Index (blend4j 0.2.0-SNAPSHOT API)

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

A

AbstractElement - Class in com.github.jmchilton.blend4j.galaxy.beans.collection.request: Description for elements used to create a dataset collection in Galaxy.
AbstractElement() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.collection.request.AbstractElement
add(String, Object) - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Adds a name/value pair to the formatted output in name=value format.
add(String, boolean) - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Adds a name/value pair to the formatted output in name=value format.
add(String, char) - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Adds a name/value pair to the formatted output in name=value format.
add(String, double) - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Adds a name/value pair to the formatted output in name=value format.
add(String, float) - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Adds a name/value pair to the formatted output in name=value format.
add(String, int) - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Adds a name/value pair to the formatted output in name=value format.
add(String, long) - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Adds a name/value pair to the formatted output in name=value format.
add(String, Object) - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Adds a name/value pair to the formatted output in name=value format.
add(String, boolean) - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Adds a name/value pair to the formatted output in name=value format.
add(String, char) - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Adds a name/value pair to the formatted output in name=value format.
add(String, double) - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Adds a name/value pair to the formatted output in name=value format.
add(String, float) - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Adds a name/value pair to the formatted output in name=value format.
add(String, int) - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Adds a name/value pair to the formatted output in name=value format.
add(String, long) - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Adds a name/value pair to the formatted output in name=value format.
addCollectionElement(AbstractElement) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.CollectionElement: Adds an element to this dataset collection.
addDatasetElement(AbstractElement) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.CollectionDescription: Adds an element to this dataset collection.
addValue(Object) - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Adds an unnamed value to the formatted output.
addValue(boolean) - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Adds an unnamed value to the formatted output.
addValue(char) - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Adds an unnamed value to the formatted output.
addValue(double) - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Adds an unnamed value to the formatted output.
addValue(float) - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Adds an unnamed value to the formatted output.
addValue(int) - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Adds an unnamed value to the formatted output.
addValue(long) - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Adds an unnamed value to the formatted output.
addValue(Object) - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Adds an unnamed value to the formatted output.
addValue(boolean) - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Adds an unnamed value to the formatted output.
addValue(char) - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Adds an unnamed value to the formatted output.
addValue(double) - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Adds an unnamed value to the formatted output.
addValue(float) - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Adds an unnamed value to the formatted output.
addValue(int) - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Adds an unnamed value to the formatted output.
addValue(long) - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Adds an unnamed value to the formatted output.
API_PATH - Static variable in class com.github.jmchilton.blend4j.galaxy.DefaultWebResourceFactoryImpl
ApiException - Exception in com.github.jmchilton.blend4j.exceptions: Base class for all API, communication, or serialization related exceptions in blend4j.
ApiException() - Constructor for exception com.github.jmchilton.blend4j.exceptions.ApiException
ApiException(Exception) - Constructor for exception com.github.jmchilton.blend4j.exceptions.ApiException

B

BaseClient - Class in com.github.jmchilton.blend4j
BaseClient(WebResource, String) - Constructor for class com.github.jmchilton.blend4j.BaseClient
buildResponseException(ClientResponse) - Method in class com.github.jmchilton.blend4j.BaseClient

C

changsetRevision - Variable in class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision
checkArgument(boolean) - Static method in class com.github.jmchilton.blend4j.util.Preconditions: Ensures the truth of an expression involving one or more parameters to the calling method.
checkArgument(boolean, Object) - Static method in class com.github.jmchilton.blend4j.util.Preconditions: Ensures the truth of an expression involving one or more parameters to the calling method.
checkArgument(boolean, String, Object...) - Static method in class com.github.jmchilton.blend4j.util.Preconditions: Ensures the truth of an expression involving one or more parameters to the calling method.
checkElementIndex(int, int) - Static method in class com.github.jmchilton.blend4j.util.Preconditions: Ensures that index specifies a valid element in an array, list or string of size size.
checkElementIndex(int, int, String) - Static method in class com.github.jmchilton.blend4j.util.Preconditions: Ensures that index specifies a valid element in an array, list or string of size size.
checkNotNull(T) - Static method in class com.github.jmchilton.blend4j.util.Preconditions: Ensures that an object reference passed as a parameter to the calling method is not null.
checkNotNull(T, Object) - Static method in class com.github.jmchilton.blend4j.util.Preconditions: Ensures that an object reference passed as a parameter to the calling method is not null.
checkNotNull(T, String, Object...) - Static method in class com.github.jmchilton.blend4j.util.Preconditions: Ensures that an object reference passed as a parameter to the calling method is not null.
checkPositionIndex(int, int) - Static method in class com.github.jmchilton.blend4j.util.Preconditions: Ensures that index specifies a valid position in an array, list or string of size size.
checkPositionIndex(int, int, String) - Static method in class com.github.jmchilton.blend4j.util.Preconditions: Ensures that index specifies a valid position in an array, list or string of size size.
checkPositionIndexes(int, int, int) - Static method in class com.github.jmchilton.blend4j.util.Preconditions: Ensures that start and end specify a valid positions in an array, list or string of size size, and are in order.
checkResponse(ClientResponse) - Method in class com.github.jmchilton.blend4j.BaseClient
checkState(boolean) - Static method in class com.github.jmchilton.blend4j.util.Preconditions: Ensures the truth of an expression involving the state of the calling instance, but not involving any parameters to the calling method.
checkState(boolean, Object) - Static method in class com.github.jmchilton.blend4j.util.Preconditions: Ensures the truth of an expression involving the state of the calling instance, but not involving any parameters to the calling method.
checkState(boolean, String, Object...) - Static method in class com.github.jmchilton.blend4j.util.Preconditions: Ensures the truth of an expression involving the state of the calling instance, but not involving any parameters to the calling method.
CollectionDescription - Class in com.github.jmchilton.blend4j.galaxy.beans.collection.request: A request to create a collection of elements (datasets or other collections) within Galaxy.
CollectionDescription() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.collection.request.CollectionDescription
CollectionElement - Class in com.github.jmchilton.blend4j.galaxy.beans.collection.request: Class defining an element in a collection that can contain other collection elements.
CollectionElement() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.collection.request.CollectionElement
CollectionElementResponse - Class in com.github.jmchilton.blend4j.galaxy.beans.collection.response: Represents a collection of elements from a dataset collection response from Galaxy.
CollectionElementResponse() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse
CollectionResponse - Class in com.github.jmchilton.blend4j.galaxy.beans.collection.response: Class for storing response information from Galaxy on a dataset collection within a History.
CollectionResponse() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionResponse
CollectionSource - Enum in com.github.jmchilton.blend4j.galaxy.beans.collection: Describes the source of data for a dataset collection.
com.github.jmchilton.blend4j - package com.github.jmchilton.blend4j
com.github.jmchilton.blend4j.exceptions - package com.github.jmchilton.blend4j.exceptions
com.github.jmchilton.blend4j.galaxy - package com.github.jmchilton.blend4j.galaxy
com.github.jmchilton.blend4j.galaxy.beans - package com.github.jmchilton.blend4j.galaxy.beans
com.github.jmchilton.blend4j.galaxy.beans.collection - package com.github.jmchilton.blend4j.galaxy.beans.collection
com.github.jmchilton.blend4j.galaxy.beans.collection.request - package com.github.jmchilton.blend4j.galaxy.beans.collection.request
com.github.jmchilton.blend4j.galaxy.beans.collection.response - package com.github.jmchilton.blend4j.galaxy.beans.collection.response
com.github.jmchilton.blend4j.toolshed - package com.github.jmchilton.blend4j.toolshed
com.github.jmchilton.blend4j.toolshed.beans - package com.github.jmchilton.blend4j.toolshed.beans
com.github.jmchilton.blend4j.util - package com.github.jmchilton.blend4j.util: Subset of Google Guava (version 17) copied into library (and modified slightly) so the functionality is available but we don't actually need to depend on another library.
Config - Class in com.github.jmchilton.blend4j
Config() - Constructor for class com.github.jmchilton.blend4j.Config
ConfigurationClient - Interface in com.github.jmchilton.blend4j.galaxy
create(Object) - Method in class com.github.jmchilton.blend4j.BaseClient
create(Object, boolean) - Method in class com.github.jmchilton.blend4j.BaseClient
create(WebResource, Object) - Method in class com.github.jmchilton.blend4j.BaseClient
create(WebResource, Object, boolean) - Method in class com.github.jmchilton.blend4j.BaseClient
create(History) - Method in interface com.github.jmchilton.blend4j.galaxy.HistoriesClient
create(History, ToolInputs) - Method in interface com.github.jmchilton.blend4j.galaxy.ToolsClient
createApiKey(String) - Method in interface com.github.jmchilton.blend4j.galaxy.UsersClient
createDatasetCollection(String, CollectionDescription) - Method in interface com.github.jmchilton.blend4j.galaxy.HistoriesClient: Creates a new Dataset Collection from the given information.
createDatasetCollectionRequest(String, CollectionDescription) - Method in interface com.github.jmchilton.blend4j.galaxy.HistoriesClient: Creates a new Dataset Collection from the given information.
createFolder(String, LibraryFolder) - Method in interface com.github.jmchilton.blend4j.galaxy.LibrariesClient
createFolderRequest(String, LibraryFolder) - Method in interface com.github.jmchilton.blend4j.galaxy.LibrariesClient
createHistoryDataset(String, HistoryDataset) - Method in interface com.github.jmchilton.blend4j.galaxy.HistoriesClient
createLibrary(Library) - Method in interface com.github.jmchilton.blend4j.galaxy.LibrariesClient
createLibraryRequest(Library) - Method in interface com.github.jmchilton.blend4j.galaxy.LibrariesClient
createRequest(History) - Method in interface com.github.jmchilton.blend4j.galaxy.HistoriesClient
createUser(String) - Method in interface com.github.jmchilton.blend4j.galaxy.UsersClient
createUser(UserCreate) - Method in interface com.github.jmchilton.blend4j.galaxy.UsersClient
createUserRequest(String) - Method in interface com.github.jmchilton.blend4j.galaxy.UsersClient
createUserRequest(UserCreate) - Method in interface com.github.jmchilton.blend4j.galaxy.UsersClient

