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(); }