A B C D E G H I M N P S

A

addCommand(String) - Method in class de.unirostock.sems.bives.webservice.client.BivesRequest

Adds another command.

addDocumentType(String) - Method in class de.unirostock.sems.bives.webservice.client.BivesSingleFileResponse

Adds another document type to the list of document types.

addError(String) - Method in class de.unirostock.sems.bives.webservice.client.BivesResponse

Adds an error.

B

baseUrl - Variable in class de.unirostock.sems.bives.webservice.client.impl.HttpBivesClient

The base url.

BivesClientException - Exception in de.unirostock.sems.bives.webservice.client.exception

The Class BivesClientException.

BivesClientException() - Constructor for exception de.unirostock.sems.bives.webservice.client.exception.BivesClientException

Instantiates a new bives client exception.

BivesClientException(String) - Constructor for exception de.unirostock.sems.bives.webservice.client.exception.BivesClientException

Instantiates a new bives client exception.

BivesClientException(Throwable) - Constructor for exception de.unirostock.sems.bives.webservice.client.exception.BivesClientException

Instantiates a new bives client exception.

BivesClientException(String, Throwable) - Constructor for exception de.unirostock.sems.bives.webservice.client.exception.BivesClientException

Instantiates a new bives client exception.

BivesClientException(String, Throwable, boolean, boolean) - Constructor for exception de.unirostock.sems.bives.webservice.client.exception.BivesClientException

Instantiates a new bives client exception.

BivesCommands - Interface in de.unirostock.sems.bives.webservice.client

The Interface BivesCommands providing some static command flags.

BivesComparisonCommands - Interface in de.unirostock.sems.bives.webservice.client

The Interface BivesComparisonCommands providing some static command flags for comparison of files.

BivesComparisonRequest - Class in de.unirostock.sems.bives.webservice.client

The Class BivesComparisonRequest to compare two versions using BiVeS web service.

BivesComparisonRequest() - Constructor for class de.unirostock.sems.bives.webservice.client.BivesComparisonRequest

The Constructor to create a comparison request.

BivesComparisonRequest(String, String) - Constructor for class de.unirostock.sems.bives.webservice.client.BivesComparisonRequest

The Constructor to create a comparison request.

BivesComparisonRequest(String, String, List<String>) - Constructor for class de.unirostock.sems.bives.webservice.client.BivesComparisonRequest

The Constructor to create a comparison request.

BivesComparisonResponse - Class in de.unirostock.sems.bives.webservice.client

The Class BivesComparisonResponse representing a response of a comparison request sent to the BiVeS web service.

BivesComparisonResponse() - Constructor for class de.unirostock.sems.bives.webservice.client.BivesComparisonResponse

BivesException - Exception in de.unirostock.sems.bives.webservice.client.exception

The Class BivesException.

BivesException() - Constructor for exception de.unirostock.sems.bives.webservice.client.exception.BivesException

Instantiates a new bives exception.

BivesException(String) - Constructor for exception de.unirostock.sems.bives.webservice.client.exception.BivesException

Instantiates a new bives exception.

BivesException(Throwable) - Constructor for exception de.unirostock.sems.bives.webservice.client.exception.BivesException

Instantiates a new bives exception.

BivesException(String, Throwable) - Constructor for exception de.unirostock.sems.bives.webservice.client.exception.BivesException

Instantiates a new bives exception.

BivesException(String, Throwable, boolean, boolean) - Constructor for exception de.unirostock.sems.bives.webservice.client.exception.BivesException

Instantiates a new bives exception.

BivesRequest - Class in de.unirostock.sems.bives.webservice.client

The Class BivesRequest to create a request for the BiVeS web service.

BivesRequest() - Constructor for class de.unirostock.sems.bives.webservice.client.BivesRequest

Instantiate a new request.

BivesResponse - Class in de.unirostock.sems.bives.webservice.client

The Class BivesResponse representing the response from a BiVeS web service.

BivesResponse() - Constructor for class de.unirostock.sems.bives.webservice.client.BivesResponse

The Constructor to create an BiVeS web service response.

bivesResults - Variable in class de.unirostock.sems.bives.webservice.client.BivesResponse

The bives results.

BivesSingleFileCommands - Interface in de.unirostock.sems.bives.webservice.client

The Interface BivesSingleFileCommands providing some static command flags to get information about certain files.

