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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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