from elementtree.SimpleXMLWriter import XMLWriter
import biogeneutil
import sys

class grimm_to_xml:
    def __init__(self, network, xmlfile):
        """ constructor to generate xml file from gene rearrangement data
        network -- RearrangementNetwork to create XML from
        xmlfile -- name of xmlfile to output to """
        fxml = open(xmlfile,'w')
        writer = XMLWriter(fxml, 'utf-8')
        xmlout = writer.start("gene-rearrangement-network")        
        for n in network:
            stepnum = str(n.get_grimmaction().get_step())
            writer.start("rearrangement-step", step=stepnum)            
            for a in n.get_annotations():
                chrname = a.get_chrcontig()
                txtchr = str(a.chrlist)
                writer.start("chromosome", name=chrname)                
                writer.data(txtchr)
                writer.end()
            writer.end("rearrangement-step")
        writer.end("gene-rearrangement-network")
        writer.close(xmlout)

if __name__ == "__main__":
    from elementtree.SimpleXMLWriter import XMLWriter
    import sys

    w = XMLWriter(sys.stdout)

    html = w.start("html")

    w.start("head")
    w.element("title", "my document")
    w.element("meta", name="generator", value="my application 1.0")
    w.end()

    w.start("body")
    w.element("h1", "this is a heading")
    w.element("p", "this is a paragraph")

    w.start("p")
    w.data("this is ")
    w.element("b", "bold")
    w.data(" and ")
    w.element("i", "italic")
    w.data(".")
    w.end("p")

    w.close(html)