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

A

add(Component, Object) - Method in class org.embl.ebi.escience.scuflui.workbench.ScrollableDesktopPane
Add an internal-frame to the desktop.
add(Component) - Method in class org.embl.ebi.escience.scuflui.workbench.ScrollableDesktopPane
 
add(Component, Object, int) - Method in class org.embl.ebi.escience.scuflui.workbench.ScrollableDesktopPane
 
add(String, Component) - Method in class org.embl.ebi.escience.scuflui.workbench.ScrollableDesktopPane
 
addScavenger(Scavenger) - Method in class org.embl.ebi.escience.scuflui.workbench.ScavengerTree
Add a new scavenger to the tree, firing appropriate model events as we do.
addScavengersFromModel() - Method in class org.embl.ebi.escience.scuflui.workbench.ScavengerTree
Examine the model, create any scavengers that would have been required to populate the model with its existing processors.
applicationname - Variable in class org.embl.ebi.escience.scuflui.workbench.SoaplabProcessorFactory
 
attachToModel(ScuflModel) - Method in class org.embl.ebi.escience.scuflui.workbench.ScavengerTree
Listen for model bind requests to set the internal ScuflModel field

C

component - Variable in class org.embl.ebi.escience.scuflui.workbench.GenericUIComponentFrame
 
count - Variable in class org.embl.ebi.escience.scuflui.workbench.ScavengerTree
A private count to avoid name duplication on created nodes
createMenuBar() - Method in class org.embl.ebi.escience.scuflui.workbench.Workbench
Create the menus required by the application
createProcessor(String, ScuflModel) - Method in interface org.embl.ebi.escience.scuflui.workbench.ProcessorFactory
Instantiate a new processor with the given name and add it to the specified ScuflModel
createProcessor(String, ScuflModel) - Method in class org.embl.ebi.escience.scuflui.workbench.SoaplabProcessorFactory
Create a new SoaplabProcessor and add it to the model
createProcessor(String, ScuflModel) - Method in class org.embl.ebi.escience.scuflui.workbench.TalismanProcessorFactory
Create a new SoaplabProcessor and add it to the model
createProcessor(String, ScuflModel) - Method in class org.embl.ebi.escience.scuflui.workbench.WSDLBasedProcessorFactory
Create a new WSDLBasedProcessor and add it to the model
createProcessor(String, ScuflModel) - Method in class org.embl.ebi.escience.scuflui.workbench.WorkflowProcessorFactory
Build a new WorkflowProcessor and add it to the model

D

DISALLOW - Static variable in class org.embl.ebi.escience.scuflui.workbench.WebScavenger
 
defaultBorderColor - Static variable in class org.embl.ebi.escience.scuflui.workbench.FileDrop
 
definitionURL - Variable in class org.embl.ebi.escience.scuflui.workbench.WorkflowProcessorFactory
 
deleteIcon - Static variable in class org.embl.ebi.escience.scuflui.workbench.Workbench
 
desktop - Variable in class org.embl.ebi.escience.scuflui.workbench.Workbench
 
detachFromModel() - Method in class org.embl.ebi.escience.scuflui.workbench.ScavengerTree
When unbound from a model, set internal model field to null
doEvent(MouseEvent) - Method in class org.embl.ebi.escience.scuflui.workbench.ScavengerTreePopupHandler
If the popup was over a ProcessorFactory implementation then present the 'add' option to the user
dropListener - Variable in class org.embl.ebi.escience.scuflui.workbench.FileDrop
 

E

endpoint - Variable in class org.embl.ebi.escience.scuflui.workbench.SoaplabProcessorFactory
 

