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

A

addParam(String, Object) - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

addSession(WorkflowAction) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

When a Goose receives a workflowAction from the Boss, it should call this function to save the workflowAction in the processing queue.

addSessionTargetData(String, int, GaggleData) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

Attach data to a goose in the next step of a workflow.

B

Boss3 - Interface in org.systemsbiology.gaggle.core

The Boss3 interface defines APIs to handle workflow related actions.

C

CompleteWorkflowAction(Boss, String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

All the data are ready, we submit the response to the boss.

D

dataSubmittedForSession(String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

Retrieve the number of data elements that have been added for the geese in the next step of the workflow.

downloadFileFromUrl(String, String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

E

equals(Object) - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

F

finalizeSessionAction(String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

G

getActionType() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowAction

getArguments() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

getCommandUri() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

getComponentID() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowAction

getComponentID() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

getComponentWorkflowNodeID() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

getCurrentRequest() - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

Retrieve a workflowAction that has not been processed yet.

getData() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowAction

getGooseInfo() - Method in interface org.systemsbiology.gaggle.core.Goose3

Get information about a goose.

getGooseInfo() - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

getGooseName() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

getJSONParams() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

getName() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

getNameList(String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

getOption() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowAction

getOptions() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

getParams() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

getSessionID() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowAction

getSessionResponse(String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

getSize(String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

getSource() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowAction

getSpecies(String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

getSubAction(String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

getTargets() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowAction

getThreadGroup(String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

Starting from Java 7 update 25, the Java Runtime is using a different threadgroup (i.e., javawsApplicationThreadGroup) to run web starts.

getType(String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

getValue() - Method in enum org.systemsbiology.gaggle.core.datatypes.WorkflowAction.Options

getValue() - Method in enum org.systemsbiology.gaggle.core.datatypes.WorkflowComponent.Options

getValue() - Method in enum org.systemsbiology.gaggle.core.datatypes.WorkflowComponent.ParamNames

getVersion() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

getWorkflowAction(String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

Get the workflowAction given the requestID

getWorkflowActionData(String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

getWorkflowID() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowAction

getWorkflowIndex() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

Goose3 - Interface in org.systemsbiology.gaggle.core

The Goose3 interface defines APIs for handling workflow related activities.

GooseWorkflowManager - Class in org.systemsbiology.gaggle.core

The GooseWorkflowManager class is a helper class for Gaggle Geese to carry out workflow related actions.

GooseWorkflowManager() - Constructor for class org.systemsbiology.gaggle.core.GooseWorkflowManager

H

handleWorkflowAction(WorkflowAction) - Method in interface org.systemsbiology.gaggle.core.Boss3

Tell the boss to handle a workflow action.

handleWorkflowAction(WorkflowAction) - Method in interface org.systemsbiology.gaggle.core.Goose3

Handles a workflowAction passed from the Boss to the goose.

handleWorkflowInformation(String, String) - Method in interface org.systemsbiology.gaggle.core.Goose3

Handles information passed from Boss.

hashCode() - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

I

invokeLater2(ThreadGroup, AppContext, Runnable) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

Starting from Java 7 update 25, the Java Runtime is using a different threadgroup (i.e., javawsApplicationThreadGroup) to run web starts.

J

JSONConstants - Interface in org.systemsbiology.gaggle.core.datatypes

Constants used by JSONReader and JSONWriter.

K

KEY_ATTRIBUTES - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_COLUMN_NAMES - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_COLUMNS - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_CONDITIONS - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_DIRECTED - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_EDGES - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_GAGGLE_DATA - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_GENES - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_INTERACTION - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_METADATA - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_NAME - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_NODE - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_NODES - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_ROW_NAMES - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_SOURCE - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_SPECIES - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_SUBTYPE - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_TARGET - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_TYPE - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_VALUES - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_WORKFLOW_EDGES - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

KEY_WORKFLOW_NODES - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

L

loadState(String) - Method in interface org.systemsbiology.gaggle.core.Boss3

Load a saved state.

loadState(String) - Method in interface org.systemsbiology.gaggle.core.Goose3

Load the state according given the state file.

O

org.systemsbiology.gaggle.core - package org.systemsbiology.gaggle.core

org.systemsbiology.gaggle.core.datatypes - package org.systemsbiology.gaggle.core.datatypes

P

pauseRecordingWorkflow(UUID) - Method in interface org.systemsbiology.gaggle.core.Boss3

Pause recording a workflow

ProcessTextFile(String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

First download a text file from the server, then parse it and output a GaggleData object.

