>) - Method in class org.jbei.ice.lib.bulkupload.ProcessedBulkUpload
setHeaders(Invocation.Builder, String) - Method in class org.jbei.ice.services.rest.IceRestClient
setHistoryCount(int) - Method in class org.jbei.ice.lib.dto.entry.PartStatistics
setHomozygosity(String) - Method in class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
setHomozygosity(String) - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
setHost(String) - Method in class org.jbei.ice.lib.dto.entry.StrainData
setHost(String) - Method in class org.jbei.ice.storage.model.Strain
setId(long) - Method in class org.jbei.ice.lib.account.AccountTransfer
setId(long) - Method in class org.jbei.ice.lib.dto.access.AccessKey
setId(long) - Method in class org.jbei.ice.lib.dto.access.AccessPermission
setId(long) - Method in class org.jbei.ice.lib.dto.comment.UserComment
setId(long) - Method in class org.jbei.ice.lib.dto.DNAFeature
setId(long) - Method in class org.jbei.ice.lib.dto.entry.AttachmentInfo
setId(long) - Method in class org.jbei.ice.lib.dto.entry.CustomField
setId(long) - Method in class org.jbei.ice.lib.dto.entry.PartData
setId(long) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
setId(long) - Method in class org.jbei.ice.lib.dto.group.UserGroup
setId(long) - Method in class org.jbei.ice.lib.dto.History
setId(long) - Method in class org.jbei.ice.lib.dto.message.MessageInfo
setId(long) - Method in class org.jbei.ice.lib.dto.sample.PartSample
setId(long) - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
setId(long) - Method in class org.jbei.ice.lib.dto.ShotgunSequenceDTO
setId(long) - Method in class org.jbei.ice.lib.dto.StorageLocation
setId(long) - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
setId(long) - Method in class org.jbei.ice.lib.experiment.Study
setId(long) - Method in class org.jbei.ice.lib.folder.AbstractFolder
setId(long) - Method in class org.jbei.ice.lib.manuscript.Manuscript
setId(long) - Method in class org.jbei.ice.storage.model.Account
setId(long) - Method in class org.jbei.ice.storage.model.AccountPreferences
setId(long) - Method in class org.jbei.ice.storage.model.AnnotationLocation
setId(long) - Method in class org.jbei.ice.storage.model.Attachment
setId(long) - Method in class org.jbei.ice.storage.model.Configuration
setId(long) - Method in class org.jbei.ice.storage.model.Entry
setId(long) - Method in class org.jbei.ice.storage.model.Feature
setId(long) - Method in class org.jbei.ice.storage.model.Folder
setId(long) - Method in class org.jbei.ice.storage.model.Group
setId(long) - Method in class org.jbei.ice.storage.model.Link
setId(long) - Method in class org.jbei.ice.storage.model.Parameter
setId(int) - Method in class org.jbei.ice.storage.model.Preference
setId(long) - Method in class org.jbei.ice.storage.model.Sample
setId(long) - Method in class org.jbei.ice.storage.model.SelectionMarker
setId(long) - Method in class org.jbei.ice.storage.model.Sequence
setId(long) - Method in class org.jbei.ice.storage.model.SequenceFeature
setId(long) - Method in class org.jbei.ice.storage.model.SequenceFeatureAttribute
setId(long) - Method in class org.jbei.ice.storage.model.ShotgunSequence
setId(long) - Method in class org.jbei.ice.storage.model.Storage
setId(long) - Method in class org.jbei.ice.storage.model.TraceSequence
setId(long) - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
setIdentification(String) - Method in class org.jbei.ice.storage.model.Feature
setIdentifier(String) - Method in class org.jbei.ice.lib.dto.DNAFeature
setIdentifier(String) - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
setIdentifier(String) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.GenbankFormatter
setIdentifier(String) - Method in class org.jbei.ice.storage.model.RemoteAccessModel
setIdentifier(String) - Method in class org.jbei.ice.storage.model.Sequence
setImportType(String) - Method in class org.jbei.ice.storage.model.BulkUpload
setInbetween(boolean) - Method in class org.jbei.ice.lib.parsers.genbank.GenbankLocation
setInbetween(boolean) - Method in class org.jbei.ice.storage.model.AnnotationLocation
setInCart(boolean) - Method in class org.jbei.ice.lib.dto.sample.PartSample
setIndex(int) - Method in class org.jbei.ice.lib.dto.entry.PartData
setIndex(String) - Method in class org.jbei.ice.storage.model.Storage
setInitials(String) - Method in class org.jbei.ice.lib.account.AccountTransfer
setInitials(String) - Method in class org.jbei.ice.storage.model.Account
setInstitution(String) - Method in class org.jbei.ice.lib.account.AccountTransfer
setInstitution(String) - Method in class org.jbei.ice.storage.model.Account
setInstitution(String) - Method in class org.jbei.ice.storage.model.Audit
setIntellectualProperty(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setIntellectualProperty(String) - Method in class org.jbei.ice.storage.model.Entry
setIp(String) - Method in class org.jbei.ice.storage.model.Account
setIsCircular(boolean) - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
setKey(String) - Method in class org.jbei.ice.lib.dto.bulkupload.PreferenceInfo
setKey(String) - Method in class org.jbei.ice.lib.dto.Setting
setKey(String) - Method in class org.jbei.ice.lib.parsers.genbank.Tag
setKey(String) - Method in class org.jbei.ice.storage.model.Configuration
setKey(String) - Method in class org.jbei.ice.storage.model.Parameter
setKey(String) - Method in class org.jbei.ice.storage.model.Preference
setKey(String) - Method in class org.jbei.ice.storage.model.SequenceFeatureAttribute
setKeywords(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setKeywords(String) - Method in class org.jbei.ice.storage.model.Entry
setLabel(String) - Method in class org.jbei.ice.lib.dto.group.UserGroup
setLabel(String) - Method in class org.jbei.ice.lib.dto.sample.PartSample
setLabel(String) - Method in class org.jbei.ice.lib.experiment.Study
setLabel(String) - Method in class org.jbei.ice.storage.model.Experiment
setLabel(String) - Method in class org.jbei.ice.storage.model.Group
setLabel(String) - Method in class org.jbei.ice.storage.model.Sample
setLastContact(Date) - Method in class org.jbei.ice.storage.model.RemotePartner
setLastContactTime(long) - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
setLastLogin(long) - Method in class org.jbei.ice.lib.account.AccountTransfer
setLastLoginTime(Date) - Method in class org.jbei.ice.storage.model.Account
setLastName(String) - Method in class org.jbei.ice.lib.account.AccountTransfer
setLastName(String) - Method in class org.jbei.ice.storage.model.Account
setLastName(String) - Method in class org.jbei.ice.storage.model.Audit
setLastUpdate(Date) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadAutoUpdate
setLastUpdate(Date) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
setLastUpdateTime(Date) - Method in class org.jbei.ice.storage.model.BulkUpload
setLength(long) - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
setLimit(int) - Method in class org.jbei.ice.lib.dto.common.PageParameters
setLink(String) - Method in class org.jbei.ice.storage.model.Link
setLinks(ArrayList<String>) - Method in class org.jbei.ice.lib.dto.entry.PartData
