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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) - Metho