F

FileDrop - class org.embl.ebi.escience.scuflui.workbench.FileDrop.
This class makes it easy to drag and drop files from the operating system to a Java program.
FileDrop(Component, FileDrop.Listener) - Constructor for class org.embl.ebi.escience.scuflui.workbench.FileDrop
Constructs a FileDrop with a default light-blue border and, if c is a java.awt.Container, recursively sets all elements contained within as drop targets, though only the top level container will change borders.
FileDrop(Component, boolean, FileDrop.Listener) - Constructor for class org.embl.ebi.escience.scuflui.workbench.FileDrop
Constructor with a default border and the option to recursively set drop targets.
FileDrop(PrintStream, Component, FileDrop.Listener) - Constructor for class org.embl.ebi.escience.scuflui.workbench.FileDrop
Constructor with a default border and debugging optionally turned on.
FileDrop(PrintStream, Component, boolean, FileDrop.Listener) - Constructor for class org.embl.ebi.escience.scuflui.workbench.FileDrop
Constructor with a default border, debugging optionally turned on and the option to recursively set drop targets.
FileDrop(Component, Border, FileDrop.Listener) - Constructor for class org.embl.ebi.escience.scuflui.workbench.FileDrop
Constructor with a specified border
FileDrop(Component, Border, boolean, FileDrop.Listener) - Constructor for class org.embl.ebi.escience.scuflui.workbench.FileDrop
Constructor with a specified border and the option to recursively set drop targets.
FileDrop(PrintStream, Component, Border, FileDrop.Listener) - Constructor for class org.embl.ebi.escience.scuflui.workbench.FileDrop
Constructor with a specified border and debugging optionally turned on.
FileDrop(PrintStream, Component, Border, boolean, FileDrop.Listener) - Constructor for class org.embl.ebi.escience.scuflui.workbench.FileDrop
Full constructor with a specified border and debugging optionally turned on.
FileDrop.Listener - interface org.embl.ebi.escience.scuflui.workbench.FileDrop.Listener.
Implement this inner interface to listen for when files are dropped.
fc - Variable in class org.embl.ebi.escience.scuflui.workbench.Workbench
 
filesDropped(File[]) - Method in interface org.embl.ebi.escience.scuflui.workbench.FileDrop.Listener
This method is called when files have been successfully dropped.

G

GenericUIComponentFrame - class org.embl.ebi.escience.scuflui.workbench.GenericUIComponentFrame.
An internal frame containing a class implementing the scuflui.ScuflUIComponent interface.
GenericUIComponentFrame(ScuflModel, ScuflUIComponent) - Constructor for class org.embl.ebi.escience.scuflui.workbench.GenericUIComponentFrame
 
getDefinitionURL() - Method in class org.embl.ebi.escience.scuflui.workbench.WorkflowProcessorFactory
Return the definition URL
getName() - Method in class org.embl.ebi.escience.scuflui.workbench.ScavengerTree
Return an apppropriate title for windows
getNextCount() - Method in class org.embl.ebi.escience.scuflui.workbench.ScavengerTree
Get the next available count and increment the counter
getProcessorClass() - Method in interface org.embl.ebi.escience.scuflui.workbench.ProcessorFactory
Return the Class object describing the processor this factory would build
getProcessorClass() - Method in class org.embl.ebi.escience.scuflui.workbench.SoaplabProcessorFactory
Return the Class object for processors that would be created by this factory
getProcessorClass() - Method in class org.embl.ebi.escience.scuflui.workbench.TalismanProcessorFactory
Return the Class object for processors that would be created by this factory
getProcessorClass() - Method in class org.embl.ebi.escience.scuflui.workbench.WSDLBasedProcessorFactory
Return the Class object for processors that would be created by this factory
getProcessorClass() - Method in class org.embl.ebi.escience.scuflui.workbench.WorkflowProcessorFactory
Return the Class object for processors that would be created by this factory
getProcessorDescription() - Method in interface org.embl.ebi.escience.scuflui.workbench.ProcessorFactory
Describe the processor that would be created by this factory were the createProcessor method invoked
getProcessorDescription() - Method in class org.embl.ebi.escience.scuflui.workbench.SoaplabProcessorFactory
Return a textual description of the factory
getProcessorDescription() - Method in class org.embl.ebi.escience.scuflui.workbench.TalismanProcessorFactory
Return a textual description of the factory
getProcessorDescription() - Method in class org.embl.ebi.escience.scuflui.workbench.WSDLBasedProcessorFactory
Return a description of the factory
getProcessorDescription() - Method in class org.embl.ebi.escience.scuflui.workbench.WorkflowProcessorFactory
Return a textual description of the factory
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.embl.ebi.escience.scuflui.workbench.ScavengerTreeRenderer
Return a custom renderer to draw the cell correctly for each node type
getXScuflURLs(String) - Method in class org.embl.ebi.escience.scuflui.workbench.WebScavenger
 

