module Modelling::SBMLModel

# File lib/modelling/sbml.rb, line 90
def _comment_repl(value)
    " " + value.gsub(/\-\-+/, "") + " "
end

# File lib/modelling/sbml.rb, line 7
def to_sbml(name)
    File.open("#{name}", "w") do |file|
        doc = REXML::Document.new 

        top = REXML::Element.new "sbml"
        top.add_attributes ({ 
            "xmlns" => "http://www.sbml.org/sbml/level1",
            "level" => "1",
            "version" => "2"
        })

        model = REXML::Element.new("model")
        model.add_attribute('name', 'Exported_Model')
        
        if @notes.length > 0
            nel = REXML::Element.new("notes")
            nel.text = @notes.gsub("%%%%-cb-%%%%", "\n# ")
            model << nel
        end

        lc = REXML::Element.new "listOfCompartments"
        cm = REXML::Element.new "compartment"
        cm.add_attributes({ "name" => "cell", "volume" => "1"})
        lc << cm
        model << lc

        ls = REXML::Element.new "listOfSpecies"
        @species.each do |n,spec|
            s = REXML::Element.new "species"
            pcc = "y(#{spec.matlab_no})"
            s << REXML::Comment.new(_comment_repl(pcc))
            s.add_attributes({
                "name" => spec.name,
                "initialAmount" => spec.initial,
                "compartment" => "cell",
                "boundaryCondition" => "true"
                })
            ls << s
        end
        model << ls

        lp = REXML::Element.new "listOfParameters"
        @parameters.each do |n,par|
            p = REXML::Element.new "parameter"
            if par.description
                pcc = par.description.gsub("%%%%-cb-%%%%", "\n# ")
                p << REXML::Comment.new(_comment_repl(pcc))
            end
            p.add_attributes({
                "name" => par.name,
                "value" => par.value
                })
            lp << p
        end
        model << lp

        lr = REXML::Element.new "listOfRules"
        @rules.each do |r|
            rt = "speciesConcentrationRule"
            re = REXML::Element.new rt
            eqc = r.equation.comments.gsub("%%%%-cb-%%%%", "\n# ")
            re << REXML::Comment.new(_comment_repl(eqc))
            re.add_attributes({
                "species" => r.output.name,
                "type" => r.type,
                "formula" => r.equation.to_s
                })
            lr << re
        end
        model << lr

        top << model

        doc << REXML::XMLDecl.new(1.0, "utf-8")
        doc << top

        # Write to file
        formatter = REXML::Formatters::Pretty.new(5)
        formatter.write(doc, file)
    end
end