setLinks(Set<Link>) - Method in class org.jbei.ice.storage.model.Entry
setLocation(StorageLocation) - Method in class org.jbei.ice.lib.dto.sample.PartSample
setLocation(List<PartSample>) - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
setLocations(List<DNAFeatureLocation>) - Method in class org.jbei.ice.lib.dto.DNAFeature
setLongDescription(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setLongDescription(String) - Method in class org.jbei.ice.storage.model.Entry
setLongDescriptionType(String) - Method in class org.jbei.ice.storage.model.Entry
setMaxScore(float) - Method in class org.jbei.ice.lib.dto.search.SearchResult
setMemberCount(long) - Method in class org.jbei.ice.lib.dto.group.UserGroup
setMessage(String) - Method in class org.jbei.ice.lib.dto.comment.UserComment
setMessage(String) - Method in class org.jbei.ice.lib.dto.message.MessageInfo
setMessage(String) - Method in class org.jbei.ice.services.rest.ErrorResponse
setMessage(String) - Method in class org.jbei.ice.storage.model.Message
setModificationTime(long) - Method in class org.jbei.ice.lib.dto.entry.PartData
setModificationTime(Date) - Method in class org.jbei.ice.storage.model.Account
setModificationTime(Date) - Method in class org.jbei.ice.storage.model.Comment
setModificationTime(Date) - Method in class org.jbei.ice.storage.model.Entry
setModificationTime(Date) - Method in class org.jbei.ice.storage.model.Folder
setModificationTime(Date) - Method in class org.jbei.ice.storage.model.Group
setModificationTime(Date) - Method in class org.jbei.ice.storage.model.Sample
setModificationTime(Date) - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
setModified(long) - Method in class org.jbei.ice.lib.dto.comment.UserComment
setName(String) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
setName(String) - Method in class org.jbei.ice.lib.dto.DNAFeature
setName(String) - Method in class org.jbei.ice.lib.dto.DNAFeatureNote
setName(String) - Method in class org.jbei.ice.lib.dto.entry.CustomField
setName(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setName(String) - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
setName(String) - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
setName(String) - Method in class org.jbei.ice.lib.dto.StorageLocation
setName(String) - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
setName(String) - Method in class org.jbei.ice.storage.model.BulkUpload
setName(String) - Method in class org.jbei.ice.storage.model.Entry
setName(String) - Method in class org.jbei.ice.storage.model.Feature
setName(String) - Method in class org.jbei.ice.storage.model.Folder
setName(String) - Method in class org.jbei.ice.storage.model.RemotePartner
setName(String) - Method in class org.jbei.ice.storage.model.SelectionMarker
setName(String) - Method in class org.jbei.ice.storage.model.SequenceFeature
setName(String) - Method in class org.jbei.ice.storage.model.Storage
setNewMessageCount(int) - Method in class org.jbei.ice.lib.account.AccountTransfer
setNident(int) - Method in class org.jbei.ice.lib.dto.search.SearchResult
setNotes(List<DNAFeatureNote>) - Method in class org.jbei.ice.lib.dto.DNAFeature
setNotes(String) - Method in class org.jbei.ice.storage.model.Sample
setOffset(int) - Method in class org.jbei.ice.lib.dto.common.PageParameters
setOriginOfReplication(String) - Method in class org.jbei.ice.lib.dto.entry.PlasmidData
setOriginOfReplication(String) - Method in class org.jbei.ice.storage.model.Plasmid
setOwner(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setOwner(AccountTransfer) - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
setOwner(String) - Method in class org.jbei.ice.storage.model.Entry
setOwner(Account) - Method in class org.jbei.ice.storage.model.Group
setOwnerEmail(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setOwnerEmail(String) - Method in class org.jbei.ice.lib.dto.group.UserGroup
setOwnerEmail(String) - Method in class org.jbei.ice.lib.experiment.Study
setOwnerEmail(String) - Method in class org.jbei.ice.storage.model.ApiKey
setOwnerEmail(String) - Method in class org.jbei.ice.storage.model.Entry
setOwnerEmail(String) - Method in class org.jbei.ice.storage.model.Experiment
setOwnerEmail(String) - Method in class org.jbei.ice.storage.model.Folder
setOwnerEmail(String) - Method in class org.jbei.ice.storage.model.Storage
setOwnerId(long) - Method in class org.jbei.ice.lib.dto.entry.PartData
setParagonUrl(String) - Method in class org.jbei.ice.lib.manuscript.Manuscript
setParagonUrl(String) - Method in class org.jbei.ice.storage.model.ManuscriptModel
setParameters(List<Parameter>) - Method in class org.jbei.ice.storage.model.Entry
setParameterValues(Map) - Method in class org.jbei.ice.storage.hibernate.bridge.EntryBooleanPropertiesBridge
setParent(FolderDetails) - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
setParent(Folder) - Method in class org.jbei.ice.storage.model.Folder
setParent(Storage) - Method in class org.jbei.ice.storage.model.Storage
setParentId(long) - Method in class org.jbei.ice.lib.dto.group.UserGroup
setParents(String) - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
setPartData(PartData) - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
setPartDataFromField(PartData, String, EntryField, boolean) - Static method in class org.jbei.ice.lib.entry.EntryUtil: Updates the partData based on the field that is specified.
setPartDefaults(PartData) - Static method in class org.jbei.ice.lib.entry.EntryUtil
setPartId(long) - Method in class org.jbei.ice.lib.dto.entry.CustomField
setPartId(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setPartId(long) - Method in class org.jbei.ice.lib.dto.sample.PartSample
setPartId(String) - Method in class org.jbei.ice.lib.experiment.Study
setPartName(String) - Method in class org.jbei.ice.lib.dto.sample.PartSample
setPartner(RegistryPartner) - Method in class org.jbei.ice.lib.dto.access.AccessPermission
setPartner(RegistryPartner) - Method in class org.jbei.ice.lib.dto.History
setPartner(RegistryPartner) - Method in class org.jbei.ice.lib.dto.search.SearchResult
setPartner(RegistryPartner) - Method in class org.jbei.ice.lib.dto.web.PartnerEntries
setPartner(RegistryPartner) - Method in class org.jbei.ice.lib.dto.web.RemoteUser
setPartner(RegistryPartner) - Method in class org.jbei.ice.lib.search.WebResult
setPartners(ArrayList<RegistryPartner>) - Method in class org.jbei.ice.lib.dto.web.WebOfRegistries
setPartnerStatus(RemotePartnerStatus) - Method in class org.jbei.ice.storage.model.RemotePartner
setPartNumber(String) - Method in class org.jbei.ice.storage.model.Entry
setPartSampleData(SampleField, PartSample, String) - Method in class org.jbei.ice.lib.bulkupload.BulkCSVUpload
setPassword(String) - Method in class org.jbei.ice.lib.account.AccountTransfer
setPassword(String) - Method in class org.jbei.ice.storage.model.Account
setPending(long) - Method in class org.jbei.ice.lib.folder.CollectionCounts
setPermission(Permission) - Method in class org.jbei.ice.storage.model.RemoteAccessModel
setPermission(Permission) - Method in class org.jbei.ice.storage.model.RemoteShareModel
