org.embl.ebi.escience.scufl
Class AnnotationTemplate

java.lang.Object
  org.embl.ebi.escience.scufl.AnnotationTemplate

public class AnnotationTemplate
extends java.lang.Object

An AnnotationTemplate object represents a single possible RDF statement that may be generated as a side effect of the invocation of a processor task instance. Any processor may have zero or more of these templates associated with it.

Author:

Tom Oinn

Field Summary

static java.lang.String

TAVERNA_PROVENANCE_NS

Constructor Summary

AnnotationTemplate()
Create a blank annotation template object

AnnotationTemplate(org.jdom.Element templateElement)
Create an annotation template object from a JDOM Element, the element being the <template> tag.

Method Summary

void	addLiteral(java.lang.String text) Add a new text literal to the template
void	addPortReference(Port p) Add a new port reference to this template
static java.lang.String	convert(java.lang.String input) Take an input string and return the string with all less than characters replaced with the appropriate XML literal
java.lang.String	getDescription() Return a chunk of HTML showing the unknowns in purple
org.jdom.Element	getElement() The JDOM Element for this AnnotationTemplate
java.lang.String	getTextAnnotation(java.util.Map inputs, java.util.Map outputs) Given two maps of inputName->LSID and outputName->LSID create a concatenated text string from all the elements in this annotation template populated with the LSID values.
static AnnotationTemplate	standardTemplate(Port subject, java.lang.String verb, Port object) Create a basic 'subject verb object' triple in RDF format

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

TAVERNA_PROVENANCE_NS

public static final java.lang.String TAVERNA_PROVENANCE_NS

See Also:

Constant Field Values

Constructor Detail

AnnotationTemplate

public AnnotationTemplate()

Create a blank annotation template object

AnnotationTemplate

public AnnotationTemplate(org.jdom.Element templateElement)

Create an annotation template object from a JDOM Element, the element being the <template> tag.

Method Detail

standardTemplate

public static AnnotationTemplate standardTemplate(Port subject,
                                                  java.lang.String verb,
                                                  Port object)

Create a basic 'subject verb object' triple in RDF format

addLiteral

public void addLiteral(java.lang.String text)

Add a new text literal to the template

addPortReference

public void addPortReference(Port p)

Add a new port reference to this template

getTextAnnotation

public java.lang.String getTextAnnotation(java.util.Map inputs,
                                          java.util.Map outputs)

Given two maps of inputName->LSID and outputName->LSID create a concatenated text string from all the elements in this annotation template populated with the LSID values. Return null if any of the values are unknown

getElement

public org.jdom.Element getElement()

The JDOM Element for this AnnotationTemplate

getDescription

public java.lang.String getDescription()

Return a chunk of HTML showing the unknowns in purple

convert

public static java.lang.String convert(java.lang.String input)

Take an input string and return the string with all less than characters replaced with the appropriate XML literal