D

Dataset - Class in com.github.jmchilton.blend4j.galaxy.beans
Dataset() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.Dataset
DEFAULT_ERROR_CODE - Static variable in exception com.github.jmchilton.blend4j.galaxy.GalaxyResponseException
DEFAULT_ERROR_MESSAGE - Static variable in exception com.github.jmchilton.blend4j.galaxy.GalaxyResponseException
DEFAULT_TRACEBACK - Static variable in exception com.github.jmchilton.blend4j.galaxy.GalaxyResponseException
DefaultWebResourceFactoryImpl - Class in com.github.jmchilton.blend4j.galaxy: Default and simplest possible implementation of WebResourceFactory.
DefaultWebResourceFactoryImpl(String, String, boolean) - Constructor for class com.github.jmchilton.blend4j.galaxy.DefaultWebResourceFactoryImpl
DefaultWebResourceFactoryImpl(String, String) - Constructor for class com.github.jmchilton.blend4j.galaxy.DefaultWebResourceFactoryImpl
DirectoryLibraryUpload - Class in com.github.jmchilton.blend4j.galaxy.beans
DirectoryLibraryUpload() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.DirectoryLibraryUpload
disableCertificateCheck() - Static method in class com.github.jmchilton.blend4j.galaxy.SslHacking

E

ElementResponse - Interface in com.github.jmchilton.blend4j.galaxy.beans.collection.response: Interface defining an element within a dataset collection.
equal(Object, Object) - Static method in class com.github.jmchilton.blend4j.util.Objects: Determines whether two possibly-null objects are equal.
equals(Object) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse
equals(Object) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionResponse
equals(Object) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
equals(Object) - Method in class com.github.jmchilton.blend4j.galaxy.beans.GalaxyObject
equals(Object) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
equals(Object) - Method in class com.github.jmchilton.blend4j.toolshed.beans.Repository
exportedWorkflows(String) - Method in interface com.github.jmchilton.blend4j.galaxy.ToolShedRepositoriesClient
exportedWorkflowsRequest(String) - Method in interface com.github.jmchilton.blend4j.galaxy.ToolShedRepositoriesClient
exportHistory(String) - Method in interface com.github.jmchilton.blend4j.galaxy.HistoriesClient
exportWorkflow(String) - Method in interface com.github.jmchilton.blend4j.galaxy.WorkflowsClient

F

FileLibraryUpload - Class in com.github.jmchilton.blend4j.galaxy.beans
FileLibraryUpload() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.FileLibraryUpload
FilesystemPathsLibraryUpload - Class in com.github.jmchilton.blend4j.galaxy.beans
FilesystemPathsLibraryUpload() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.FilesystemPathsLibraryUpload
FilesystemPathsLibraryUpload(boolean) - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.FilesystemPathsLibraryUpload
fileUploadRequest(String, String, String, File) - Method in interface com.github.jmchilton.blend4j.galaxy.ToolsClient: Deprecated.
Use uploadRequest now.
firstNonNull(T, T) - Static method in class com.github.jmchilton.blend4j.util.MoreObjects: Returns the first of two given parameters that is not null, if either is, or otherwise throws a NullPointerException.
firstNonNull(T, T) - Static method in class com.github.jmchilton.blend4j.util.Objects: Deprecated.
Use MoreObjects.firstNonNull(T, T) instead. This method is scheduled for removal in June 2016.
fromText(String) - Static method in enum com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository.InstallationStatus

