module Modelling::VFGenModel

# File lib/modelling/vfgen.rb, line 9
def to_vfgen(basepath)
    File.open("#{basepath}", "w") do |f|
        mname = basepath.gsub(%r((.*[\/])?([^/\]+)$), "\\2").gsub(%r(\.vf$), "").gsub(%r([^A-Za-z0-9\-\_]), "_")
        doc = REXML::Document.new 

        top = REXML::Element.new "VectorField"
        top.add_attributes({
            "Name" => mname,
            "Description" => @notes.gsub("%%%%-cb-%%%%", " ")
            })

        mno = 1
        @species = (@species.sort {|x,y| x[1].matlab_no <=> y[1].matlab_no })
        @species.each do |n, sp|
            # redo matlab numbers
            sp.matlab_no=(mno)
            mno = mno + 1
        end

        @rules.each do |rule|
            if rule.type == 'rate' and rule.output.kind_of?(Parameter)
                raise "Parameters cannot have rate rules"
            end
        end

        species_eqns = []
        species_comments = []
        ((@rules.reject { |e| e.output.kind_of? Parameter})                      .sort {|x,y| x.output.matlab_no <=> y.output.matlab_no})                      .each do |rule|
                eq = rule.equation.clone

                species_comments[rule.output.matlab_no] = eq.comments.gsub("%%%%-cb-%%%%", " ")
                species_eqns[rule.output.matlab_no] = eq.to_s
            end

        para_has_rule = {}

        (@rules.reject { |e| e.output.kind_of? Species})                      .each do |rule|
                eq = rule.equation.clone
                eqstr = eq.to_s

                rel = REXML::Element.new "Expression"
                rel.add_attributes({
                    "Name" => rule.output.name,
                    "Formula" => eqstr,
                    "Description" => eq.comments.gsub("%%%%-cb-%%%%", " ")
                    })

                top << rel

                para_has_rule[rule.output.name] = 1
            end

        (@parameters.reject {|p| para_has_rule[p]}).each do |p, par|

            rel = REXML::Element.new "Parameter"

            if par.description
                pcc = par.description.gsub("%%%%-cb-%%%%", "\n# ")
            else
                pcc = ""
            end

            rel.add_attributes({
                "Name" => par.name,
                "DefaultValue" => par.value,
                "Description" => pcc
                })

            top << rel
        end

        @species.each do |n,s|
            pcc = ""
            if species_comments[s.matlab_no]
                pcc = species_comments[s.matlab_no]
            end
            
            speq = "0"
            if species_eqns[s.matlab_no]
                speq = species_eqns[s.matlab_no]
            else
                puts("[W] Species #{s.name} has no rate rule, setting to zero.")
            end
            rel = REXML::Element.new "StateVariable"

            rel.add_attributes({
                "Name" => s.name,
                "DefaultInitialCondition" => s.initial,
                "Formula" => speq,
                "Description" => pcc
                })

            top << rel

        end

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

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