setPermissions(long, ArrayList<AccessPermission>) - Method in class org.jbei.ice.services.rest.FolderResource
setPersonal(long) - Method in class org.jbei.ice.lib.folder.CollectionCounts
setPlantType(PlantType) - Method in class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
setPlantType(PlantType) - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
setPlasmidData(PlasmidData) - Method in class org.jbei.ice.lib.dto.entry.PartData
setPlasmidFields(PlasmidData, Entry) - Static method in class org.jbei.ice.servlet.InfoToModelFactory
setPlateDescription(String) - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
setPlateDescription(String) - Method in class org.jbei.ice.storage.model.Request
setPreferences(String) - Method in class org.jbei.ice.storage.model.AccountPreferences
setPrincipalInvestigator(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setPrincipalInvestigator(String) - Method in class org.jbei.ice.storage.model.Entry
setPrincipalInvestigatorEmail(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setPrincipalInvestigatorEmail(String) - Method in class org.jbei.ice.storage.model.Entry
setPrincipalInvestigatorId(long) - Method in class org.jbei.ice.lib.dto.entry.PartData
setPromoters(String) - Method in class org.jbei.ice.lib.dto.entry.PlasmidData
setPromoters(String) - Method in class org.jbei.ice.storage.model.Plasmid
setPropagatePermission(boolean) - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
setPropagatePermissions(boolean) - Method in class org.jbei.ice.storage.model.Folder
setPropertyValue(ConfigurationKey, String) - Method in class org.jbei.ice.lib.config.ConfigurationController
setPublicRead(boolean) - Method in class org.jbei.ice.lib.dto.entry.PartData
setPublicReadAccess(boolean) - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
setQuery(SearchQuery) - Method in class org.jbei.ice.lib.dto.search.SearchResults
setQuery(SearchQuery) - Method in class org.jbei.ice.lib.search.WebSearchResults
setQueryAlignment(String) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
setQueryAlignment(String) - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
setQueryEnd(int) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
setQueryEnd(int) - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
setQueryLength(int) - Method in class org.jbei.ice.lib.dto.search.SearchResult
setQueryStart(int) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
setQueryStart(int) - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
setQueryString(String) - Method in class org.jbei.ice.lib.dto.search.SearchQuery
setQuoted(boolean) - Method in class org.jbei.ice.lib.dto.DNAFeatureNote
setQuoted(Boolean) - Method in class org.jbei.ice.storage.model.SequenceFeatureAttribute
setRawBody(String) - Method in class org.jbei.ice.lib.parsers.genbank.Tag
setRead(boolean) - Method in class org.jbei.ice.lib.dto.message.MessageInfo
setRead(boolean) - Method in class org.jbei.ice.storage.model.Message
setRecordId(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setRecordId(String) - Method in class org.jbei.ice.storage.model.Entry
setRecordType(String) - Method in class org.jbei.ice.storage.model.Entry
setReferences(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setReferences(ArrayList<Tag>) - Method in class org.jbei.ice.lib.parsers.genbank.ReferenceTag
setReferences(String) - Method in class org.jbei.ice.storage.model.Entry
setRegisterDate(long) - Method in class org.jbei.ice.lib.account.AccountTransfer
setRemoteClientModel(RemoteClientModel) - Method in class org.jbei.ice.storage.model.Audit
setRemoteClientModel(RemoteClientModel) - Method in class org.jbei.ice.storage.model.RemoteAccessModel
setRemotePartner(RegistryPartner) - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
setRemotePartner(RemotePartner) - Method in class org.jbei.ice.storage.model.RemoteClientModel
setRemoteShare(RemoteShareModel) - Method in class org.jbei.ice.storage.model.Permission
setReplicatesIn(String) - Method in class org.jbei.ice.lib.dto.entry.PlasmidData
setReplicatesIn(String) - Method in class org.jbei.ice.storage.model.Plasmid
setRequested(Date) - Method in class org.jbei.ice.storage.model.Request
setRequester(AccountTransfer) - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
setRequests(ArrayList<SampleRequest>) - Method in class org.jbei.ice.lib.dto.sample.UserSamples
setRequestsStatus(String, ArrayList<Long>, SampleRequestStatus) - Method in class org.jbei.ice.lib.entry.sample.RequestRetriever
setRequestStatus(SampleRequestStatus, ArrayList<Long>) - Method in class org.jbei.ice.services.rest.SampleResource: Sets the status of sample requests.
setRequestTime(long) - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
setRequestType(SampleRequestType) - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
setRestrictionEnzymes(String) - Method in class org.jbei.ice.storage.model.AccountPreferences
setResultCount(long) - Method in class org.jbei.ice.lib.dto.AccountResults
setResultCount(long) - Method in class org.jbei.ice.lib.dto.common.Results
setResultCount(long) - Method in class org.jbei.ice.lib.dto.search.SearchResults
setResults(List<SearchResult>) - Method in class org.jbei.ice.lib.dto.search.SearchResults
setResults(List<SearchResult>) - Method in class org.jbei.ice.lib.search.WebResult
setRetrieveCount(int) - Method in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
setRevHash(String) - Method in class org.jbei.ice.storage.model.Sequence
setRow(int) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadAutoUpdate
setSalt(String) - Method in class org.jbei.ice.storage.model.Account
setSalt(String) - Method in class org.jbei.ice.storage.model.RemotePartner
setSampleCount(int) - Method in class org.jbei.ice.lib.dto.entry.PartStatistics
setSamples(ArrayList<PartSample>) - Method in class org.jbei.ice.lib.dto.comment.UserComment
setScore(int) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
setScore(float) - Method in class org.jbei.ice.lib.dto.search.SearchResult
setScore(int) - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
setSearchQuery(SearchQuery) - Method in class org.jbei.ice.lib.entry.EntrySelection
setSecret(String) - Method in class org.jbei.ice.lib.dto.access.AccessKey
setSecret(String) - Method in class org.jbei.ice.lib.dto.access.AccessPermission
setSecret(String) - Method in class org.jbei.ice.storage.model.ApiKey
setSecret(String) - Method in class org.jbei.ice.storage.model.RemoteShareModel
setSeedFields(ArabidopsisSeedData, Entry) - Static method in class org.jbei.ice.servlet.InfoToModelFactory
setSeedParents(String) - Method in class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
setSelectedEntries(EntrySelection, EntryField...) - Method in class org.jbei.ice.lib.entry.EntriesAsCSV: Set source of entries, extract to csv
setSelectionMarkers(ArrayList<String>) - Method in class org.jbei.ice.lib.dto.entry.PartData
setSelectionMarkers(Set<SelectionMarker>) - Method in class org.jbei.ice.storage.model.Entry
setSelectionType(EntrySelectionType) - Method in class org.jbei.ice.lib.entry.EntrySelection
