IDMapperOrthoXml.java 文件源码

private void readMappings(Reader in) throws FileNotFoundException, XMLStreamException, XMLParseException
{
    //open the orthoXML for reading
    OrthoXMLReader reader = new OrthoXMLReader(in);

    // get species from reader
    for (Species species : reader.getSpecies())
    {
        System.out.printf(species.getName() + "\t");
        System.out.printf(species.getNcbiTaxId() + "\t");
    }
    System.out.printf("#");
    //read the group iteratively
    Group group;

    while ((group = reader.next()) != null)
    {       
        Set<Xref> groupRefs = new HashSet<Xref>();

        for(Gene gene : group.getNestedGenes())
        {
            Database database = gene.getDatabase();

            DataSource ds = aliases.get(database.getName());
            if (ds == null) ds = DataSource.getByFullName(database.getName());

            dataSources.add(ds);
            groupRefs.add (new Xref(gene.getGeneIdentifier(), ds));
            groupRefs.add (new Xref(gene.getProteinIdentifier(), ds));      
        }

        for (Xref ref : groupRefs)
        {
            allIds.put (ref, groupRefs);
        }           
    }
}