module Modelling::XPPModel

# File lib/modelling/xpp.rb, line 225
def _split_assignment_list(lstr)
    tokens = lstr.split(/[\s,;\n\r]+/)
    current = ""
    state = "n"
    ret = []
    tokens.each do |tok|
        case state
        when "n"
            if tok.match(/\=[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/)
                ret.push "#{tok}"
                current = ""
            elsif tok.match(/\=$/)
                current = "#{tok}="
                state = "v"
            else
                current = "#{tok}"
                state = "="
            end
        when "="
            if not tok.match(/^\=/)
                raise "invalid assignment list, expected '=', but got '#{tok}'"
            else
                current = current + tok
            end
            if tok.match(/\=[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/)
                state = "n"
                ret.push(current + tok)
                current = ""
            else
                state = "v"
            end
        when "v"
            ret.push(current + tok)
            current = ""
            state = "n"
        else
            raise "internal parsing error: unknown state #{state}"
        end
    end
    ret
end

# File lib/modelling/xpp.rb, line 9
def from_xpp(filename)
    lines = []
    current_line = ""
    cont = false
    # handle line continuations
    File.foreach(filename) do |line|
        if line.match(/^(.*)\\s*$/)
            current_line= current_line + $1
            cont = true
        else
            current_line= current_line + line
            cont = false
        end
        if not cont
            lines.push current_line
            current_line = ""
        end
    end
    if current_line != ""
        lines.push current_line
    end

    lines = lines.map { |e| e.strip  }

    last_comment = ""
    comment_used = false
    @xpp_extra = []
    lines.each do |l|
        # xpp options -- we don't really know what to do with them but save
        # them in case someone else does
        if l.match(/^[\"\@]/)
            @xpp_extra.push l unless l == ""
            if not comment_used and last_comment != ""
                if @notes == ""
                    @notes = @notes + "%%%%-cb-%%%%"
                end
                @notes = @notes + last_comment
            end
            last_comment = ""
            comment_used = false
            next
        end

        if l.match(/^(.*)\#(.*)$/)
            if comment_used
                last_comment = ""
                comment_used = false
            end
            last_comment = last_comment + $2
            l = $1
        end

        # parameters or numbers
        if l.match(/^[pn][a-zA-Z]*\s+([a-zA-Z].*)$/)
            ll = $1
            ps = _split_assignment_list(ll)
            ps.each do |pl|
                if pl.strip.match(/([a-zA-Z\_][a-zA-Z\_0-9]*)\s*\=\s*([0-9eE+\-\.]+)/)
                    @parameters[$1] = Parameter.new($1, $2.to_f, last_comment)
                elsif pl.strip.match(/([a-zA-Z\_][a-zA-Z\_0-9]*)/)
                    @parameters[$1] = Parameter.new($1, 0.0, last_comment)
                else
                    puts "[W] ignoring invalid parameter #{pl}\n"
                end
    #            puts "Par:  (#{@parameters[$1].to_s})\n"
            end
            comment_used = true
        elsif l.match(%r(d([a-zA-Z0-9\_]+)/dt\s*\=(.*)))
            pname = $1
            eqn = $2

            if !@species[pname]
                @species[pname] = Species.new(pname, 0.0)
            end

            @rules.push Rule.new(@species[pname], Equation.new(eqn, last_comment), 'rate')
            comment_used = true

    #        puts "dxdt:  (d#{@species[pname].to_s}/dt <- #{eqn})\n"
        # species rate rule of the form x' = ...
        elsif l.match(%r(([a-zA-Z0-9\_]+)'\s*\=(.*)))
            pname = $1
            eqn = $2

            if !@species[pname]
                @species[pname] = Species.new(pname, 0.0)
            end

            @rules.push Rule.new(@species[pname], Equation.new(eqn, last_comment), 'rate')
            comment_used = true

