module Modelling::SassyModel

# File lib/modelling/sassy.rb, line 15
        def from_sassy(basepath, parameters = nil, initvals = nil)
            # reset object
            initialize
            if parameters.nil?
                parameters = "#{basepath}.par"
            end
            if initvals.nil?
                initvals = "#{basepath}.y"
            end
            model = "#{basepath}_model.m"
            unless File.exists?(model) and File.exists?(parameters)
                raise "Both #{model} and #{parameters} must exist."
            end
            mdata = @@sassyparser.parse(File.read(model))
            if mdata.nil? or mdata.value.nil?
                raise <<-END
Error parsing #{model}, reason:
#{@@sassyparser.failure_reason}
#{@@sassyparser.failure_line}:#{@@sassyparser.failure_column}
END
            end
            mdata = mdata.value

            if @model == "" || @model.nil?
                @model = basepath.gsub(/^.*[\\/]/, "")
                if @model == ""
                    @model = "Imported from #{basepath}"
                end
            else
                @model = @model + " " + basepath.gsub(/^.*[\\/]/, "")
            end

            if @notes.nil?
                @notes = mdata[:comments_top]
            else
                @notes = @notes + mdata[:comments_top]
            end

            @sassy_extra = mdata[:sassyfooter]

            species_offset = @species.length

            mdata[:equations].each_with_index.map do |e, i|
                if @species["y_#{i+1}"]
                    raise "Duplicate species y_#{i+1}\n"
                end
                @species["y_#{i+1}"] = Species.new("y_#{i+1}", 0, i+1+species_offset)
            end

            @parameters['force'] = Parameter.new('force', 0, "SASSy force parameter")
            @parameters['dawn'] = Parameter.new('dawn', 6, "SASSy dawn parameter")
            @parameters['dusk'] = Parameter.new('dusk', 18, "SASSy dusk parameter")
            File.open(parameters, "r").each do |l|
                lspl = l.split(/\s+/)
                pname = lspl.shift
                pval = lspl.shift
                comment = lspl.join(" ").gsub(/^"/, "").gsub(/"$/, "").gsub(/\"/, "\"")
                if pname != 'force' and pname != 'dawn' and pname != 'dusk' and @parameters[pname]
                    puts "[W] Identical name for parameter #{pname}\n"
                end
                @parameters[pname] = Parameter.new(pname, pval.to_f, comment)
            end

            if File.exists?(initvals)
                File.open(initvals).each do |l|
                    l.match(/^y([0-9]+)\s+(.*)$/) {|m| @species["y_#{$1}"].initial=($2).to_f}
                end
            end

            # rename species
            eqns = mdata[:equations].map { |e| Equation.new(e[:equation], e[:comments]) }
            eqns.each do |eq|
                @species.each do |name, spec|
                    eq.replace_ident("y(#{spec.matlab_no})", spec.name)
                end
            end

            idx = -mdata[:rules].length
            mdata[:rules].each do |r|
                if @species.key? r[:output]
                    raise "Cannot assign species values in sassy rules"
                end
                if not @parameters.key? r[:output]
                    @parameters[r[:output]] = Parameter.new(r[:output], 0, r[:comment])
                end
                eq = Equation.new(r[:equation], r[:comment])
                @species.each do |name, spec|
                    eq.replace_ident("y(#{spec.matlab_no})", spec.name)
                end

                @rules.push (Rule.new(@parameters[r[:output]], eq, 'scalar'))
            end

            mdata[:equations].each_with_index.map { |e, i|
                 @rules.push (Rule.new(@species["y_#{i+1}"], eqns[i], 'rate'))
            }

            # fix parameters
            @parameters.each do |k, p|
                p.name=(k)
            end

            self.validate
            self
        end

# File lib/modelling/sassy.rb, line 124
        def to_sassy(basepath)
            File.open("#{basepath}.par", "w") do |f|
                @parameters.each do |n, p|
                    f.puts(p.to_par)
                end
            end
            File.open("#{basepath}.y", "w") do |f|
                mno = 1
                @species = (@species.sort {|x,y| x[1].matlab_no <=> y[1].matlab_no })
                @species.each do |n, sp|
                    f.puts("y#{sp.matlab_no} #{sp.initial}\n")
                    # redo matlab numbers
                    sp.matlab_no=(mno)
                    mno = mno + 1
                end
            end
            File.open("#{basepath}_model.m", "w") do |f|
                @rules.each do |rule|
                    if rule.type == 'scalar' and rule.output.kind_of?(Species)
                        raise "Cannot export scalar species rules to Sassy format"
                    end
                    if rule.type == 'rate' and rule.output.kind_of?(Parameter)
                        raise "Parameters cannot have rate rules"
                    end
                end
                f.puts <<-END
function dydt = f(t, y, p)

% #{@notes.gsub("%%%%-cb-%%%%", "\n% ")}

eval(p);

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.each do |n,s|
                            eq.replace_ident(s.name, "y(#{s.matlab_no})")
                        end
                        species_comments[rule.output.matlab_no] = eq.comments.gsub("%%%%-cb-%%%%", " ")
                        species_eqns[rule.output.matlab_no] = eq.to_s
                    end

                (@rules.reject { |e| e.output.kind_of? Species})                      .each do |rule|
                        eq = rule.equation.clone
                        @species.each do |n,s|
                            eq.replace_ident(s.name, "y(#{s.matlab_no})")
                        end

                        f.puts ("% " + eq.comments.gsub("%%%%-cb-%%%%", " ") + "\n#{rule.output.name} = "  + eq.to_s + ";\n")
                    end

                f.puts("\ndydt = [ \n")

                @species.each do |n,s|
                    if species_comments[s.matlab_no]
                        f.puts("     % #{species_comments[s.matlab_no]}\n")
                    end
                    if species_eqns[s.matlab_no]
                        f.puts("     #{species_eqns[s.matlab_no]} ;\n")
                    else
                        puts("[W] Species #{s.name} has no rate rule, setting to zero.")
                        f.puts("     0 ;\n")
                    end
                end
                formatted_sassy_extra = @sassy_extra.gsub("%%%%-cb-%%%%", "\n%")                      .gsub(/\n%$/, '')                       .gsub(/%([^%])/, '% \1')
                f.puts <<-END
]; 

% #{formatted_sassy_extra}

END
            end
        end