setSent(long) - Method in class org.jbei.ice.lib.dto.message.MessageInfo
setSent(long) - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
setSent(long) - Method in class org.jbei.ice.storage.model.RemotePartner
setSentToAbrc(Boolean) - Method in class org.jbei.ice.lib.dto.entry.ArabidopsisSeedData
setSentToABRC(Boolean) - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
setSequence(String) - Method in class org.jbei.ice.lib.dto.DNAFeature
setSequence(String) - Method in class org.jbei.ice.lib.dto.DNASequence
setSequence(DNASequence) - Method in class org.jbei.ice.lib.dto.entry.SequenceInfo
setSequence(String) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
setSequence(String) - Method in class org.jbei.ice.lib.dto.search.BlastQuery
setSequence(String) - Method in class org.jbei.ice.lib.parsers.genbank.OriginTag
setSequence(Sequence) - Method in class org.jbei.ice.storage.model.Entry
setSequence(String) - Method in class org.jbei.ice.storage.model.Feature
setSequence(String) - Method in class org.jbei.ice.storage.model.Sequence
setSequence(Sequence) - Method in class org.jbei.ice.storage.model.SequenceFeature
setSequence(String) - Method in class org.jbei.ice.storage.model.TraceSequence
setSequenceCount(int) - Method in class org.jbei.ice.lib.dto.entry.PartStatistics
setSequenceFeature(SequenceFeature) - Method in class org.jbei.ice.storage.model.AnnotationLocation
setSequenceFeature(SequenceFeature) - Method in class org.jbei.ice.storage.model.SequenceFeatureAttribute
setSequenceFeatures(Set<SequenceFeature>) - Method in class org.jbei.ice.storage.model.Sequence
setSequenceFileName(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setSequenceHash(String) - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
setSequenceUser(String) - Method in class org.jbei.ice.storage.model.Sequence
setSessionId(String) - Method in class org.jbei.ice.lib.account.AccountTransfer
setShared(long) - Method in class org.jbei.ice.lib.folder.CollectionCounts
setSharer(Account) - Method in class org.jbei.ice.storage.model.RemoteShareModel
setShortDescription(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setShortDescription(String) - Method in class org.jbei.ice.storage.model.Entry
setSingleResidue(boolean) - Method in class org.jbei.ice.lib.parsers.genbank.GenbankLocation
setSingleResidue(boolean) - Method in class org.jbei.ice.storage.model.AnnotationLocation
setSortAscending(boolean) - Method in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
setSortField(ColumnField) - Method in class org.jbei.ice.lib.dto.common.PageParameters
setSortField(ColumnField) - Method in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
setStart(int) - Method in class org.jbei.ice.lib.dto.search.SearchQuery.Parameters
setStatus(BulkUploadStatus) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
setStatus(String) - Method in class org.jbei.ice.lib.dto.entry.PartData
setStatus(SampleRequestStatus) - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
setStatus(RemotePartnerStatus) - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
setStatus(ManuscriptStatus) - Method in class org.jbei.ice.lib.manuscript.Manuscript
setStatus(AccessStatus) - Method in class org.jbei.ice.storage.model.ApiKey
setStatus(BulkUploadStatus) - Method in class org.jbei.ice.storage.model.BulkUpload
setStatus(String) - Method in class org.jbei.ice.storage.model.Entry
setStatus(ManuscriptStatus) - Method in class org.jbei.ice.storage.model.ManuscriptModel
setStatus(MessageStatus) - Method in class org.jbei.ice.storage.model.Message
setStatus(SampleRequestStatus) - Method in class org.jbei.ice.storage.model.Request
setStorage(Storage) - Method in class org.jbei.ice.storage.model.Sample
setStorageType(Storage.StorageType) - Method in class org.jbei.ice.storage.model.Storage
setStrainData(StrainData) - Method in class org.jbei.ice.lib.dto.entry.PartData
setStrainFields(StrainData, Entry) - Static method in class org.jbei.ice.servlet.InfoToModelFactory
setStrand(int) - Method in class org.jbei.ice.lib.dto.DNAFeature
setStrand(int) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
setStrand(int) - Method in class org.jbei.ice.storage.model.SequenceFeature: +1 for forward, -1 for reverse.
setStrand(int) - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
setSubjectAlignment(String) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
setSubjectAlignment(String) - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
setSubjectEnd(int) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
setSubjectEnd(int) - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
setSubjects(Set<Entry>) - Method in class org.jbei.ice.storage.model.Experiment
setSubjectStart(int) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
setSubjectStart(int) - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
setSuccess(boolean) - Method in class org.jbei.ice.lib.bulkupload.ProcessedBulkUpload
setTime(long) - Method in class org.jbei.ice.lib.dto.History
setTime(Date) - Method in class org.jbei.ice.storage.model.Audit
Setting - Class in org.jbei.ice.lib.dto: POJO for site-wide Configuration setting
Setting(String, String) - Constructor for class org.jbei.ice.lib.dto.Setting
setTitle(String) - Method in class org.jbei.ice.lib.dto.message.MessageInfo
setTitle(String) - Method in class org.jbei.ice.lib.manuscript.Manuscript
setTitle(String) - Method in class org.jbei.ice.storage.model.ManuscriptModel
setTitle(String) - Method in class org.jbei.ice.storage.model.Message
setToken(String, String) - Static method in class org.jbei.ice.lib.access.AccessTokens
setToken(String) - Method in class org.jbei.ice.lib.dto.access.AccessKey
setToken(String) - Method in class org.jbei.ice.storage.model.RemoteAccessModel
setTotalCount(long) - Method in class org.jbei.ice.lib.search.WebSearchResults
setTraceSequence(TraceSequence) - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
setTraceSequenceAlignment(TraceSequenceAlignmentInfo) - Method in class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
setTraceSequenceAlignment(TraceSequenceAlignment) - Method in class org.jbei.ice.storage.model.TraceSequence
setTransferred(long) - Method in class org.jbei.ice.lib.folder.CollectionCounts
setType(String) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadInfo
setType(AccessPermission.Type) - Method in class org.jbei.ice.lib.dto.access.AccessPermission
setType(String) - Method in class org.jbei.ice.lib.dto.DNAFeature
setType(EntryType) - Method in class org.jbei.ice.lib.dto.entry.PartData
setType(FolderType) - Method in class org.jbei.ice.lib.dto.folder.FolderDetails
setType(GroupType) - Method in class org.jbei.ice.lib.dto.group.UserGroup
setType(SampleType) - Method in class org.jbei.ice.lib.dto.StorageLocation
setType(AccountType) - Method in class org.jbei.ice.storage.model.Account
setType(FolderType) - Method in class org.jbei.ice.storage.model.Folder
setType(GroupType) - Method in class org.jbei.ice.storage.model.Group
setType(SampleRequestType) - Method in class org.jbei.ice.storage.model.Request
setTypeId(long) - Method in class org.jbei.ice.lib.dto.access.AccessPermission