G

GalaxyAuthWebResourceFactoryImpl - Class in com.github.jmchilton.blend4j.galaxy: Build a WebResourceFactory from Galaxy credentials (username/password).
GalaxyAuthWebResourceFactoryImpl(String, String, String, boolean) - Constructor for class com.github.jmchilton.blend4j.galaxy.GalaxyAuthWebResourceFactoryImpl
GalaxyAuthWebResourceFactoryImpl(String, String, String) - Constructor for class com.github.jmchilton.blend4j.galaxy.GalaxyAuthWebResourceFactoryImpl
GalaxyInstance - Interface in com.github.jmchilton.blend4j.galaxy
GalaxyInstanceFactory - Class in com.github.jmchilton.blend4j.galaxy: This class contains static factory methods for producing GalaxyInstance objects.
GalaxyInstanceFactory() - Constructor for class com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory
GalaxyObject - Class in com.github.jmchilton.blend4j.galaxy.beans
GalaxyObject() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.GalaxyObject
GalaxyResponseException - Exception in com.github.jmchilton.blend4j.galaxy
GalaxyResponseException(ClientResponse) - Constructor for exception com.github.jmchilton.blend4j.galaxy.GalaxyResponseException
get(WebResource, TypeReference<List<T>>) - Method in class com.github.jmchilton.blend4j.BaseClient
get(TypeReference<List<T>>) - Method in class com.github.jmchilton.blend4j.BaseClient
get() - Method in class com.github.jmchilton.blend4j.galaxy.DefaultWebResourceFactoryImpl
get(String, String) - Static method in class com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory
get(String, String, boolean) - Static method in class com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory
get(WebResourceFactory) - Static method in class com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory
get() - Method in interface com.github.jmchilton.blend4j.galaxy.WebResourceFactory
get(String, String) - Static method in class com.github.jmchilton.blend4j.toolshed.ToolShedInstanceFactory
get(WebResourceFactory) - Static method in class com.github.jmchilton.blend4j.toolshed.ToolShedInstanceFactory
getAccessInRoles() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryPermissions
getAddInRoles() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryPermissions
getAnnotation() - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryWorkflow
getApiKey() - Method in class com.github.jmchilton.blend4j.galaxy.DefaultWebResourceFactoryImpl
getApiKey() - Method in class com.github.jmchilton.blend4j.galaxy.GalaxyAuthWebResourceFactoryImpl
getApiKey() - Method in interface com.github.jmchilton.blend4j.galaxy.GalaxyInstance
getApiKey() - Method in interface com.github.jmchilton.blend4j.galaxy.WebResourceFactory
getBlurb() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
getChangesetRevision() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
getChangsetRevision() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision
getCollectionElements() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.CollectionElement: Gets the list of contained collection elements.
getCollectionType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.CollectionDescription: Gets the collection type.
getCollectionType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.CollectionElement: Gets the type of this collection.
getCollectionType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse: Gets the type of this collection.
getCollectionType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionResponse: Gets the type of this collection.
getConfigurationClient() - Method in interface com.github.jmchilton.blend4j.galaxy.GalaxyInstance
getContent() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryDataset
getContent() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload
getContextRevision() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
getCreateType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryFolder
getCreateType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload
getDatasetElements() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.CollectionDescription: Gets a list of elements within this dataset collection.
getDatasetName() - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
getDataType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
getDbkey() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload
getDbKey() - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
getDescription() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Library
getDescription() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryFolder
getDescription() - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
getDestination() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
getDirectory() - Method in class com.github.jmchilton.blend4j.galaxy.beans.DirectoryLibraryUpload
getDownloadUrl() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
getDownloadUrl() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryExport
getElementIdentifier() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse: Gets the identifier of the elements in this collection.
getElementIndex() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse: Gets the index of this particular element in a collection.
getElements() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionResponse: Gets a list of elements within this collection.
getElementType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse: Gets the type of elements in this collection.
getEmail() - Method in class com.github.jmchilton.blend4j.galaxy.beans.User
getEmail() - Method in class com.github.jmchilton.blend4j.galaxy.beans.UserCreate
getErrorMessage() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
getExtraParameters() - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
getFile() - Method in class com.github.jmchilton.blend4j.galaxy.beans.FileLibraryUpload
getFile() - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.UploadFile
getFileObjects() - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
getFiles() - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
getFileSize() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
getFilesystemPaths() - Method in class com.github.jmchilton.blend4j.galaxy.beans.FilesystemPathsLibraryUpload
getFileType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload
getFileType() - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
getFolderId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryFolder
getFolderId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload
getFormatVersion() - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryWorkflow
getFromCredentials(String, String, String) - Static method in class com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory
getFromCredentials(String, String, String, boolean) - Static method in class com.github.jmchilton.blend4j.galaxy.GalaxyInstanceFactory
getFullDownloadUrl() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
getGalaxyUrl() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
getGalaxyUrl() - Method in interface com.github.jmchilton.blend4j.galaxy.beans.HasGalaxyUrl
getGalaxyUrl() - Method in class com.github.jmchilton.blend4j.galaxy.DefaultWebResourceFactoryImpl: Deprecated.
getGalaxyUrl() - Method in interface com.github.jmchilton.blend4j.galaxy.GalaxyInstance
getGalaxyUrl() - Method in interface com.github.jmchilton.blend4j.galaxy.WebResourceFactory: Deprecated.
getGenomeBuild() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
getHid() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
getHistories() - Method in interface com.github.jmchilton.blend4j.galaxy.HistoriesClient
getHistoriesClient() - Method in interface com.github.jmchilton.blend4j.galaxy.GalaxyInstance
getHistoryContentType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
getHistoryId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionResponse: Gets the id of the history this collection exists within.
getHistoryId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.ToolInputs
getHistoryId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowOutputs
getHistoryId() - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
getId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.SimpleElement: Gets the id of this element.
getId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse: Gets the id of this collection element.
getId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.GalaxyObject
getId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
getId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.WorkflowInput
getImportInputsToHistory() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
getIndex() - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryWorkflow
getInfo() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
getInputs() - Method in class com.github.jmchilton.blend4j.galaxy.beans.ToolInputs
getInputs() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails
getInputs() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
getInputSteps() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowStepDefinition
getInstallableRevisions(Repository) - Method in interface com.github.jmchilton.blend4j.toolshed.RepositoriesClient
getInstallableRevisions(Repository) - Method in class com.github.jmchilton.blend4j.toolshed.RepositoriesClientImpl
getInstallableRevisionsRequest(Repository) - Method in interface com.github.jmchilton.blend4j.toolshed.RepositoriesClient
getInstallableRevisionsRequest(Repository) - Method in class com.github.jmchilton.blend4j.toolshed.RepositoriesClientImpl
getInstallationStatus() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
getInstalledChangesetRevision() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
getJerseyClient() - Method in class com.github.jmchilton.blend4j.galaxy.DefaultWebResourceFactoryImpl: Return a configured Jersey client for Galaxy API code to interact with.
getJobId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
getJson(WebResource) - Method in class com.github.jmchilton.blend4j.BaseClient