BivesSingleFileRequest - Class in de.unirostock.sems.bives.webservice.client

The Class BivesSingleFileRequest to retrieve some information of a single file from the BiVeS web service.

BivesSingleFileRequest() - Constructor for class de.unirostock.sems.bives.webservice.client.BivesSingleFileRequest

The Constructor to create a single-file-request.

BivesSingleFileRequest(String) - Constructor for class de.unirostock.sems.bives.webservice.client.BivesSingleFileRequest

The Constructor to create a single-file-request.

BivesSingleFileRequest(String, List<String>) - Constructor for class de.unirostock.sems.bives.webservice.client.BivesSingleFileRequest

The Constructor to create a single-file-request.

BivesSingleFileResponse - Class in de.unirostock.sems.bives.webservice.client

The Class BivesSingleFileResponse representing a response of a single-file-request sent to the BiVeS web service.

BivesSingleFileResponse() - Constructor for class de.unirostock.sems.bives.webservice.client.BivesSingleFileResponse

Instantiates a new bives single file response.

BivesWs - Interface in de.unirostock.sems.bives.webservice.client

The Interface to send a request to the BiVeS web service.

C

COMMAND_COMPONENT_HIERARCHY_DOT - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesComparisonCommands

get the component hierarchy encoded in DOT (only available for CellML files)

COMMAND_COMPONENT_HIERARCHY_GRAPHML - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesComparisonCommands

get the component hierarchy encoded in GraphML (only available for CellML files)

COMMAND_COMPONENT_HIERARCHY_JSON - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesComparisonCommands

get the component hierarchy encoded in JSON (only available for CellML files)

COMMAND_DOCUMENT_TYPE - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesSingleFileCommands

get the document type of the file

COMMAND_FORCE_CELLML - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesCommands

force CellML file interpretation

COMMAND_FORCE_REGULAR - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesCommands

force regular file interpretation (don't try to read as SBML or CellML)

COMMAND_FORCE_SBML - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesCommands

force SBML file interpretation

COMMAND_META - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesSingleFileCommands

get some meta information about the file

COMMAND_REACTIONS_DOT - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesComparisonCommands

get the reaction network encoded in DOT

COMMAND_REACTIONS_GRAPHML - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesComparisonCommands

get the reaction network encoded in GraphML

COMMAND_REACTIONS_JSON - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesComparisonCommands

get the reaction network encoded in JSON

COMMAND_REPORT_HTML - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesComparisonCommands

get the human readable report encoded in HTML

COMMAND_REPORT_MARKDOWN - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesComparisonCommands

get the human readable report encoded in MarkDown

COMMAND_REPORT_RESTRUCTURED_TEXT - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesComparisonCommands

get the human readable report encoded in reStructuredText

COMMAND_SET_LOG_STACKTRACE - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesCommands

just intended to help server administrators to fix issues

COMMAND_SET_VERBOSE - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesCommands

just intended to help server administrators to fix problems

COMMAND_SINGLE_FILE_COMPONENT_HIERARCHY_DOT - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesSingleFileCommands

get the component hierarchy encoded in DOT (only available for CellML files)

COMMAND_SINGLE_FILE_COMPONENT_HIERARCHY_GRAPHML - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesSingleFileCommands

get the component hierarchy encoded in GraphML (only available for CellML files)

COMMAND_SINGLE_FILE_COMPONENT_HIERARCHY_JSON - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesSingleFileCommands

get the component hierarchy encoded in JSON (only available for CellML files)

COMMAND_SINGLE_FILE_REACTIONS_DOT - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesSingleFileCommands

get the reaction network encoded in DOT

COMMAND_SINGLE_FILE_REACTIONS_GRAPHML - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesSingleFileCommands

get the reaction network encoded in GraphML

COMMAND_SINGLE_FILE_REACTIONS_JSON - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesSingleFileCommands

get the reaction network encoded in JSON

COMMAND_SINGLE_FLATTEN - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesSingleFileCommands

get the flattened model

COMMAND_XML_DIFF - Static variable in interface de.unirostock.sems.bives.webservice.client.BivesComparisonCommands

get the diff encoded in xml

commands - Variable in class de.unirostock.sems.bives.webservice.client.BivesRequest

The commands.