setUpdated(Date) - Method in class org.jbei.ice.storage.model.Request
setUpdateTime(long) - Method in class org.jbei.ice.lib.dto.sample.SampleRequest
setUpload(BulkUpload) - Method in class org.jbei.ice.storage.model.Permission
setUploadId(long) - Method in class org.jbei.ice.lib.bulkupload.ProcessedBulkUpload
setUri(String) - Method in class org.jbei.ice.lib.dto.DNAFeature
setUri(String) - Method in class org.jbei.ice.lib.dto.DNAFeatureLocation
setUri(String) - Method in class org.jbei.ice.lib.dto.FeaturedDNASequence
setUri(String) - Method in class org.jbei.ice.storage.model.Feature
setUri(String) - Method in class org.jbei.ice.storage.model.Sequence
setUri(String) - Method in class org.jbei.ice.storage.model.SequenceFeature
setUrl(String) - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
setUrl(String) - Method in class org.jbei.ice.lib.experiment.Study
setUrl(String) - Method in class org.jbei.ice.storage.model.Experiment
setUrl(String) - Method in class org.jbei.ice.storage.model.Link
setUrl(String) - Method in class org.jbei.ice.storage.model.RemotePartner
setUser(AccountTransfer) - Method in class org.jbei.ice.lib.dto.web.RemoteUser
setUserEntryCount(long) - Method in class org.jbei.ice.lib.account.AccountTransfer
setUserId(String) - Method in class org.jbei.ice.lib.dto.access.AccessPermission
setUserId(String) - Method in class org.jbei.ice.lib.dto.History
setUserId(String) - Method in class org.jbei.ice.lib.dto.user.UserPreferences
setUserId(String) - Method in class org.jbei.ice.storage.model.Audit
setUserMessage(String) - Method in class org.jbei.ice.lib.bulkupload.ProcessedBulkUpload
setUuid(String) - Method in class org.jbei.ice.lib.dto.group.UserGroup
setUuid(String) - Method in class org.jbei.ice.storage.model.Group
setUuid(String) - Method in class org.jbei.ice.storage.model.Sample
setUuid(String) - Method in class org.jbei.ice.storage.model.Storage
setValue(String) - Method in class org.jbei.ice.lib.dto.bulkupload.PreferenceInfo
setValue(String) - Method in class org.jbei.ice.lib.dto.DNAFeatureNote
setValue(String) - Method in class org.jbei.ice.lib.dto.entry.CustomField
setValue(String) - Method in class org.jbei.ice.lib.dto.Setting
setValue(String) - Method in class org.jbei.ice.lib.parsers.genbank.Tag
setValue(String) - Method in class org.jbei.ice.storage.model.Configuration
setValue(String) - Method in class org.jbei.ice.storage.model.Parameter
setValue(String) - Method in class org.jbei.ice.storage.model.Preference
setValue(String) - Method in class org.jbei.ice.storage.model.SequenceFeatureAttribute
setVersion(String) - Method in class org.jbei.ice.lib.config.SiteSettings
setVersionId(String) - Method in class org.jbei.ice.storage.model.Entry
setViewCount(long) - Method in class org.jbei.ice.lib.dto.entry.PartData
setVisibility(Visibility) - Method in class org.jbei.ice.lib.dto.entry.PartData
setVisibility(Integer) - Method in class org.jbei.ice.storage.model.Entry
setVisibleEntryCount(long) - Method in class org.jbei.ice.lib.account.AccountTransfer
setWebEnabled(boolean) - Method in class org.jbei.ice.lib.dto.web.WebOfRegistries
setZipFileName(String) - Method in class org.jbei.ice.lib.manuscript.Manuscript
SharedEntries - Class in org.jbei.ice.lib.entry: Entries that have been shared with the specified user or with groups that the specified user is a member of
SharedEntries(String) - Constructor for class org.jbei.ice.lib.entry.SharedEntries
sharedEntryCount(Account, Set<Group>, String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO: An entry is shared if requester has explicit read or write permissions of belongs to a group that have explicit read or write permissions
sharedWithUserEntries(Account, Set<Group>, ColumnField, boolean, int, int, String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
sharedWithUserEntryIds(Account, Set<Group>) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
shareFolder(String, AccessPermission, String) - Method in class org.jbei.ice.lib.net.RemoteContact
SHOTGUN_DIR_NAME - Static variable in class org.jbei.ice.lib.entry.sequence.SequenceAnalysisController
SHOTGUN_SEQUENCES_DIR - Static variable in class org.jbei.ice.storage.hibernate.dao.ShotgunSequenceDAO
ShotgunSequence - Class in org.jbei.ice.storage.model
ShotgunSequence() - Constructor for class org.jbei.ice.storage.model.ShotgunSequence
ShotgunSequence(Entry, String, String, String, Date) - Constructor for class org.jbei.ice.storage.model.ShotgunSequence
ShotgunSequenceDAO - Class in org.jbei.ice.storage.hibernate.dao
ShotgunSequenceDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.ShotgunSequenceDAO
ShotgunSequenceDTO - Class in org.jbei.ice.lib.dto
ShotgunSequenceDTO(ShotgunSequence) - Constructor for class org.jbei.ice.lib.dto.ShotgunSequenceDTO
sirName - Variable in class org.jbei.ice.lib.account.authentication.LblLdapAuthentication
SiteSettings - Class in org.jbei.ice.lib.config: Settings for the site
SiteSettings() - Constructor for class org.jbei.ice.lib.config.SiteSettings
sort(ColumnField, LinkedList<SearchResult>) - Static method in class org.jbei.ice.lib.dto.search.SearchResults
SOURCE_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
stackTraceToString(Throwable) - Static method in class org.jbei.ice.lib.utils.Utils: Retrieve the stack trace from the given Throwable, and output the string.
startUp() - Static method in class org.jbei.ice.ApplicationInitialize: Responsible for initializing the system and checking for the existence of needed data (such as settings) and creating as needed
StatusType - Enum in org.jbei.ice.lib.shared
stop() - Method in class org.jbei.ice.lib.entry.sequence.annotation.AutoAnnotationBlastDbBuildTask
stopService() - Method in class org.jbei.ice.lib.executor.IceExecutorService
Storage - Class in org.jbei.ice.storage.model: Store sample storage location information as well as the hierarchical structure information.
Storage() - Constructor for class org.jbei.ice.storage.model.Storage
Storage.StorageType - Enum in org.jbei.ice.storage.model
StorageDAO - Class in org.jbei.ice.storage.hibernate.dao: Manager to manipulate Storage objects in the database.
StorageDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.StorageDAO
StorageLocation - Class in org.jbei.ice.lib.dto: Storage location information that specifies display (which can be a unique identifier) and the location type (e.g.
StorageLocation() - Constructor for class org.jbei.ice.lib.dto.StorageLocation
Strain - Class in org.jbei.ice.storage.model: Store Strain specific fields.
Strain() - Constructor for class org.jbei.ice.storage.model.Strain
StrainData - Class in org.jbei.ice.lib.dto.entry
StrainData() - Constructor for class org.jbei.ice.lib.dto.entry.StrainData
Study - Class in org.jbei.ice.lib.experiment: Data transfer object for experiments
Study() - Constructor for class org.jbei.ice.lib.experiment.Study
Study(String, String) - Constructor for class org.jbei.ice.lib.experiment.Study
submitBulkImportDraft(String, BulkUpload, ProcessedBulkUpload) - Method in class org.jbei.ice.lib.bulkupload.BulkEntryCreator: Submits a bulk import that has been saved.