getJson(WebResource, boolean) - Method in class com.github.jmchilton.blend4j.BaseClient
getLabel() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition
getLatestInstallableRevision(Repository) - Static method in class com.github.jmchilton.blend4j.toolshed.ToolShedUtils
getLatestInstallableRevision(ToolShedInstance, Repository) - Static method in class com.github.jmchilton.blend4j.toolshed.ToolShedUtils
getLatestRepositoryRevision(RepositoriesClient, String, String) - Static method in class com.github.jmchilton.blend4j.toolshed.RepositoryUtils
getLatestRepositoryRevision(RepositoriesClient, Repository) - Static method in class com.github.jmchilton.blend4j.toolshed.RepositoryUtils
getLibraries() - Method in interface com.github.jmchilton.blend4j.galaxy.LibrariesClient
getLibrariesClient() - Method in interface com.github.jmchilton.blend4j.galaxy.GalaxyInstance
getLibraryContents(String) - Method in interface com.github.jmchilton.blend4j.galaxy.LibrariesClient
getLinkDataOnly() - Method in class com.github.jmchilton.blend4j.galaxy.beans.FilesystemPathsLibraryUpload
getMainToolShedInstance() - Static method in class com.github.jmchilton.blend4j.toolshed.ToolShedInstanceFactory
getMainToolShedInstance(String) - Static method in class com.github.jmchilton.blend4j.toolshed.ToolShedInstanceFactory
getManageInRoles() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryPermissions
getModelClass() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse: Gets the class of this collection.
getModifyInRoles() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryPermissions
getName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.AbstractElement: Gets the name of this element.
getName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.CollectionDescription: Gets the name of this dataset collection.
getName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.History
getName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
getName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision
getName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
getName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Library
getName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryContent
getName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryFolder
getName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload
getName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryWorkflow
getName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Role
getName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Workflow
getName() - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.UploadFile
getName() - Method in class com.github.jmchilton.blend4j.toolshed.beans.Repository
getName() - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
getNewToolPanelSectionLabel() - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryInstall
getNoAddToHistory() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
getOutputIds() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowOutputs
getOutputName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.OutputDataset
getOutputs() - Method in class com.github.jmchilton.blend4j.galaxy.beans.ToolExecution
getOwner() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision
getOwner() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
getOwner() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails
getOwner() - Method in class com.github.jmchilton.blend4j.toolshed.beans.Repository
getOwner() - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
getParameterName() - Method in class com.github.jmchilton.blend4j.galaxy.beans.ToolParameter
getParameters() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
getParameters() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
getParameterValue() - Method in class com.github.jmchilton.blend4j.galaxy.beans.ToolParameter
getPassword() - Method in class com.github.jmchilton.blend4j.galaxy.beans.UserCreate
getRawConfiguration() - Method in interface com.github.jmchilton.blend4j.galaxy.ConfigurationClient
getRawWebResource() - Method in class com.github.jmchilton.blend4j.galaxy.DefaultWebResourceFactoryImpl: Build Jersey client, and get WebResource targeting Galaxy API.
getRepositories() - Method in interface com.github.jmchilton.blend4j.galaxy.ToolShedRepositoriesClient
getRepositories() - Method in interface com.github.jmchilton.blend4j.toolshed.RepositoriesClient
getRepositories() - Method in class com.github.jmchilton.blend4j.toolshed.RepositoriesClientImpl
getRepositoriesClient() - Method in interface com.github.jmchilton.blend4j.galaxy.GalaxyInstance
getRepositoriesClient() - Method in interface com.github.jmchilton.blend4j.toolshed.ToolShedInstance
getRepositoryRevisionInstallInfoRequest(RepositoryRevision) - Method in interface com.github.jmchilton.blend4j.toolshed.RepositoriesClient
getRepositoryRevisionInstallInfoRequest(RepositoryRevision) - Method in class com.github.jmchilton.blend4j.toolshed.RepositoriesClientImpl
getResponse(WebResource) - Method in class com.github.jmchilton.blend4j.BaseClient
getResponse(WebResource, boolean) - Method in class com.github.jmchilton.blend4j.BaseClient
getResponseBody() - Method in exception com.github.jmchilton.blend4j.exceptions.ResponseException
getResponseElement() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse: Gets the response element within this collection.
getResults() - Method in class com.github.jmchilton.blend4j.galaxy.SearchClient.SearchResponse
getRevision() - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryRevision
getRole(String) - Method in interface com.github.jmchilton.blend4j.galaxy.RolesClient
getRoles() - Method in interface com.github.jmchilton.blend4j.galaxy.RolesClient
getRolesClient() - Method in interface com.github.jmchilton.blend4j.galaxy.GalaxyInstance
getRootFolder(String) - Method in interface com.github.jmchilton.blend4j.galaxy.LibrariesClient
getSearchClient() - Method in interface com.github.jmchilton.blend4j.galaxy.GalaxyInstance
getServerDirectory() - Method in class com.github.jmchilton.blend4j.galaxy.beans.DirectoryLibraryUpload
getSource() - Method in enum com.github.jmchilton.blend4j.galaxy.beans.collection.CollectionSource
getSource() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.AbstractElement: Gets the source of this element.
getSource() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryDataset
getSourceStep() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowStepDefinition.WorkflowStepOutput
getSourceType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.WorkflowInput
getStandardError() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
getStandardOutput() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
getState() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
getState() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryDetails
getStateIds() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryDetails
getStatus() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
getStatusCode() - Method in exception com.github.jmchilton.blend4j.exceptions.ResponseException
getStepOutput() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowStepDefinition.WorkflowStepOutput
getSteps() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails
getSynopsis() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Library
getTimesDownloaded() - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
getToolId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
getToolId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.ToolInputs
getToolId() - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
getToolPanelSectionId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryInstall
getToolsClient() - Method in interface com.github.jmchilton.blend4j.galaxy.GalaxyInstance
getToolShed() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
getToolShedUrl() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision
getType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.CollectionDescription: Gets the type of this request.
getType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents: Deprecated.
getType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryContent
getType() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowStepDefinition
getType() - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
getUploadOption() - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload
getUrl() - Method in class com.github.jmchilton.blend4j.galaxy.beans.GalaxyObject
getUrl() - Method in class com.github.jmchilton.blend4j.galaxy.beans.UrlLibraryUpload
getUrl() - Method in class com.github.jmchilton.blend4j.galaxy.DefaultWebResourceFactoryImpl
getUrl() - Method in interface com.github.jmchilton.blend4j.galaxy.WebResourceFactory
getUrl() - Method in interface com.github.jmchilton.blend4j.toolshed.ToolShedInstance
getUserId() - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
getUsername() - Method in class com.github.jmchilton.blend4j.galaxy.beans.User
getUsername() - Method in class com.github.jmchilton.blend4j.galaxy.beans.UserCreate
getUsers() - Method in interface com.github.jmchilton.blend4j.galaxy.UsersClient
getUsersClient() - Method in interface com.github.jmchilton.blend4j.galaxy.GalaxyInstance
getUuid() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
getValue() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition
getVisible() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
getWebResource() - Method in class com.github.jmchilton.blend4j.BaseClient
getWebResource(String) - Method in class com.github.jmchilton.blend4j.BaseClient
getWebResource() - Method in interface com.github.jmchilton.blend4j.galaxy.GalaxyInstance
getWebResourceContents(String) - Method in class com.github.jmchilton.blend4j.BaseClient
getWorkflowId() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
getWorkflows() - Method in interface com.github.jmchilton.blend4j.galaxy.WorkflowsClient
getWorkflowsClient() - Method in interface com.github.jmchilton.blend4j.galaxy.GalaxyInstance