    #        puts "dxdt:  (d#{@species[pname].to_s}/dt <- #{eqn})\n"
        # aux vars and shortcuts are translated to scalar rules
        elsif l.match(/^([a][a-zA-Z]*\s+)?([a-zA-Z0-9][a-zA-Z0-9]*)\s*\=\s*(.+)/)
            pname = $2
            eqn = $3
            if not @parameters[pname]
                @parameters[pname] = Parameter.new(pname, 0.0, last_comment)
            end
    #        puts "aux:  (#{@parameters[pname].to_s} <- #{eqn})\n"
            @rules.push Rule.new(@parameters[pname], Equation.new(eqn, last_comment), 'scalar')
            comment_used = true
        # initial value assignment
        elsif l.match(/^i[a-zA-Z]*\s+([a-zA-Z0-9\_]+\s*\=.*)$/)
            ll = $1
            ps = _split_assignment_list(ll)
            ps.each do |pl|
                if pl.strip.match(/([a-zA-Z\_][a-zA-Z\_0-9]*)\s*\=\s*([0-9eE\+\-\.]+)/)
                    @species[$1] = Species.new($1, $2.to_f)
                elsif pl.strip.match(/([a-zA-Z\_][a-zA-Z\_0-9]*)/)
                    @species[$1] = Species.new($1, 0.0)
                else
                    puts "[W] ignoring invalid species #{pl}\n"
                end
    #            puts "X0i:  (#{@species[$1].to_s})\n"
            end
        # x(0) = ...
        elsif l.match(/^([a-zA-Z][a-zA-Z0-9\_]*)\(0\)\s*\=(.*)/)
            @species[$1] = Species.new($1, $2.to_f)
    #        puts "X0:  (#{@species[$1].to_s})\n"
        # single parameter assignments
        elsif l.match(/^!?([a-zA-Z][a-zA-Z0-9\_]*)\s*\=\s*(.*)/)
            pname = $1
            eqn = $2
            if eqn.strip.match(/^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/)
                @parameters[pname] = Parameter.new(pname, eqn.to_f, last_comment)
    #            puts "Par:  (#{@parameters[$1].to_s})\n"
            else
                if not @parameters[pname]
                    @parameters[pname] = Parameter.new(pname, 0.0, last_comment)
                end
                @rules.push Rule.new(@parameters[pname], Equation.new(eqn, last_comment), 'scalar')
    #            puts "auxa:  (#{@parameters[pname].to_s} <- #{eqn})\n"
            end
            comment_used = true
            # puts "X0:  (#{@parameters[$1].to_s})\n"
        elsif l == "done"
            break
        elsif l != ""
            puts "[W] unmatched xpp line: #{l}\n"
        end
    end
    if not comment_used and last_comment != ""
        if @notes == ""
            @notes = @notes + "%%%%-cb-%%%%"
        end
        @notes = @notes + last_comment
    end
    no = 1
    @species.each do |n, s|
        s.matlab_no=(no)
        no = no + 1
    end

    # fix rule outputs
    @rules.each do |r|
        if @species.key? r.output.name
            r.output=(@species[r.output.name])
        elsif @parameters.key? r.output.name
            r.output=(@parameters[r.output.name])
        else
            raise "invalid rule #{r} \n"
        end

    end

    self.validate
end

# File lib/modelling/xpp.rb, line 179
        def to_xpp(filename)
            if not filename.match(%r(.ode$))
                filename = filename + ".ode"
            end
            xextra = ""
            if @xpp_extra
                xextra = @xpp_extra.join("\n")
            end
            File.open("#{filename}", "w") do |f|
                f.puts <<-END
# #{@notes.gsub("%%%%-cb-%%%%", "\n# ")}

#{xextra}

END
                f.puts("# Parameters \n")
                f.puts("# ---------- \n\n")
                @parameters.each do |n,par|
                    if par.description
                        pcc = par.description.gsub("%%%%-cb-%%%%", "\n# ")
                        f.puts("# #{pcc}\n")
                    end
                    f.puts("par #{par.name} = #{par.value}\n")
                end
                f.puts("\n")
                f.puts("# Initial values \n")
                f.puts("# -------------- \n\n")
                @species.each do |n,spec|
                    f.puts("# y(#{spec.matlab_no}) \n")
                    f.puts("init #{spec.name} = #{spec.initial}\n")
                end
                f.puts("\n")
                f.puts("# Rules \n")
                f.puts("# ----- \n\n")
                @rules.each do |r|
                    eqc = r.equation.comments.gsub("%%%%-cb-%%%%", "\n# ")
                    f.puts "# #{eqc}\n"
                    f.puts "#{r.to_s}\n\n"
                end
            end
        end