I

importIcon - Static variable in class org.embl.ebi.escience.scuflui.workbench.Workbench
 
isDragOk(PrintStream, DropTargetDragEvent) - Method in class org.embl.ebi.escience.scuflui.workbench.FileDrop
Determine if the dragged data is a file list.

L

listeners - Variable in class org.embl.ebi.escience.scuflui.workbench.ScrollableDesktopPane
 
log(PrintStream, String) - Static method in class org.embl.ebi.escience.scuflui.workbench.FileDrop
Outputs message to out if it's not null.
logo - Static variable in class org.embl.ebi.escience.scuflui.workbench.SplashScreen
 

M

main(String[]) - Static method in class org.embl.ebi.escience.scuflui.workbench.FileDrop
Runs a sample program that shows dropped files
main(String[]) - Static method in class org.embl.ebi.escience.scuflui.workbench.WebScavenger
 
main(String[]) - Static method in class org.embl.ebi.escience.scuflui.workbench.Workbench
Launch the model workbench, shows the default set of UI components in internal frames and waits for the user to load a model from file
makeDropTarget(PrintStream, Component, boolean) - Method in class org.embl.ebi.escience.scuflui.workbench.FileDrop
 
model - Variable in class org.embl.ebi.escience.scuflui.workbench.ScavengerTree
The model that this scavenger will create processor for
model - Variable in class org.embl.ebi.escience.scuflui.workbench.Workbench
 
mousePressed(MouseEvent) - Method in class org.embl.ebi.escience.scuflui.workbench.ScavengerTreePopupHandler
Handle the mouse pressed event in case this is the platform specific trigger for a popup menu
mouseReleased(MouseEvent) - Method in class org.embl.ebi.escience.scuflui.workbench.ScavengerTreePopupHandler
Similarly handle the mouse released event

N

normalBorder - Variable in class org.embl.ebi.escience.scuflui.workbench.FileDrop
 

O

openIcon - Static variable in class org.embl.ebi.escience.scuflui.workbench.Workbench
 
openurlIcon - Static variable in class org.embl.ebi.escience.scuflui.workbench.Workbench
 
operationName - Variable in class org.embl.ebi.escience.scuflui.workbench.WSDLBasedProcessorFactory
 
org.embl.ebi.escience.scuflui.workbench - package org.embl.ebi.escience.scuflui.workbench
Provides Java Swing components that show or allow manipulation of subsets of the ScuflModel state.

P

ProcessorFactory - interface org.embl.ebi.escience.scuflui.workbench.ProcessorFactory.
Implementing classes are capable of creating a new processor and attaching it to a model when supplied with the new processor name and a reference to the model.
paint(Graphics) - Method in class org.embl.ebi.escience.scuflui.workbench.ScrollableDesktopPane
 
portTypeName - Variable in class org.embl.ebi.escience.scuflui.workbench.WSDLBasedProcessorFactory
 
preferredSizeOfAllFrames() - Method in class org.embl.ebi.escience.scuflui.workbench.ScrollableDesktopPane
Set the preferred size of the desktop to the right-bottom-corner of the internal-frame with the "largest" right-bottom-corner.