subType - Variable in class org.jbei.ice.lib.bulkupload.BulkCSVUpload

T

Tag - Class in org.jbei.ice.lib.parsers.genbank
Tag(Tag.Type) - Constructor for class org.jbei.ice.lib.parsers.genbank.Tag
Tag.Type - Enum in org.jbei.ice.lib.parsers.genbank
Task - Class in org.jbei.ice.lib.executor: Abstract class representing tasks that are run by the ice executor service
Task() - Constructor for class org.jbei.ice.lib.executor.Task
TaskStatus - Enum in org.jbei.ice.lib.executor: Represents the current status of a task that has been submitted to the ICE task service
timeTillRun() - Method in class org.jbei.ice.lib.entry.sequence.annotation.AutoAnnotationBlastDbBuildTask
toDataTransferObject() - Method in interface org.jbei.ice.storage.DataModel
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Account
toDataTransferObject() - Method in class org.jbei.ice.storage.model.AccountPreferences
toDataTransferObject() - Method in class org.jbei.ice.storage.model.AnnotationLocation
toDataTransferObject() - Method in class org.jbei.ice.storage.model.ApiKey
toDataTransferObject() - Method in class org.jbei.ice.storage.model.ArabidopsisSeed
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Attachment
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Audit
toDataTransferObject() - Method in class org.jbei.ice.storage.model.BulkUpload
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Comment
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Configuration
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Entry
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Experiment
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Feature
toDataTransferObject() - Method in class org.jbei.ice.storage.model.FeatureCurationModel
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Folder
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Group
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Link
toDataTransferObject() - Method in class org.jbei.ice.storage.model.ManuscriptModel
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Message
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Parameter
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Permission
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Plasmid
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Preference
toDataTransferObject() - Method in class org.jbei.ice.storage.model.RemoteAccessModel
toDataTransferObject() - Method in class org.jbei.ice.storage.model.RemoteClientModel
toDataTransferObject() - Method in class org.jbei.ice.storage.model.RemotePartner
toDataTransferObject() - Method in class org.jbei.ice.storage.model.RemoteShareModel
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Request
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Sample
toDataTransferObject() - Method in class org.jbei.ice.storage.model.SelectionMarker
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Sequence
toDataTransferObject() - Method in class org.jbei.ice.storage.model.SequenceFeature
toDataTransferObject() - Method in class org.jbei.ice.storage.model.SequenceFeatureAttribute
toDataTransferObject() - Method in class org.jbei.ice.storage.model.ShotgunSequence
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Storage
toDataTransferObject() - Method in class org.jbei.ice.storage.model.Strain
toDataTransferObject() - Method in class org.jbei.ice.storage.model.TraceSequence
toDataTransferObject() - Method in class org.jbei.ice.storage.model.TraceSequenceAlignment
TokenHash - Class in org.jbei.ice.lib.account
TokenHash() - Constructor for class org.jbei.ice.lib.account.TokenHash
TokenVerification - Class in org.jbei.ice.lib.access: Verifies the different tokens that ICE handles including API token, Web of registries token
TokenVerification() - Constructor for class org.jbei.ice.lib.access.TokenVerification
toResponse(Exception) - Method in class org.jbei.ice.services.rest.ICEExceptionMapper
toSampleType(String) - Static method in enum org.jbei.ice.lib.dto.sample.SampleType
toString() - Method in enum org.jbei.ice.lib.account.AccountType
toString() - Method in class org.jbei.ice.lib.bulkupload.BulkUploadAutoUpdate
toString() - Method in class org.jbei.ice.lib.dto.access.AccessPermission
toString() - Method in class org.jbei.ice.lib.dto.bulkupload.PreferenceInfo
toString() - Method in enum org.jbei.ice.lib.dto.entry.EntryField
toString() - Method in enum org.jbei.ice.lib.dto.entry.EntryType
toString() - Method in enum org.jbei.ice.lib.dto.entry.PlantType
toString() - Method in class org.jbei.ice.lib.dto.sample.PartSample
toString() - Method in enum org.jbei.ice.lib.dto.sample.SampleRequestType
toString() - Method in class org.jbei.ice.lib.dto.StorageLocation
toString() - Method in enum org.jbei.ice.lib.dto.user.PreferenceKey
toString() - Method in class org.jbei.ice.lib.dto.web.RegistryPartner
toString() - Method in class org.jbei.ice.lib.experiment.Study
toString() - Method in enum org.jbei.ice.lib.shared.StatusType
TRACES_DIR_NAME - Static variable in class org.jbei.ice.lib.entry.sequence.SequenceAnalysisController
TRACES_DIR_NAME - Static variable in class org.jbei.ice.lib.entry.sequence.TraceSequences
TraceSequence - Class in org.jbei.ice.storage.model: Store sequence trace file information.
TraceSequence() - Constructor for class org.jbei.ice.storage.model.TraceSequence
TraceSequence(Entry, String, String, String, String, Date) - Constructor for class org.jbei.ice.storage.model.TraceSequence
TraceSequenceAlignment - Class in org.jbei.ice.storage.model: Store computed trace alignment information.
TraceSequenceAlignment() - Constructor for class org.jbei.ice.storage.model.TraceSequenceAlignment
TraceSequenceAlignment(TraceSequence, int, int, int, int, int, int, String, String, String, Date) - Constructor for class org.jbei.ice.storage.model.TraceSequenceAlignment
TraceSequenceAlignmentInfo - Class in org.jbei.ice.lib.dto.entry
TraceSequenceAlignmentInfo() - Constructor for class org.jbei.ice.lib.dto.entry.TraceSequenceAlignmentInfo
TraceSequenceAnalysis - Class in org.jbei.ice.lib.dto.entry
TraceSequenceAnalysis() - Constructor for class org.jbei.ice.lib.dto.entry.TraceSequenceAnalysis
TraceSequenceDAO - Class in org.jbei.ice.storage.hibernate.dao: Data accessor for TraceSequences
TraceSequenceDAO() - Constructor for class org.jbei.ice.storage.hibernate.dao.TraceSequenceDAO
TraceSequences - Class in org.jbei.ice.lib.entry.sequence: Trace sequence for alignment against a specific sequence
TraceSequences(String, long) - Constructor for class org.jbei.ice.lib.entry.sequence.TraceSequences
transfer(PartData) - Method in class org.jbei.ice.services.rest.PartResource
transferEntries(String, long, EntrySelection) - Method in class org.jbei.ice.lib.net.RemoteEntries: Schedules a task to handle the transfer
transferEntries(long, List<PartData>) - Method in class org.jbei.ice.lib.net.RemoteTransfer: Performs the transfer of the entry objects to the remote partner specified.
transferEntries(long, EntrySelection) - Method in class org.jbei.ice.services.rest.PartnerResource: Schedules a task to transfer a list of entries (explicit or context for generating them) to a specified partner
transferFolder(String, FolderDetails) - Method in class org.jbei.ice.lib.net.RemoteContact
transferFolder(long, FolderDetails, List<Long>) - Method in class org.jbei.ice.lib.net.RemoteTransfer
transferPart(String, PartData) - Method in class org.jbei.ice.lib.net.RemoteContact
TransferredParts - Class in org.jbei.ice.lib.net: This class represents one or more entries that have been transferred from another registry
TransferredParts() - Constructor for class org.jbei.ice.lib.net.TransferredParts
transferSequence(String, String, EntryType, String) - Method in class org.jbei.ice.lib.net.RemoteContact
TransferTask - Class in org.jbei.ice.lib.executor: Task for transferring parts to a another registry
TransferTask(String, long, EntrySelection) - Constructor for class org.jbei.ice.lib.executor.TransferTask
translateToProtein(String) - Static method in class org.jbei.ice.lib.utils.SequenceUtils: Calculate the amino acid translation of the given dnaSequence string.
Type - Enum in org.jbei.ice.lib.email

U

UI_CONFIG_DIR - Static variable in class org.jbei.ice.lib.config.ConfigurationController
update(String, Entry) - Method in class org.jbei.ice.lib.entry.EntryController
update(String, Sequence) - Method in class org.jbei.ice.lib.entry.sequence.SequenceController: Update the Sequence in the database, with the option to rebuild the search index.
update(String, long, FolderDetails) - Method in class org.jbei.ice.lib.folder.FolderController: Updates the folder referenced by the folderId with the passed folder details.
