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);
}
/**
* Add subpart to a SequenceAnnotation
*
* @param sub Subpart to create SequenceAnnotation
* @param place
* @return
*/
private SequenceAnnotation createAnnotation(Subpart sub, int place) {
SequenceAnnotation annotation2 = SBOLFactory.createSequenceAnnotation();
annotation2.setURI(
URI.create("http://sbols.org/anot/an_" + this.partId + "_" + sub.id + "_" + place));
DnaComponent dnaComponent2 = SBOLFactory.createDnaComponent();
dnaComponent2.setURI(URI.create("http://partsregistry.org/Part/" + sub.getPart_name()));
dnaComponent2.setDescription(sub.description);
dnaComponent2.setDisplayId(sub.getPart_name());
dnaComponent2.setName(sub.nickName);
dnaComponent2.addType(SequenceOntology.type(sub.getType().toString()));
annotation2.setSubComponent(dnaComponent2);
return annotation2;
}
private SequenceAnnotation createAnnotation(feature sub, int place) {
SequenceAnnotation annotation2 = SBOLFactory.createSequenceAnnotation();
annotation2.setBioStart(sub.startpos);
annotation2.setBioEnd(sub.endpos);
if (sub.direction.equals("forward")) annotation2.setStrand(StrandType.POSITIVE);
else annotation2.setStrand(StrandType.NEGATIVE);
annotation2.setURI(URI.create("http://sbols.org/anot/f_" + sub.id));
DnaComponent dnaComponent2 = SBOLFactory.createDnaComponent();
dnaComponent2.setURI(URI.create("http://partsregistry.org/feat/f_" + sub.id));
dnaComponent2.setDisplayId("f_" + sub.id);
dnaComponent2.setName(sub.type);
dnaComponent2.addType(SequenceOntology.type(sub.type));
annotation2.setSubComponent(dnaComponent2);
return annotation2;
}
private SBOLRootObject createDnaComponent(String xml, SBOLDocument document) {
SAXBuilder builder = new SAXBuilder();
DnaComponent dnaComponent = SBOLFactory.createDnaComponent();
try {
Document doc = builder.build(new File(xml));
Element rootEl = doc.getRootElement();
Element list = rootEl.getChild("part_list").getChild("part");
partId = Integer.parseInt(list.getChildText("part_id"));
dnaComponent.setURI(URI.create(list.getChildText("part_url")));
dnaComponent.setDisplayId(list.getChildText("part_name"));
dnaComponent.setName(list.getChildText("part_short_name"));
dnaComponent.setDescription(list.getChildText("part_short_desc"));
Element seq = rootEl.getChild("part_list").getChild("part").getChild("sequences");
dnaComponent.setDnaSequence(this.createDnaSequence(seq.getChildText("seq_data")));
List<SequenceAnnotation> seqs = createAllDnaSubComponent(xml);
System.out.println(seqs.size());
for (int i = 0; i < seqs.size(); i++) dnaComponent.addAnnotation(seqs.get(i));
} catch (JDOMException e) {
// e.printStackTrace();
} catch (IOException e) {
// e.printStackTrace();
}
return dnaComponent;
}
// 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();
}
public DnaSequence createDnaSequence(String seq) {
DnaSequence dnaSequence = SBOLFactory.createDnaSequence();
dnaSequence.setURI(URI.create("http://partsregistry.org/seq/partseq_" + this.partId));
dnaSequence.setNucleotides(strToSeq(seq));
return dnaSequence;
}
/** Creates a document with a single DnaComponent. */
public SBOLDocument createDocument(String xml) {
SBOLDocument document = SBOLFactory.createDocument();
document.addContent(createDnaComponent(xml, document));
return document;
}