R

registerListener(Component) - Method in class org.embl.ebi.escience.scuflui.workbench.ScrollableDesktopPane
 
remove(Component) - Static method in class org.embl.ebi.escience.scuflui.workbench.FileDrop
Removes the drag-and-drop hooks from the component and optionally from the all children.
remove(PrintStream, Component, boolean) - Static method in class org.embl.ebi.escience.scuflui.workbench.FileDrop
Removes the drag-and-drop hooks from the component and optionally from the all children.
remove(Component) - Method in class org.embl.ebi.escience.scuflui.workbench.ScrollableDesktopPane
Remove an internal-frame from the desktop.
robotSafe(URL) - Method in class org.embl.ebi.escience.scuflui.workbench.WebScavenger
 
robotSafeOld(URL) - Method in class org.embl.ebi.escience.scuflui.workbench.WebScavenger
Check whether there is a robots.txt that would ban access to the URL and those below it
root - Variable in class org.embl.ebi.escience.scuflui.workbench.ScavengerTree
The root node

S

Scavenger - class org.embl.ebi.escience.scuflui.workbench.Scavenger.
A subclass of DefaultMutableTreeNode that should be subclassed to create particular scavengers for different types of processor
Scavenger(Object) - Constructor for class org.embl.ebi.escience.scuflui.workbench.Scavenger
 
ScavengerCreationException - exception org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException.
Signifies that a scavenger failed during instantiation, most commonly because of network unavailability.
ScavengerCreationException(String) - Constructor for class org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException
 
ScavengerTree - class org.embl.ebi.escience.scuflui.workbench.ScavengerTree.
A JTree subclass showing available processors from some set of external libraries or searches.
ScavengerTree() - Constructor for class org.embl.ebi.escience.scuflui.workbench.ScavengerTree
Create a new scavenger tree
ScavengerTreePopupHandler - class org.embl.ebi.escience.scuflui.workbench.ScavengerTreePopupHandler.
A class to handle popup menus on nodes on the ScavengerTree tree
ScavengerTreePopupHandler(ScavengerTree) - Constructor for class org.embl.ebi.escience.scuflui.workbench.ScavengerTreePopupHandler
 
ScavengerTreeRenderer - class org.embl.ebi.escience.scuflui.workbench.ScavengerTreeRenderer.
A cell renderer that paints the appropriate icons depending on the component of the model being displayed.
ScavengerTreeRenderer() - Constructor for class org.embl.ebi.escience.scuflui.workbench.ScavengerTreeRenderer
 
ScrollableDesktopPane - class org.embl.ebi.escience.scuflui.workbench.ScrollableDesktopPane.
ScrollableDesktopPane.java This class gives a DesktopPane which responds properly when placed within a scrollpane.
ScrollableDesktopPane() - Constructor for class org.embl.ebi.escience.scuflui.workbench.ScrollableDesktopPane
 
SoaplabProcessorFactory - class org.embl.ebi.escience.scuflui.workbench.SoaplabProcessorFactory.
Implementation of ProcessorFactory that creates SoaplabProcessor nodes
SoaplabProcessorFactory(String, String) - Constructor for class org.embl.ebi.escience.scuflui.workbench.SoaplabProcessorFactory
Create a new factory configured with the specified endpoint base and application name, which will be concatenated to produce the endpoint URL.
SoaplabScavenger - class org.embl.ebi.escience.scuflui.workbench.SoaplabScavenger.
A Scavenger that knows how to get all the Soaplab services from a specified installation
SoaplabScavenger(String) - Constructor for class org.embl.ebi.escience.scuflui.workbench.SoaplabScavenger
Create a new Soaplab scavenger, the base parameter should be the base URL of the Soaplab service, i.e.
SplashScreen - class org.embl.ebi.escience.scuflui.workbench.SplashScreen.
A splash screen for the workbench, code derived heavily from http://www.javaworld.com/javaworld/javatips/jw-javatip104.html
SplashScreen(int) - Constructor for class org.embl.ebi.escience.scuflui.workbench.SplashScreen
 
saveIcon - Static variable in class org.embl.ebi.escience.scuflui.workbench.Workbench
 
scavenger - Variable in class org.embl.ebi.escience.scuflui.workbench.ScavengerTreePopupHandler
 
scavengerList - Variable in class org.embl.ebi.escience.scuflui.workbench.ScavengerTree
A list of the names of all the scavengers contained within this tree
scriptURL - Variable in class org.embl.ebi.escience.scuflui.workbench.TalismanProcessorFactory
 
search(String) - Method in class org.embl.ebi.escience.scuflui.workbench.WebScavenger
Return an array of strings of URLs of XScufl files found by a web crawl from the initial URL.
supportsDnD - Static variable in class org.embl.ebi.escience.scuflui.workbench.FileDrop
Discover if the running JVM is modern enough to have drag and drop.
supportsDnD() - Static method in class org.embl.ebi.escience.scuflui.workbench.FileDrop
 