update(long, UserGroup) - Method in class org.jbei.ice.lib.group.Groups
update(long, Manuscript) - Method in class org.jbei.ice.lib.manuscript.Manuscripts
update(String, long, RegistryPartner) - Method in class org.jbei.ice.lib.net.WebPartners
update(Setting) - Method in class org.jbei.ice.services.rest.ConfigResource
update(long, CustomField) - Method in class org.jbei.ice.services.rest.CustomFieldResource
update(long, FolderDetails) - Method in class org.jbei.ice.services.rest.FolderResource: Updates the specified folder resource
update(long, Manuscript) - Method in class org.jbei.ice.services.rest.ManuscriptResource
update(long, PartData) - Method in class org.jbei.ice.services.rest.PartResource: Update the part information at the specified resource identifier
update(long, AccountTransfer) - Method in class org.jbei.ice.services.rest.UserResource
update(T) - Method in class org.jbei.ice.storage.hibernate.HibernateRepository: Updates an existing object in the database, if found
update(T) - Method in interface org.jbei.ice.storage.IRepository
updateAccount(String, long, AccountTransfer) - Method in class org.jbei.ice.lib.account.AccountController
updateAPIKey(String, long) - Method in class org.jbei.ice.lib.net.WebPartners: Refreshes the API key for the referenced partner
updateBlastIndex() - Method in class org.jbei.ice.services.rest.SearchResource: Rebuild the blast database
updateComment(long, long, UserComment) - Method in class org.jbei.ice.services.rest.PartResource
updateConfigValue(Setting) - Method in class org.jbei.ice.services.rest.ConfigResource
updateEntries(Visibility, List<Long>) - Method in class org.jbei.ice.services.rest.PartResource
updateEntry(String, long, long, PartData) - Method in class org.jbei.ice.lib.bulkupload.BulkEntryCreator
updateEntry(long, long, PartData) - Method in class org.jbei.ice.services.rest.BulkUploadResource
updateEntryComment(String, long, long, UserComment) - Method in class org.jbei.ice.lib.entry.EntryController
updateEntryField(PartData, Entry) - Static method in class org.jbei.ice.servlet.InfoToModelFactory: sets the corresponding fields in data only if they are not null
updateField(String, long, CustomField) - Method in class org.jbei.ice.lib.dto.entry.CustomFields
updateGroup(long, UserGroup) - Method in class org.jbei.ice.services.rest.GroupResource
updateList(long, BulkUploadInfo) - Method in class org.jbei.ice.services.rest.BulkUploadResource: Creates or updates a list of entries that are to be associated with the specified bulk upload
updateLuceneIndex() - Method in class org.jbei.ice.services.rest.SearchResource: Rebuild the lucene indexes used for searching
updateName(long, BulkUploadInfo) - Method in class org.jbei.ice.services.rest.BulkUploadResource
updatePart(String, long, PartData) - Method in class org.jbei.ice.lib.entry.EntryController: Update the information associated with the specified part.
Note that any missing information will be deleted from the original entry.
updatePassword(String, long, AccountTransfer) - Method in class org.jbei.ice.lib.account.AccountController: Updates the specified user account's password
updatePassword(long, AccountTransfer) - Method in class org.jbei.ice.services.rest.UserResource
updatePreference(String, long, String, String) - Method in class org.jbei.ice.lib.account.PreferencesController
updatePreference(long, String, String) - Method in class org.jbei.ice.services.rest.UserResource
updateRemoteAPIKey(String, RegistryPartner) - Method in class org.jbei.ice.lib.net.WebPartners: Updates the api token of a remote partner using information sent by that partner
updateRemotePartnerAPIKey(RegistryPartner) - Method in class org.jbei.ice.services.rest.PartnerResource: Request from a remote ICE instance to update it's api key Verification uses the existing API key.
updateSampleRequest(long, SampleRequestStatus) - Method in class org.jbei.ice.services.rest.SampleResource
updateSequence(String, long, FeaturedDNASequence, boolean) - Method in class org.jbei.ice.lib.entry.sequence.SequenceController
updateSequence(long, boolean, FeaturedDNASequence) - Method in class org.jbei.ice.services.rest.PartResource
updateSequence(Sequence, Set<SequenceFeature>) - Method in class org.jbei.ice.storage.hibernate.dao.SequenceDAO: Updates an existing feature with a new set of features
updateSetting(String, Setting, String) - Method in class org.jbei.ice.lib.config.ConfigurationController
updateStatus(String, long, BulkUploadStatus) - Method in class org.jbei.ice.lib.bulkupload.BulkEntryCreator
updateStatus(String, long, SampleRequestStatus) - Method in class org.jbei.ice.lib.entry.sample.RequestRetriever
updateStatus(long, BulkUploadInfo) - Method in class org.jbei.ice.services.rest.BulkUploadResource: Updates the status of the bulk upload
updateVisibility(List<Long>, Visibility) - Method in class org.jbei.ice.lib.entry.Entries
updateWebPartner(String, String, RegistryPartner) - Method in class org.jbei.ice.lib.net.WoRController
updateWebPartner(long, RegistryPartner) - Method in class org.jbei.ice.services.rest.PartnerResource
updateWebPartner(String, RegistryPartner) - Method in class org.jbei.ice.services.rest.WebResource
updateWebPartnerAPIKey(long) - Method in class org.jbei.ice.services.rest.PartnerResource
uploadAttachmentFile(long, InputStream, long, FormDataContentDisposition) - Method in class org.jbei.ice.services.rest.BulkUploadResource
uploadSequence(InputStream, String, String, boolean, FormDataContentDisposition) - Method in class org.jbei.ice.services.rest.FileResource: this creates an entry if an id is not specified in the form data
uploadSequenceFile(long, InputStream, long, FormDataContentDisposition) - Method in class org.jbei.ice.services.rest.BulkUploadResource
UserApiKeys - Class in org.jbei.ice.lib.account: API keys generated by users
UserApiKeys(String) - Constructor for class org.jbei.ice.lib.account.UserApiKeys
UserComment - Class in org.jbei.ice.lib.dto.comment: Comments are tied to specific entries and the entryId field is used to uniquely identify the entry this comment is tied to
UserComment() - Constructor for class org.jbei.ice.lib.dto.comment.UserComment
UserFolder - Class in org.jbei.ice.lib.folder: Represents a folder created or owned by a user
UserFolder(String) - Constructor for class org.jbei.ice.lib.folder.UserFolder
UserGroup - Class in org.jbei.ice.lib.dto.group: DTO for groups
UserGroup() - Constructor for class org.jbei.ice.lib.dto.group.UserGroup
userId - Variable in class org.jbei.ice.lib.bulkupload.BulkCSVUpload
userId - Variable in class org.jbei.ice.lib.parsers.AbstractParser
UserIdAuthentication - Class in org.jbei.ice.lib.account.authentication: Authentication implementation that only validates the user id with any non empty string as password
UserIdAuthentication() - Constructor for class org.jbei.ice.lib.account.authentication.UserIdAuthentication
UserPreferences - Class in org.jbei.ice.lib.dto.user: Wrapper for user preferences
UserPreferences() - Constructor for class org.jbei.ice.lib.dto.user.UserPreferences
UserResource - Class in org.jbei.ice.services.rest: REST Resource for users
UserResource() - Constructor for class org.jbei.ice.services.rest.UserResource
UserSamples - Class in org.jbei.ice.lib.dto.sample: Wrapper around user sample requests to include information such as the total count
UserSamples() - Constructor for class org.jbei.ice.lib.dto.sample.UserSamples
UserSessions - Class in org.jbei.ice.lib.account: Creates and maintains the web application sessions for users who have successfully authenticated
UserSessions() - Constructor for class org.jbei.ice.lib.account.UserSessions
UtilityException - Exception in org.jbei.ice.lib.utils: Exception class for Utilities.
UtilityException(Throwable) - Constructor for exception org.jbei.ice.lib.utils.UtilityException
UtilityException(String) - Constructor for exception org.jbei.ice.lib.utils.UtilityException
Utils - Class in org.jbei.ice.lib.utils: General utility methods.