D

de.unirostock.sems.bives.webservice.client - package de.unirostock.sems.bives.webservice.client

de.unirostock.sems.bives.webservice.client.exception - package de.unirostock.sems.bives.webservice.client.exception

de.unirostock.sems.bives.webservice.client.impl - package de.unirostock.sems.bives.webservice.client.impl

documentTypes - Variable in class de.unirostock.sems.bives.webservice.client.BivesSingleFileResponse

The document types.

E

error - Variable in class de.unirostock.sems.bives.webservice.client.BivesResponse

The errors.

G

getCommands() - Method in class de.unirostock.sems.bives.webservice.client.BivesRequest

Gets the commands.

getDocumentTypes() - Method in class de.unirostock.sems.bives.webservice.client.BivesSingleFileResponse

Gets the document types.

getErrors() - Method in class de.unirostock.sems.bives.webservice.client.BivesResponse

Gets the errors.

getMeta() - Method in class de.unirostock.sems.bives.webservice.client.BivesSingleFileResponse

Gets the meta informations.

getModels() - Method in class de.unirostock.sems.bives.webservice.client.BivesRequest

Gets the models.

getNodeStats() - Method in class de.unirostock.sems.bives.webservice.client.BivesSingleFileResponse

Gets the node statistics as a map: NODE_NAME => OCCURRENCES.

getResult(String) - Method in class de.unirostock.sems.bives.webservice.client.BivesResponse

Gets a result.

H

hasError() - Method in class de.unirostock.sems.bives.webservice.client.BivesResponse

Checks for errors.

HttpBivesClient - Class in de.unirostock.sems.bives.webservice.client.impl

The Implementation of a BiVeS web service Client.

HttpBivesClient(String) - Constructor for class de.unirostock.sems.bives.webservice.client.impl.HttpBivesClient

The Constructor.

I

isReady() - Method in class de.unirostock.sems.bives.webservice.client.BivesComparisonRequest

Checks if the request is ready.

isReady() - Method in class de.unirostock.sems.bives.webservice.client.BivesRequest

Checks if is this request is ready.

isReady() - Method in class de.unirostock.sems.bives.webservice.client.BivesSingleFileRequest

Checks if the request is ready.

M

meta - Variable in class de.unirostock.sems.bives.webservice.client.BivesSingleFileResponse

The meta informations.

models - Variable in class de.unirostock.sems.bives.webservice.client.BivesRequest

The models.

N

nodeStats - Variable in class de.unirostock.sems.bives.webservice.client.BivesSingleFileResponse

The node statistics.

P

performRequest(BivesSingleFileRequest) - Method in interface de.unirostock.sems.bives.webservice.client.BivesWs

Perform a single-file-request.

performRequest(BivesComparisonRequest) - Method in interface de.unirostock.sems.bives.webservice.client.BivesWs

Perform comparison request.

performRequest(BivesRequest, BivesResponse) - Method in class de.unirostock.sems.bives.webservice.client.impl.HttpBivesClient

Performs the request.

performRequest(BivesSingleFileRequest) - Method in class de.unirostock.sems.bives.webservice.client.impl.HttpBivesClient

performRequest(BivesComparisonRequest) - Method in class de.unirostock.sems.bives.webservice.client.impl.HttpBivesClient

postProcess() - Method in class de.unirostock.sems.bives.webservice.client.BivesComparisonResponse

postProcess() - Method in class de.unirostock.sems.bives.webservice.client.BivesResponse

Post process a response.

postProcess() - Method in class de.unirostock.sems.bives.webservice.client.BivesSingleFileResponse

S

setDocumentTypes(List<String>) - Method in class de.unirostock.sems.bives.webservice.client.BivesSingleFileResponse

Sets the document types.

setMeta(String, String) - Method in class de.unirostock.sems.bives.webservice.client.BivesSingleFileResponse

Sets the meta informations.

setModel(String) - Method in class de.unirostock.sems.bives.webservice.client.BivesSingleFileRequest

Sets the model.

setModels(String, String) - Method in class de.unirostock.sems.bives.webservice.client.BivesComparisonRequest

Sets the models.

setNodeStats(String, int) - Method in class de.unirostock.sems.bives.webservice.client.BivesSingleFileResponse

Sets the statistics for a certain node type.

setResult(String, String) - Method in class de.unirostock.sems.bives.webservice.client.BivesResponse

Sets a result.

A B C D E G H I M N P S