T

TalismanProcessorFactory - class org.embl.ebi.escience.scuflui.workbench.TalismanProcessorFactory.
Implementation of ProcessorFactory that creates TalismanProcessor nodes
TalismanProcessorFactory(String) - Constructor for class org.embl.ebi.escience.scuflui.workbench.TalismanProcessorFactory
Create a new factory configured with the specified script URL
TalismanScavenger - class org.embl.ebi.escience.scuflui.workbench.TalismanScavenger.
A Scavenger that knows how to load Talisman scripts
TalismanScavenger(String) - Constructor for class org.embl.ebi.escience.scuflui.workbench.TalismanScavenger
Create a new Talisman scavenger, the single parameter should be resolvable to a location from which the tscript could be fetched.
toString() - Method in class org.embl.ebi.escience.scuflui.workbench.SoaplabProcessorFactory
Return the application name as the toString result
toString() - Method in class org.embl.ebi.escience.scuflui.workbench.TalismanProcessorFactory
Return the leaf of the path as the factory name
toString() - Method in class org.embl.ebi.escience.scuflui.workbench.WSDLBasedProcessorFactory
Return the operation name as the toString result
toString() - Method in class org.embl.ebi.escience.scuflui.workbench.WorkflowProcessorFactory
Return the leaf of the path as the factory name
treeModel - Variable in class org.embl.ebi.escience.scuflui.workbench.ScavengerTree
The tree model

W

WSDLBasedProcessorFactory - class org.embl.ebi.escience.scuflui.workbench.WSDLBasedProcessorFactory.
Implementation of ProcessorFactory that creates WSDLBasedProcessor nodes
WSDLBasedProcessorFactory(String, String, String) - Constructor for class org.embl.ebi.escience.scuflui.workbench.WSDLBasedProcessorFactory
Create a new factory with the specified wsdl location, port type name and operation name
WSDLBasedScavenger - class org.embl.ebi.escience.scuflui.workbench.WSDLBasedScavenger.
A Scavenger that knows how to inspect a given wsdl document for all available port types and operations within them.
WSDLBasedScavenger(String) - Constructor for class org.embl.ebi.escience.scuflui.workbench.WSDLBasedScavenger
Create a new WSDLBased scavenger, the single parameter should be resolvable to a location from which the wsdl document can be fetched.
WebScavenger - class org.embl.ebi.escience.scuflui.workbench.WebScavenger.
A scavenger that does a web crawl starting at the specified URL to find scufl xml files.
WebScavenger(String) - Constructor for class org.embl.ebi.escience.scuflui.workbench.WebScavenger
 
Workbench - class org.embl.ebi.escience.scuflui.workbench.Workbench.
A sample workbench application to allow editing and visualization of Scufl workflows
Workbench() - Constructor for class org.embl.ebi.escience.scuflui.workbench.Workbench
Create a new top level application.
WorkflowProcessorFactory - class org.embl.ebi.escience.scuflui.workbench.WorkflowProcessorFactory.
Implementation of ProcessorFactory that creates WorkflowProcessor nodes
WorkflowProcessorFactory(String) - Constructor for class org.embl.ebi.escience.scuflui.workbench.WorkflowProcessorFactory
Create a new factory configured with the specified definition URL
WorkflowScavenger - class org.embl.ebi.escience.scuflui.workbench.WorkflowScavenger.
A Scavenger that knows how to load nested workflow scripts
WorkflowScavenger(String) - Constructor for class org.embl.ebi.escience.scuflui.workbench.WorkflowScavenger
Create a new Talisman scavenger, the single parameter should be resolvable to a location from which the tscript could be fetched.
wsdlLocation - Variable in class org.embl.ebi.escience.scuflui.workbench.WSDLBasedProcessorFactory
 

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