Difference between revisions of "InterMine Presentation"

public class BakeOff {
    public static void main(String[] args) throws Exception {
        // code to get the "xfile" gene
        ObjectStore os = ObjectStoreFactory.getObjectStore("os.production");
        Query q = new Query();
        QueryClass qcObj = new QueryClass(Gene.class);
        q.addFrom(qcObj);
        QueryField qf = new QueryField(qcObj, "identifier");
        q.addToSelect(qf);
        SimpleConstraint sc = new SimpleConstraint(qf, ConstraintOp.EQUALS, new QueryValue("xfile"));
        q.setConstraint(sc);
        System.err.println("query: " + q);
        Results res = os.execute(q);
 
        // a Results object is a List of Lists
        List rr = (List) res.get(0);
        Gene gene = (Gene) rr.get(0);
 
        System.err.println ("symbol: " + gene.getIdentifier());
 
        // a BioEntity in FlyMine has a collection of Synonym objects -
        // we need Synonym.value for each Synonym
        System.err.print ("synonyms: ");
        Iterator synIter = gene.getSynonyms().iterator();
        while (synIter.hasNext()) {
            Synonym syn = (Synonym) synIter.next();
            System.err.print (syn.getValue() + ' ');
        }
 
        System.err.println ("description: " + gene.getDescription());
 
        // get the class name, but we already know that the gene is a Gene
        System.err.println ("type: " + gene.getClass().getName());
 
        // make a List from a the Set of exons for this Gene
        List exons = new ArrayList(gene.getExons());
        Exon exon1 = (Exon) exons.get(0);
        Exon exon2 = (Exon) exons.get(1);
 
        // get the start and end via the Location object
        System.err.println ("exon1 start: " + exon1.getChromosomeLocation().getStart());
        System.err.println ("exon1 end: " + exon1.getChromosomeLocation().getEnd());
        System.err.println ("exon2 start: " + exon2.getChromosomeLocation().getStart());
        System.err.println ("exon2 end: " + exon2.getChromosomeLocation().getEnd());
 
        // write out the first cds
        List cdss = new ArrayList(gene.getCDSs());
        FlyMineSequence flymineSequence = FlyMineSequenceFactory.make((CDS) cdss.get(0));
 
        // use BioJava to output the sequence
        Annotation annotation = flymineSequence.getAnnotation();
        annotation.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE,
                               gene.getIdentifier() + " cds");
        SeqIOTools.writeFasta(System.err, flymineSequence);
    }
}

  Query q = new Query();
  QueryClass qcObj = new QueryClass(Gene.class);
  q.addFrom(qcObj);
  q.addToSelect(qcObj);
 
  QueryField qf = new QueryField(qcObj, "identifier");
 
  SimpleConstraint sc = new SimpleConstraint(qf, ConstraintOp.MATCHES, new QueryValue("x-%"));
  q.setConstraint(sc);