Utils() - Constructor for class org.jbei.ice.lib.utils.Utils
uuid - Variable in class org.jbei.ice.storage.model.Group

V

validate(HttpServletRequest) - Method in class org.jbei.auth.hmac.HmacAuthorizor: Validates a request based on HTTP Authorization header.
validateEntries(InputStream) - Method in class org.jbei.ice.lib.entry.Entries
validateEntry(Entry) - Method in class org.jbei.ice.lib.bulkupload.BulkUploadValidation
validates(PartData) - Static method in class org.jbei.ice.lib.entry.EntryUtil: Validates the required fields in the Data Transfer Object
valueOf(String) - Static method in enum org.jbei.ice.lib.access.AccessStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.access.AccessType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.access.Article: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.account.AccountType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.bulkupload.BulkUploadStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.access.AccessPermission.Article: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.access.AccessPermission.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.AuditType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.bulkupload.EditMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.bulkupload.SampleField: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.ConfigurationKey: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.entry.AutoCompleteField: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.entry.EntryField: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.entry.EntryType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.entry.Generation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.entry.PlantType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.entry.Visibility: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.folder.FolderType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.group.GroupType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.sample.SampleRequestStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.sample.SampleRequestType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.sample.SampleType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.search.BlastProgram: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.search.IndexType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.search.SearchBoostField: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.user.PreferenceKey: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.dto.web.RemotePartnerStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.email.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.entry.EntrySelectionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.entry.LinkType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.entry.sequence.SequenceFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.executor.TaskStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.folder.collection.CollectionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.manuscript.ManuscriptStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.message.MessageStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.parsers.genbank.Tag.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.search.QueryType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.shared.BioSafetyOption: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.shared.ColumnField: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.lib.shared.StatusType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.storage.model.Part.AssemblyStandard: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.storage.model.SequenceFeature.AnnotationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.jbei.ice.storage.model.Storage.StorageType: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.jbei.ice.lib.access.AccessStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.access.AccessType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.access.Article: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.account.AccountType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.bulkupload.BulkUploadStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.access.AccessPermission.Article: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.access.AccessPermission.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.AuditType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.bulkupload.EditMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.bulkupload.SampleField: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.ConfigurationKey: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.entry.AutoCompleteField: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.entry.EntryField: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.entry.EntryType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.entry.Generation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.entry.PlantType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.entry.Visibility: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.folder.FolderType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.group.GroupType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.sample.SampleRequestStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.sample.SampleRequestType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.sample.SampleType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.search.BlastProgram: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.search.IndexType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.search.SearchBoostField: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.user.PreferenceKey: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.dto.web.RemotePartnerStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.email.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.entry.EntrySelectionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.entry.LinkType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.entry.sequence.SequenceFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.executor.TaskStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.folder.collection.CollectionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.manuscript.ManuscriptStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.message.MessageStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.parsers.genbank.Tag.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.search.QueryType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.shared.BioSafetyOption: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.shared.ColumnField: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.lib.shared.StatusType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.storage.model.Part.AssemblyStandard: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.storage.model.SequenceFeature.AnnotationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.jbei.ice.storage.model.Storage.StorageType: Returns an array containing the constants of this enum type, in the order they are declared.
valueToEnum(Integer) - Static method in enum org.jbei.ice.lib.dto.entry.Visibility
verifyAPIKey(String, String, String) - Method in class org.jbei.ice.lib.access.TokenVerification
verifyPartnerToken(String, String) - Method in class org.jbei.ice.lib.access.TokenVerification
VERSION_TAG - Static variable in class org.jbei.ice.lib.parsers.genbank.GenBankParser
Visibility - Enum in org.jbei.ice.lib.dto.entry: Type of visibility for entries in the system.
VisibleEntries - Class in org.jbei.ice.lib.entry: Entries that a specified user has read permissions on by virtue of account status (e.g.
VisibleEntries(String) - Constructor for class org.jbei.ice.lib.entry.VisibleEntries
visibleEntryCount(Account, Set<Group>, String) - Method in class org.jbei.ice.storage.hibernate.dao.EntryDAO
visit(Sequence) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.SBOL2Visitor
visit(SequenceFeature) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.SBOL2Visitor
visit(Sequence) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.SBOLVisitor
visit(SequenceFeature) - Method in class org.jbei.ice.lib.entry.sequence.composers.formatters.SBOLVisitor
visit(DnaComponent) - Method in class org.jbei.ice.lib.parsers.sbol.ICESBOLParserVisitor

W

waitUntil(Date) - Method in class org.jbei.ice.lib.entry.sequence.annotation.AutoAnnotationBlastDbBuildTask: Uses the defined lock object to wait until a specified time
warn(String) - Static method in class org.jbei.ice.lib.common.logging.Logger
WebEntries - Class in org.jbei.ice.lib.dto.web: Represents entries that are available for the web (public) These entries can reside on this instance or on other instances
WebEntries() - Constructor for class org.jbei.ice.lib.dto.web.WebEntries
WebOfRegistries - Class in org.jbei.ice.lib.dto.web: Wrapper around web of registries settings and partners
WebOfRegistries() - Constructor for class org.jbei.ice.lib.dto.web.WebOfRegistries
WebOfRegistriesTask - Class in org.jbei.ice.lib.net: Task to enable or disable web of registries by contacting a master node to obtain a (potentially curated) list of other ICE instances.
WebOfRegistriesTask(String, String, boolean) - Constructor for class org.jbei.ice.lib.net.WebOfRegistriesTask
WebPartners - Class in org.jbei.ice.lib.net: Partners for web of registries
WebPartners() - Constructor for class org.jbei.ice.lib.net.WebPartners
WebPartners(RemoteContact) - Constructor for class org.jbei.ice.lib.net.WebPartners
WebResource - Class in org.jbei.ice.services.rest: Resource for web of registries requests
This is particularly useful for third party tools to tap into the web of registries functionality without having specific API keys to each of the instances
WebResource() - Constructor for class org.jbei.ice.services.rest.WebResource
WebResult - Class in org.jbei.ice.lib.search
WebResult() - Constructor for class org.jbei.ice.lib.search.WebResult
WebSearch - Class in org.jbei.ice.lib.search: Search for other ICE instances
WebSearch() - Constructor for class org.jbei.ice.lib.search.WebSearch
WebSearch.SearchTask - Class in org.jbei.ice.lib.search
WebSearchResults - Class in org.jbei.ice.lib.search: Wrapper around search results received from a remote ICE instance
WebSearchResults(int) - Constructor for class org.jbei.ice.lib.search.WebSearchResults
WOR_API_KEY_TOKEN - Static variable in class org.jbei.ice.services.rest.Headers
WOR_PARTNER_TOKEN - Static variable in class org.jbei.ice.services.rest.Headers
WOR_PARTNER_TOKEN - Variable in class org.jbei.ice.services.rest.RestResource
WoRController - Class in org.jbei.ice.lib.net: Controller for Web of Registries functionality
WoRController() - Constructor for class org.jbei.ice.lib.net.WoRController
worPartnerToken - Variable in class org.jbei.ice.services.rest.RestResource
write(int) - Method in class org.jbei.auth.hmac.HmacOutputStream
write(byte[], int, int) - Method in class org.jbei.auth.hmac.HmacOutputStream
writeDataEntries(RemotePartner, List<PartData>, List<EntryField>, CSVWriter, ZipOutputStream) - Method in class org.jbei.ice.lib.net.RemoteEntriesAsCSV
writeLocalEntries(List<Entry>, List<EntryField>, CSVWriter, ZipOutputStream) - Method in class org.jbei.ice.lib.net.RemoteEntriesAsCSV
writeSequenceFileToDisk(String, InputStream) - Method in class org.jbei.ice.storage.hibernate.dao.ShotgunSequenceDAO
writeTo(ArrayList<IDataTransferModel>, Class<?>, Type, Annotation[], MediaType, MultivaluedMap<String, Object>, OutputStream) - Method in class org.jbei.ice.services.rest.ArrayDataJSONHandler
writeTo(IDataTransferModel, Class<?>, Type, Annotation[], MediaType, MultivaluedMap<String, Object>, OutputStream) - Method in class org.jbei.ice.services.rest.PartDataJSONHandler

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