/** {@inheritDoc} */
@Override
public SBOLDocument read(InputStream in) throws IOException, SBOLValidationException {
try {
Unmarshaller unmarshaller = JAXB.CONTEXT.createUnmarshaller();
if (validate) {
unmarshaller.setSchema(JAXB.SCHEMA);
}
SBOLDocument doc = (SBOLDocument) unmarshaller.unmarshal(in);
doc.accept(new PrecedeReferenceFinder());
doc.accept(new DuplicateRemover());
if (validate) {
new SBOLValidatorImpl().validateWithoutSchema(doc);
}
return doc;
} catch (SBOLValidationException e) {
throw e;
} catch (UnmarshalException e) {
if (e.getLinkedException() != null) {
throw new SBOLValidationException(e.getLinkedException());
} else {
throw new SBOLValidationException(e);
}
} catch (Exception e) {
throw new IOException(e);
}
}
public static void main(String[] args) throws Exception {
System.out.format("Create a very simple SBOL document%n%n");
// create a DnaComponent and set some of its properties
DnaComponent dnaComponent = SBOLFactory.createDnaComponent();
dnaComponent.setURI(URI.create("http://example.com/MyDnaComponent"));
dnaComponent.setDisplayId("MyDnaComponent");
dnaComponent.setName("myDNA");
dnaComponent.setDescription("This is a very simple example");
// create an empty document populated with some SBOL objects
SBOLDocument document = SBOLFactory.createDocument();
// add the DnaComponent to this document
document.addContent(dnaComponent);
// write the contents of the document as an XML file to stdout
System.out.format("Serialize the SBOL document in the official XML format:%n");
SBOLFactory.write(document, System.out);
// now serialize the contents into a buffer so we can read it back
ByteArrayOutputStream buffer = new ByteArrayOutputStream();
SBOLFactory.write(document, buffer);
// create a new document using the byte buffer as our input
SBOLDocument newDocument = SBOLFactory.read(new ByteArrayInputStream(buffer.toByteArray()));
// write the contents of the new document in amore human-readable format
System.out.format("%nSerialize the SBOL document in a more readable presentation format:%n");
new SBOLPrettyWriter().write(newDocument, System.out);
}
// public static URI getTypeBySubpartType(subpart_type type)
// {
// switch(type)
// {
// case Terminator:return SequenceOntology.TERMINATOR;
// case Primers:return SequenceOntology.PRIMER_BINDING_SITE;
// }
// return SequenceOntology.CDS;
// }
public xmlToSbol(String xml, String sbol) throws IOException {
SBOLDocument document = createDocument(xml);
System.out.println(
"Created a new SBOL document with " + document.getContents().size() + " element(s)");
FileOutputStream fileoutStream = new FileOutputStream(sbol);
SBOLFactory.write(document, fileoutStream);
fileoutStream.close();
}
/** Creates a document with a single DnaComponent. */
public SBOLDocument createDocument(String xml) {
SBOLDocument document = SBOLFactory.createDocument();
document.addContent(createDnaComponent(xml, document));
return document;
}
@Override
public void visit(SBOLDocument doc) {
super.visit(doc);
removeDuplicates(doc.getContents());
}