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D E H M N O P R S T X

D

doCoordinationDefinition(String, String, String, String, String, Element) - Static method in class org.embl.ebi.escience.scufl.parser.Scufl2XScuflParser
Create a coordination definition
doLine(String, Element) - Static method in class org.embl.ebi.escience.scufl.parser.Scufl2XScuflParser
Process a single line of scufl, creating appropriate element declarations and adding them onto the supplied element.
doLinkDefinition(String, String, Element) - Static method in class org.embl.ebi.escience.scufl.parser.Scufl2XScuflParser
Create a data link definition
doProcessorDefinition(String, String, String, Element) - Static method in class org.embl.ebi.escience.scufl.parser.Scufl2XScuflParser
Create a processor definition

E

ExceptionHolder - class org.embl.ebi.escience.scufl.parser.ExceptionHolder.
Used to carry an exception between the worker threads loading the processors and the main thread that actually cares
ExceptionHolder() - Constructor for class org.embl.ebi.escience.scufl.parser.ExceptionHolder
 

H

holder - Variable in class org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread
 

M

model - Variable in class org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread
 

N

name - Variable in class org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread
 
namespace - Variable in class org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread
 

O

org.embl.ebi.escience.scufl.parser - package org.embl.ebi.escience.scufl.parser
Provides the object model for the Simple Conceptual Unified Flow Language (Scufl).

P

ProcessorLoaderThread - class org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.
A thread subclass to load a processor without blocking everything
ProcessorLoaderThread(ScuflModel, Element, String, Namespace, ExceptionHolder) - Constructor for class org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread
 
parse(InputStream) - Static method in class org.embl.ebi.escience.scufl.parser.Scufl2XScuflParser
Read the Scufl format on the supplied InputStream, return a new InputStream from which may be read the XScufl representation.
parse(String) - Static method in class org.embl.ebi.escience.scufl.parser.Scufl2XScuflParser
Read the Scufl format contained within the String and produce a String containing the XML format XScufl
parseScufl(String) - Static method in class org.embl.ebi.escience.scufl.parser.Scufl2XScuflParser
Create a JDOM Document containing the XML format representation of the Scufl file passed in as the single string parameter
populate(String, ScuflModel, String) - Static method in class org.embl.ebi.escience.scufl.parser.XScuflParser
Read from the given String containing an XScufl document and populate the given ScuflModel with data from the definition.
populate(InputStream, ScuflModel, String) - Static method in class org.embl.ebi.escience.scufl.parser.XScuflParser
Read from the given InputStream and populate the given ScuflModel with data from the definition.
populate(Document, ScuflModel, String) - Static method in class org.embl.ebi.escience.scufl.parser.XScuflParser
Read from the given JDOM Document and populate the given ScuflModel with data from the definition.
processorNode - Variable in class org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread
 

R

run() - Method in class org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread
 

S

Scufl2XScuflParser - class org.embl.ebi.escience.scufl.parser.Scufl2XScuflParser.
Given an input stream from which to read a Scufl definition file, this class exposes an InputStream that contains the corresponding XScufl representation.
Scufl2XScuflParser() - Constructor for class org.embl.ebi.escience.scufl.parser.Scufl2XScuflParser
 
scuflNS() - Static method in class org.embl.ebi.escience.scufl.parser.Scufl2XScuflParser
The namespace for the Scufl elements

T

theException - Variable in class org.embl.ebi.escience.scufl.parser.ExceptionHolder
 

X

XScuflFormatException - exception org.embl.ebi.escience.scufl.parser.XScuflFormatException.
Thrown by the ScuflModel when it can't find a particular named processor.
XScuflFormatException(String) - Constructor for class org.embl.ebi.escience.scufl.parser.XScuflFormatException
 
XScuflParser - class org.embl.ebi.escience.scufl.parser.XScuflParser.
Reads a definition in XScufl format and populates the supplied model with it.
XScuflParser() - Constructor for class org.embl.ebi.escience.scufl.parser.XScuflParser
 

D E H M N O P R S T X