H

HasGalaxyUrl - Interface in com.github.jmchilton.blend4j.galaxy.beans
hashCode() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse
hashCode() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionResponse
hashCode() - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
hashCode() - Method in class com.github.jmchilton.blend4j.galaxy.beans.GalaxyObject
hashCode() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
hashCode() - Method in class com.github.jmchilton.blend4j.toolshed.beans.Repository
hashCode(Object...) - Static method in class com.github.jmchilton.blend4j.util.Objects: Generates a hash code for multiple values.
HistoriesClient - Interface in com.github.jmchilton.blend4j.galaxy
History - Class in com.github.jmchilton.blend4j.galaxy.beans
History() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.History
History(String) - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.History
HistoryContents - Class in com.github.jmchilton.blend4j.galaxy.beans
HistoryContents() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
HistoryContentsProvenance - Class in com.github.jmchilton.blend4j.galaxy.beans
HistoryContentsProvenance() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
HistoryDataset - Class in com.github.jmchilton.blend4j.galaxy.beans
HistoryDataset() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.HistoryDataset
HistoryDataset.Source - Enum in com.github.jmchilton.blend4j.galaxy.beans
HistoryDatasetElement - Class in com.github.jmchilton.blend4j.galaxy.beans.collection.request: Class describing a history dataset to be placed within a collection.
HistoryDatasetElement() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.collection.request.HistoryDatasetElement: Builds a new HistoryDatasetElement.
HistoryDetails - Class in com.github.jmchilton.blend4j.galaxy.beans
HistoryDetails() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.HistoryDetails
HistoryExport - Class in com.github.jmchilton.blend4j.galaxy.beans
HistoryExport() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.HistoryExport
HistoryExport(String) - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.HistoryExport

I

importWorkflow(String, int) - Method in interface com.github.jmchilton.blend4j.galaxy.ToolShedRepositoriesClient
importWorkflow(String) - Method in interface com.github.jmchilton.blend4j.galaxy.WorkflowsClient
importWorkflowRequest(String, int) - Method in interface com.github.jmchilton.blend4j.galaxy.ToolShedRepositoriesClient
importWorkflowResponse(String) - Method in interface com.github.jmchilton.blend4j.galaxy.WorkflowsClient
importWorkflows(String) - Method in interface com.github.jmchilton.blend4j.galaxy.ToolShedRepositoriesClient
importWorkflowsRequest(String) - Method in interface com.github.jmchilton.blend4j.galaxy.ToolShedRepositoriesClient
InstallableRepositoryRevision - Class in com.github.jmchilton.blend4j.galaxy.beans
InstallableRepositoryRevision() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision
InstallableRepositoryRevision(String, RepositoryRevision) - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision
InstallableRepositoryRevision(InstallableRepositoryRevision) - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision
InstalledRepository - Class in com.github.jmchilton.blend4j.galaxy.beans
InstalledRepository() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
InstalledRepository.InstallationStatus - Enum in com.github.jmchilton.blend4j.galaxy.beans
installRepository(RepositoryInstall) - Method in interface com.github.jmchilton.blend4j.galaxy.ToolShedRepositoriesClient
installRepositoryRequest(RepositoryInstall) - Method in interface com.github.jmchilton.blend4j.galaxy.ToolShedRepositoriesClient
isComplete() - Method in enum com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository.InstallationStatus
isDeleted() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
isDeleted() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
isDeleted() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails
isDeleted() - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
isDeprecated() - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
isDistToShed() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
isIncludedDatatypes() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
isInstallRepositoryDependencies() - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryInstall
isInstallToolDependencies() - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryInstall
isLinkData() - Method in class com.github.jmchilton.blend4j.galaxy.beans.FilesystemPathsLibraryUpload
isPrivate_() - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
isPublished() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails
isPurged() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
isReady() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryDetails
isReady() - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryExport
isUninstalled() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
isUpdateAvailable() - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
isVisible() - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionResponse: Gets the visible status of this collection.

L

LibrariesClient - Interface in com.github.jmchilton.blend4j.galaxy
Library - Class in com.github.jmchilton.blend4j.galaxy.beans
Library() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.Library
Library(String) - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.Library
LibraryContent - Class in com.github.jmchilton.blend4j.galaxy.beans
LibraryContent() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.LibraryContent
LibraryFolder - Class in com.github.jmchilton.blend4j.galaxy.beans
LibraryFolder() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.LibraryFolder
LibraryPermissions - Class in com.github.jmchilton.blend4j.galaxy.beans
LibraryPermissions() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.LibraryPermissions
LibraryUpload - Class in com.github.jmchilton.blend4j.galaxy.beans
LibraryUpload(String) - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload
LibraryUpload.CreateType - Enum in com.github.jmchilton.blend4j.galaxy.beans
listTypeReference(Class<T>) - Method in class com.github.jmchilton.blend4j.BaseClient
loadBlendProperties() - Static method in class com.github.jmchilton.blend4j.Config

M

mapper - Variable in class com.github.jmchilton.blend4j.BaseClient
MoreObjects - Class in com.github.jmchilton.blend4j.util: Helper functions that operate on any Object, and are not already provided in Objects.
MoreObjects.ToStringHelper - Class in com.github.jmchilton.blend4j.util: Support class for MoreObjects.toStringHelper(java.lang.Object).
multipartPost(WebResource, Map<String, Object>, Iterable<BodyPart>) - Method in class com.github.jmchilton.blend4j.BaseClient

N

name - Variable in class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision

O

Objects - Class in com.github.jmchilton.blend4j.util: Helper functions that can operate on any Object.
Objects.ToStringHelper - Class in com.github.jmchilton.blend4j.util: Deprecated.
Use MoreObjects.ToStringHelper instead. This class is scheduled for removal in June 2016.
omitNullValues() - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Configures the MoreObjects.ToStringHelper so MoreObjects.ToStringHelper.toString() will ignore properties with null value.
omitNullValues() - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Configures the Objects.ToStringHelper so Objects.ToStringHelper.toString() will ignore properties with null value.
OutputDataset - Class in com.github.jmchilton.blend4j.galaxy.beans
OutputDataset() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.OutputDataset
owner - Variable in class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision

P

path(String) - Method in class com.github.jmchilton.blend4j.BaseClient
Preconditions - Class in com.github.jmchilton.blend4j.util: Static convenience methods that help a method or constructor check whether it was invoked correctly (whether its preconditions have been met).
prepareUpload(File) - Method in class com.github.jmchilton.blend4j.BaseClient
prepareUploads(Iterable<File>) - Method in class com.github.jmchilton.blend4j.BaseClient

R

read(ClientResponse, TypeReference<T>) - Method in class com.github.jmchilton.blend4j.BaseClient
read(ClientResponse, Class<T>) - Method in class com.github.jmchilton.blend4j.BaseClient
readJson(String, TypeReference<T>) - Method in class com.github.jmchilton.blend4j.BaseClient
readJson(String, Class<T>) - Method in class com.github.jmchilton.blend4j.BaseClient
repairRepositoryRequest(InstallableRepositoryRevision) - Method in interface com.github.jmchilton.blend4j.galaxy.ToolShedRepositoriesClient
RepositoriesClient - Interface in com.github.jmchilton.blend4j.toolshed
RepositoriesClientImpl - Class in com.github.jmchilton.blend4j.toolshed
Repository - Class in com.github.jmchilton.blend4j.toolshed.beans
Repository() - Constructor for class com.github.jmchilton.blend4j.toolshed.beans.Repository
Repository(String, String) - Constructor for class com.github.jmchilton.blend4j.toolshed.beans.Repository
RepositoryDetails - Class in com.github.jmchilton.blend4j.toolshed.beans
RepositoryDetails() - Constructor for class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
RepositoryInstall - Class in com.github.jmchilton.blend4j.galaxy.beans
RepositoryInstall() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.RepositoryInstall
RepositoryInstall(InstallableRepositoryRevision) - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.RepositoryInstall
RepositoryRevision - Class in com.github.jmchilton.blend4j.toolshed.beans
RepositoryRevision() - Constructor for class com.github.jmchilton.blend4j.toolshed.beans.RepositoryRevision
RepositoryRevision(Repository, String) - Constructor for class com.github.jmchilton.blend4j.toolshed.beans.RepositoryRevision
RepositoryRevision(String, String, String) - Constructor for class com.github.jmchilton.blend4j.toolshed.beans.RepositoryRevision
RepositoryUtils - Class in com.github.jmchilton.blend4j.toolshed
RepositoryUtils() - Constructor for class com.github.jmchilton.blend4j.toolshed.RepositoryUtils
RepositoryWorkflow - Class in com.github.jmchilton.blend4j.galaxy.beans
RepositoryWorkflow() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.RepositoryWorkflow
ResponseException - Exception in com.github.jmchilton.blend4j.exceptions
ResponseException(ClientResponse) - Constructor for exception com.github.jmchilton.blend4j.exceptions.ResponseException
Role - Class in com.github.jmchilton.blend4j.galaxy.beans
Role() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.Role
RolesClient - Interface in com.github.jmchilton.blend4j.galaxy
runWorkflow(WorkflowInputs) - Method in interface com.github.jmchilton.blend4j.galaxy.WorkflowsClient
runWorkflowResponse(WorkflowInputs) - Method in interface com.github.jmchilton.blend4j.galaxy.WorkflowsClient