R

recordAction(String, String, Object, int, HashMap<String, String>, HashMap<String, String>, HashMap<String, String>) - Method in interface org.systemsbiology.gaggle.core.Boss3

Record a broadcast action.

removeRequest(String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

Remove a workflowAction from the processing queue.

RemoveSessionData(String) - Method in class org.systemsbiology.gaggle.core.GooseWorkflowManager

Remove the workflowAction after finishing handling it.

resumeRecordingWorkflow(UUID) - Method in interface org.systemsbiology.gaggle.core.Boss3

Resume recording a workflow

S

saveState(Goose3, String, String, String, String) - Method in interface org.systemsbiology.gaggle.core.Boss3

Save the current state.

saveState(String, String) - Method in interface org.systemsbiology.gaggle.core.Goose3

This API is called by the Boss during state saving.

setData(GaggleData[]) - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowAction

setParams(HashMap) - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

setTargets(WorkflowComponent[]) - Method in class org.systemsbiology.gaggle.core.datatypes.WorkflowAction

startRecordingWorkflow() - Method in interface org.systemsbiology.gaggle.core.Boss3

Tell the boss to start recording a workflow.

submitWorkflow(Goose3, String) - Method in interface org.systemsbiology.gaggle.core.Boss3

Submit a workflow to the boss.

T

terminateRecordingWorkflow(UUID) - Method in interface org.systemsbiology.gaggle.core.Boss3

Tell the boss to stop recording a workflow

TYPE_ANY - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

TYPE_BICLUSTER - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

TYPE_MATRIX - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

TYPE_NAMELIST - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

TYPE_NETWORK - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

TYPE_TABLE - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

TYPE_TUPLE - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

TYPE_WORKFLOW - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

V

valueOf(String) - Static method in enum org.systemsbiology.gaggle.core.datatypes.WorkflowAction.ActionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.systemsbiology.gaggle.core.datatypes.WorkflowAction.DataType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.systemsbiology.gaggle.core.datatypes.WorkflowAction.Options

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.systemsbiology.gaggle.core.datatypes.WorkflowComponent.Options

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.systemsbiology.gaggle.core.datatypes.WorkflowComponent.ParamNames

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.systemsbiology.gaggle.core.datatypes.WorkflowAction.ActionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.systemsbiology.gaggle.core.datatypes.WorkflowAction.DataType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.systemsbiology.gaggle.core.datatypes.WorkflowAction.Options

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.systemsbiology.gaggle.core.datatypes.WorkflowComponent.Options

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.systemsbiology.gaggle.core.datatypes.WorkflowComponent.ParamNames

Returns an array containing the constants of this enum type, in the order they are declared.

W

WORKDLOW_COMPONENT_ARGUMENTS - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_COMPONENT_DATAURI - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_COMPONENT_ID - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_COMPONENT_SERVICEURI - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_COMPONENT_SUBACTION - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_EDGE_DATATYPE - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_EDGE_PARALLELTYPE - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_EDGE_SOURCEID - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_EDGE_STARTNODE - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_EDGE_TARGETID - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_EMPTY_ARGUMENT - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_ID - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_NAME - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_ORGANISMINFO - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_RECORDING_FILE - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_RESET - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_SAVESTATERESULTKEY - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_STATEID - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WORKFLOW_USERID - Static variable in interface org.systemsbiology.gaggle.core.datatypes.JSONConstants

WorkflowAction - Class in org.systemsbiology.gaggle.core.datatypes

A workflow action consists of a source component, a list of target components, and data passed by the source component to the target.

WorkflowAction(String, String, String, WorkflowAction.ActionType, WorkflowComponent, WorkflowComponent[], int, GaggleData[]) - Constructor for class org.systemsbiology.gaggle.core.datatypes.WorkflowAction

WorkflowAction.ActionType - Enum in org.systemsbiology.gaggle.core.datatypes

WorkflowAction.DataType - Enum in org.systemsbiology.gaggle.core.datatypes

WorkflowAction.Options - Enum in org.systemsbiology.gaggle.core.datatypes

WorkflowComponent - Class in org.systemsbiology.gaggle.core.datatypes

Each WorkflowComponent corresponds to a goose.

WorkflowComponent(String, String, String, String, String, String, String, String, HashMap, int) - Constructor for class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

WorkflowComponent(String, String, String, String, String, String, HashMap) - Constructor for class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

WorkflowComponent(WorkflowComponent) - Constructor for class org.systemsbiology.gaggle.core.datatypes.WorkflowComponent

Copy constructor

WorkflowComponent.Options - Enum in org.systemsbiology.gaggle.core.datatypes

WorkflowComponent.ParamNames - Enum in org.systemsbiology.gaggle.core.datatypes

Parameter names SubTarget is for goose that have subactions.

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