S

search(String) - Method in interface com.github.jmchilton.blend4j.galaxy.SearchClient
search(String) - Method in class com.github.jmchilton.blend4j.galaxy.SearchClientImpl
SearchClient - Interface in com.github.jmchilton.blend4j.galaxy
SearchClient.SearchResponse - Class in com.github.jmchilton.blend4j.galaxy
SearchClient.SearchResponse() - Constructor for class com.github.jmchilton.blend4j.galaxy.SearchClient.SearchResponse
SearchClientImpl - Class in com.github.jmchilton.blend4j.galaxy
SerializationException - Exception in com.github.jmchilton.blend4j.exceptions
SerializationException() - Constructor for exception com.github.jmchilton.blend4j.exceptions.SerializationException
SerializationException(Exception) - Constructor for exception com.github.jmchilton.blend4j.exceptions.SerializationException
setAccessInRoles(List<String>) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryPermissions
setAddInRoles(List<String>) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryPermissions
setAnnotation(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryWorkflow
setApiKey(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
setApiKey(String) - Method in interface com.github.jmchilton.blend4j.galaxy.beans.HasGalaxyUrl
setBlurb(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
setChangesetRevision(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
setChangsetRevision(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision
setCollectionType(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.CollectionDescription: Sets the collection type.
setCollectionType(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.CollectionElement: Sets the type of this collection.
setCollectionType(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse: Sets the type of this collection.
setCollectionType(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionResponse: Sets the type of this collection.
setContent(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryDataset
setContent(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload
setContextRevision(int) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
setCreateType(LibraryUpload.CreateType) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload
setDatasetName(String) - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
setDataType(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
setDbkey(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload
setDbKey(String) - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
setDeleted(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
setDeleted(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
setDeleted(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails
setDeleted(boolean) - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
setDeprecated(boolean) - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
setDescription(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Library
setDescription(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryFolder
setDescription(String) - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
setDestination(WorkflowInputs.WorkflowDestination) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
setDistToShed(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
setDownloadUrl(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
setDownloadUrl(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryExport
setElementIdentifier(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse: Sets the identifer of elements in this collection.
setElementIndex(int) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse: Sets the index of this element in a collection.
setElements(List<CollectionElementResponse>) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionResponse: Sets the list of elements within this collection.
setElementType(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse: Sets the type of elements in this collection.
setEmail(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.User
setEmail(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.UserCreate
setErrorMessage(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
setExtraParameters(Map<String, String>) - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
setFile(File) - Method in class com.github.jmchilton.blend4j.galaxy.beans.FileLibraryUpload
setFileSize(Integer) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
setFileType(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload
setFileType(String) - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
setFolderId(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryFolder
setFolderId(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload
setFormatVersion(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryWorkflow
setGalaxyUrl(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
setGalaxyUrl(String) - Method in interface com.github.jmchilton.blend4j.galaxy.beans.HasGalaxyUrl
setGenomeBuild(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
setHid(int) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
setHistoryContentType(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
setHistoryId(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionResponse: Sets the id of the history this collection exists within.
setHistoryId(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.ToolInputs
setHistoryId(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowOutputs
setId(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.SimpleElement: Sets the id of this element.
setId(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse: Sets the id of this collection element.
setId(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.GalaxyObject
setId(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
setImportInputsToHistory(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
setIncludedDatatypes(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
setIndex(int) - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryWorkflow
setInfo(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
setInput(String, WorkflowInputs.WorkflowInput) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
setInputs(Map<String, WorkflowInputDefinition>) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails
setInputSteps(Map<String, WorkflowStepDefinition.WorkflowStepOutput>) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowStepDefinition
setInstalledChangesetRevision(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
setInstallRepositoryDependencies(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryInstall
setInstallToolDependencies(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryInstall
setJobId(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
setLabel(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition
setLibraryPermissions(String, LibraryPermissions) - Method in interface com.github.jmchilton.blend4j.galaxy.LibrariesClient
setLinkData(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.FilesystemPathsLibraryUpload
setManageInRoles(List<String>) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryPermissions
setModelClass(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse: Sets the class of this collection.
setModifyInRoles(List<String>) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryPermissions
setName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.AbstractElement: Sets the name of this element.
setName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.CollectionDescription: Sets the name of this dataset collection.
setName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.History
setName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
setName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision
setName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
setName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Library
setName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryContent
setName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryFolder
setName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload
setName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryWorkflow
setName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Role
setName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Workflow
setName(String) - Method in class com.github.jmchilton.blend4j.toolshed.beans.Repository
setName(String) - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
setNewToolPanelSectionLabel(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryInstall
setNiceTotalDiskUsage(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.User
setOutputIds(List<String>) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowOutputs
setOutputName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.OutputDataset
setOutputs(List<OutputDataset>) - Method in class com.github.jmchilton.blend4j.galaxy.beans.ToolExecution
setOwner(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision
setOwner(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
setOwner(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails
setOwner(String) - Method in class com.github.jmchilton.blend4j.toolshed.beans.Repository
setOwner(String) - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
setParameter(String, ToolParameter) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs: Deprecated.
setParameterName(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.ToolParameter
setParameters(Map<String, Object>) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
setParameterValue(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.ToolParameter
setPassword(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.UserCreate
setPrivate_(boolean) - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
setPublished(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails
setPurged(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
setResponseObject(ElementResponse) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse: Sets the data element within this collection.
setResults(List<Map<String, Object>>) - Method in class com.github.jmchilton.blend4j.galaxy.SearchClient.SearchResponse
setRevision(String) - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryRevision
setSource(CollectionSource) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.AbstractElement: Sets the source of this element.
setSource(HistoryDataset.Source) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryDataset
setSourceStep(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowStepDefinition.WorkflowStepOutput
setStandardError(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
setStandardOutput(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
setState(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
setState(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryDetails
setStateIds(Map<String, List<String>>) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryDetails
setStatus(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
setStepOutput(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowStepDefinition.WorkflowStepOutput
setStepParameter(String, String, Object) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
setStepParameter(int, String, Object) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
setStepParameter(String, ToolParameter) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
setStepParameter(int, ToolParameter) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
setSteps(Map<String, WorkflowStepDefinition>) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails
setSynopsis(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Library
setTimesDownloaded(int) - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
setToolId(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
setToolId(String) - Method in class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
setToolPanelSectionId(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.RepositoryInstall
setToolParameter(String, String, Object) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
setToolParameter(String, ToolParameter) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
setToolShed(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
setToolShedUrl(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision
setTotalDiskUsage(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.User
setType(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.request.CollectionDescription: Sets the type of this request.
setType(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContents
setType(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.LibraryContent
setType(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowStepDefinition
setType(String) - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
setUninstalled(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
setUpdateAvailable(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository
setUrl(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.GalaxyObject
setUserId(String) - Method in class com.github.jmchilton.blend4j.toolshed.beans.RepositoryDetails
setUsername(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.User
setUsername(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.UserCreate
setUuid(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.HistoryContentsProvenance
setValue(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition
setVisible(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionResponse: Sets the visible status of this collection.
setVisible(boolean) - Method in class com.github.jmchilton.blend4j.galaxy.beans.Dataset
setWorkflowId(String) - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
show(String, Class<T>) - Method in class com.github.jmchilton.blend4j.BaseClient
showDataset(String, String) - Method in interface com.github.jmchilton.blend4j.galaxy.HistoriesClient
showDatasetCollection(String, String) - Method in interface com.github.jmchilton.blend4j.galaxy.HistoriesClient: Gets a Dataset collection for the given historyId and datasetCollectionId.
showHistory(String) - Method in interface com.github.jmchilton.blend4j.galaxy.HistoriesClient
showHistoryContents(String) - Method in interface com.github.jmchilton.blend4j.galaxy.HistoriesClient
showHistoryRequest(String) - Method in interface com.github.jmchilton.blend4j.galaxy.HistoriesClient
showProvenance(String, String) - Method in interface com.github.jmchilton.blend4j.galaxy.HistoriesClient
showRepository(String) - Method in interface com.github.jmchilton.blend4j.galaxy.ToolShedRepositoriesClient
showRepository(String) - Method in interface com.github.jmchilton.blend4j.toolshed.RepositoriesClient
showRepository(String) - Method in class com.github.jmchilton.blend4j.toolshed.RepositoriesClientImpl
showUser(String) - Method in interface com.github.jmchilton.blend4j.galaxy.UsersClient
showWorkflow(String) - Method in interface com.github.jmchilton.blend4j.galaxy.WorkflowsClient
SimpleElement - Class in com.github.jmchilton.blend4j.galaxy.beans.collection.request: Class describing requests for the creation of a simple element in a dataset (no sub elements).
SimpleElement() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.collection.request.SimpleElement
SslHacking - Class in com.github.jmchilton.blend4j.galaxy
SslHacking() - Constructor for class com.github.jmchilton.blend4j.galaxy.SslHacking

T

toJson() - Method in enum com.github.jmchilton.blend4j.galaxy.beans.HistoryDataset.Source
toJson() - Method in enum com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload.CreateType
ToolExecution - Class in com.github.jmchilton.blend4j.galaxy.beans
ToolExecution() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.ToolExecution
ToolInputs - Class in com.github.jmchilton.blend4j.galaxy.beans
ToolInputs(String, Map<String, String>) - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.ToolInputs
ToolParameter - Class in com.github.jmchilton.blend4j.galaxy.beans
ToolParameter(String, String) - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.ToolParameter
ToolsClient - Interface in com.github.jmchilton.blend4j.galaxy
ToolsClient.FileUploadRequest - Class in com.github.jmchilton.blend4j.galaxy
ToolsClient.FileUploadRequest(String, File) - Constructor for class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
ToolsClient.FileUploadRequest(String, ToolsClient.UploadFile) - Constructor for class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
ToolsClient.FileUploadRequest(String, Iterable<ToolsClient.UploadFile>) - Constructor for class com.github.jmchilton.blend4j.galaxy.ToolsClient.FileUploadRequest
ToolsClient.UploadFile - Class in com.github.jmchilton.blend4j.galaxy
ToolsClient.UploadFile(File) - Constructor for class com.github.jmchilton.blend4j.galaxy.ToolsClient.UploadFile
ToolsClient.UploadFile(File, String) - Constructor for class com.github.jmchilton.blend4j.galaxy.ToolsClient.UploadFile
ToolShedInstance - Interface in com.github.jmchilton.blend4j.toolshed
ToolShedInstanceFactory - Class in com.github.jmchilton.blend4j.toolshed
ToolShedInstanceFactory() - Constructor for class com.github.jmchilton.blend4j.toolshed.ToolShedInstanceFactory
ToolShedRepositoriesClient - Interface in com.github.jmchilton.blend4j.galaxy
toolShedUrl - Variable in class com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision
ToolShedUtils - Class in com.github.jmchilton.blend4j.toolshed
ToolShedUtils() - Constructor for class com.github.jmchilton.blend4j.toolshed.ToolShedUtils
toString() - Method in exception com.github.jmchilton.blend4j.exceptions.ResponseException
toString() - Method in class com.github.jmchilton.blend4j.toolshed.beans.Repository
toString() - Method in class com.github.jmchilton.blend4j.util.MoreObjects.ToStringHelper: Returns a string in the format specified by MoreObjects.toStringHelper(Object).
toString() - Method in class com.github.jmchilton.blend4j.util.Objects.ToStringHelper: Deprecated.

Returns a string in the format specified by Objects.toStringHelper(Object).
toStringHelper() - Method in exception com.github.jmchilton.blend4j.exceptions.ResponseException
toStringHelper() - Method in exception com.github.jmchilton.blend4j.galaxy.GalaxyResponseException
toStringHelper(Object) - Static method in class com.github.jmchilton.blend4j.util.MoreObjects: Creates an instance of MoreObjects.ToStringHelper.
toStringHelper(Class<?>) - Static method in class com.github.jmchilton.blend4j.util.MoreObjects: Creates an instance of MoreObjects.ToStringHelper in the same manner as MoreObjects.toStringHelper(Object), but using the simple name of clazz instead of using an instance's Object.getClass().
toStringHelper(String) - Static method in class com.github.jmchilton.blend4j.util.MoreObjects: Creates an instance of MoreObjects.ToStringHelper in the same manner as MoreObjects.toStringHelper(Object), but using className instead of using an instance's Object.getClass().
toStringHelper(Object) - Static method in class com.github.jmchilton.blend4j.util.Objects: Deprecated.
Use MoreObjects.toStringHelper(Object) instead. This method is scheduled for removal in June 2016.
toStringHelper(Class<?>) - Static method in class com.github.jmchilton.blend4j.util.Objects: Deprecated.
Use MoreObjects.toStringHelper(Class) instead. This method is scheduled for removal in June 2016.
toStringHelper(String) - Static method in class com.github.jmchilton.blend4j.util.Objects: Deprecated.
Use MoreObjects.toStringHelper(String) instead. This method is scheduled for removal in June 2016.

U

upload(ToolsClient.FileUploadRequest) - Method in interface com.github.jmchilton.blend4j.galaxy.ToolsClient
uploadFile(String, FileLibraryUpload) - Method in interface com.github.jmchilton.blend4j.galaxy.LibrariesClient
uploadFileFromUrl(String, FilesystemPathsLibraryUpload) - Method in interface com.github.jmchilton.blend4j.galaxy.LibrariesClient
uploadFileFromUrlRequest(String, UrlLibraryUpload) - Method in interface com.github.jmchilton.blend4j.galaxy.LibrariesClient
uploadFilesystemPathsRequest(String, FilesystemPathsLibraryUpload) - Method in interface com.github.jmchilton.blend4j.galaxy.LibrariesClient
uploadRequest(ToolsClient.FileUploadRequest) - Method in interface com.github.jmchilton.blend4j.galaxy.ToolsClient
uploadServerDirectoryRequest(String, DirectoryLibraryUpload) - Method in interface com.github.jmchilton.blend4j.galaxy.LibrariesClient
UrlLibraryUpload - Class in com.github.jmchilton.blend4j.galaxy.beans
UrlLibraryUpload() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.UrlLibraryUpload
User - Class in com.github.jmchilton.blend4j.galaxy.beans
User() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.User
UserCreate - Class in com.github.jmchilton.blend4j.galaxy.beans
UserCreate() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.UserCreate
UsersClient - Interface in com.github.jmchilton.blend4j.galaxy

V

value() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.ExistingHistory
value() - Method in enum com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.InputSourceType
value() - Method in class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.NewHistory
valueOf(String) - Static method in enum com.github.jmchilton.blend4j.galaxy.beans.collection.CollectionSource: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.jmchilton.blend4j.galaxy.beans.HistoryDataset.Source: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository.InstallationStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload.CreateType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.InputSourceType: Returns the enum constant of this type with the specified name.
values() - Static method in enum com.github.jmchilton.blend4j.galaxy.beans.collection.CollectionSource: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.jmchilton.blend4j.galaxy.beans.HistoryDataset.Source: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository.InstallationStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.jmchilton.blend4j.galaxy.beans.LibraryUpload.CreateType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.InputSourceType: Returns an array containing the constants of this enum type, in the order they are declared.

W

webResource - Variable in class com.github.jmchilton.blend4j.BaseClient
WebResourceFactory - Interface in com.github.jmchilton.blend4j.galaxy
Workflow - Class in com.github.jmchilton.blend4j.galaxy.beans
Workflow() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.Workflow
WorkflowDetails - Class in com.github.jmchilton.blend4j.galaxy.beans
WorkflowDetails() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.WorkflowDetails
WorkflowInputDefinition - Class in com.github.jmchilton.blend4j.galaxy.beans
WorkflowInputDefinition() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputDefinition
WorkflowInputs - Class in com.github.jmchilton.blend4j.galaxy.beans
WorkflowInputs() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs
WorkflowInputs.ExistingHistory - Class in com.github.jmchilton.blend4j.galaxy.beans
WorkflowInputs.ExistingHistory(String) - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.ExistingHistory
WorkflowInputs.InputSourceType - Enum in com.github.jmchilton.blend4j.galaxy.beans: Defines the different Workflow Input source types.
WorkflowInputs.NewHistory - Class in com.github.jmchilton.blend4j.galaxy.beans
WorkflowInputs.NewHistory(String) - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.NewHistory
WorkflowInputs.WorkflowDestination - Class in com.github.jmchilton.blend4j.galaxy.beans
WorkflowInputs.WorkflowDestination() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.WorkflowDestination
WorkflowInputs.WorkflowInput - Class in com.github.jmchilton.blend4j.galaxy.beans
WorkflowInputs.WorkflowInput(String, WorkflowInputs.InputSourceType) - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.WorkflowInputs.WorkflowInput
WorkflowOutputs - Class in com.github.jmchilton.blend4j.galaxy.beans
WorkflowOutputs() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.WorkflowOutputs
WorkflowsClient - Interface in com.github.jmchilton.blend4j.galaxy
WorkflowStepDefinition - Class in com.github.jmchilton.blend4j.galaxy.beans
WorkflowStepDefinition() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.WorkflowStepDefinition
WorkflowStepDefinition.WorkflowStepOutput - Class in com.github.jmchilton.blend4j.galaxy.beans
WorkflowStepDefinition.WorkflowStepOutput() - Constructor for class com.github.jmchilton.blend4j.galaxy.beans.WorkflowStepDefinition.WorkflowStepOutput
write(Object) - Method in class com.github.jmchilton.blend4j.BaseClient

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