function [VOI, STATES, ALGEBRAIC, CONSTANTS] = mainFunction()
    % This is the "main function".  In Matlab, things work best if you rename this function to match the filename.
   [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel();
end

function [algebraicVariableCount] = getAlgebraicVariableCount() 
    % Used later when setting a global variable with the number of algebraic variables.
    % Note: This is not the "main method".  
    algebraicVariableCount =17;
end
% There are a total of 10 entries in each of the rate and state variable arrays.
% There are a total of 19 entries in the constant variable array.
%

function [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel()
    % Create ALGEBRAIC of correct size
    global algebraicVariableCount;  algebraicVariableCount = getAlgebraicVariableCount();
    % Initialise constants and state variables
    [INIT_STATES, CONSTANTS] = initConsts;

    % Set timespan to solve over 
    tspan = [0, 10];

    % Set numerical accuracy options for ODE solver
    options = odeset('RelTol', 1e-06, 'AbsTol', 1e-06, 'MaxStep', 1);

    % Solve model with ODE solver
    [VOI, STATES] = ode15s(@(VOI, STATES)computeRates(VOI, STATES, CONSTANTS), tspan, INIT_STATES, options);

    % Compute algebraic variables
    [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS);
    ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI);

    % Plot state variables against variable of integration
    [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends();
    figure();
    plot(VOI, STATES);
    xlabel(LEGEND_VOI);
    l = legend(LEGEND_STATES);
    set(l,'Interpreter','none');
end

function [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends()
    LEGEND_STATES = ''; LEGEND_ALGEBRAIC = ''; LEGEND_VOI = ''; LEGEND_CONSTANTS = '';
    LEGEND_VOI = strpad('time in component environment (second)');
    LEGEND_STATES(:,1) = strpad('C_6PG in component C_6PG (millimolar)');
    LEGEND_CONSTANTS(:,1) = strpad('mu in component model_constants (per_hour)');
    LEGEND_ALGEBRAIC(:,4) = strpad('rG6PDH in component rG6PDH (flux)');
    LEGEND_ALGEBRAIC(:,10) = strpad('r6PGDH in component r6PGDH (flux)');
    LEGEND_STATES(:,2) = strpad('C_Ru5P in component C_Ru5P (millimolar)');
    LEGEND_ALGEBRAIC(:,12) = strpad('rRu5PE in component rRu5PE (flux)');
    LEGEND_ALGEBRAIC(:,11) = strpad('rR5PI in component rR5PI (flux)');
    LEGEND_STATES(:,3) = strpad('C_R5P in component C_R5P (millimolar)');
    LEGEND_ALGEBRAIC(:,13) = strpad('rTKL1 in component rTKL1 (flux)');
    LEGEND_ALGEBRAIC(:,14) = strpad('rRPPK in component rRPPK (flux)');
    LEGEND_STATES(:,4) = strpad('C_X5P in component C_X5P (millimolar)');
    LEGEND_ALGEBRAIC(:,16) = strpad('rTKL2 in component rTKL2 (flux)');
    LEGEND_STATES(:,5) = strpad('C_S7P in component C_S7P (millimolar)');
    LEGEND_ALGEBRAIC(:,15) = strpad('rTAL in component rTAL (flux)');
    LEGEND_STATES(:,6) = strpad('C_E4P in component C_E4P (millimolar)');
    LEGEND_ALGEBRAIC(:,17) = strpad('rPKDA in component rPKDA (flux)');
    LEGEND_STATES(:,7) = strpad('C_G6P in component C_G6P (millimolar)');
    LEGEND_ALGEBRAIC(:,1) = strpad('dC_G6P_dt in component C_G6P (flux)');
    LEGEND_STATES(:,8) = strpad('C_NADP in component C_NADP (millimolar)');
    LEGEND_STATES(:,9) = strpad('C_NADPH in component C_NADPH (millimolar)');
    LEGEND_STATES(:,10) = strpad('C_MgATP in component C_MgATP (millimolar)');
    LEGEND_CONSTANTS(:,2) = strpad('K_NADP_1 in component rG6PDH (millimolar)');
    LEGEND_CONSTANTS(:,3) = strpad('Ki_NADPH_1 in component rG6PDH (millimolar)');
    LEGEND_CONSTANTS(:,4) = strpad('Ki_MgATP_1 in component rG6PDH (millimolar)');
    LEGEND_ALGEBRAIC(:,2) = strpad('I_NADPH_1 in component rG6PDH (dimensionless)');
    LEGEND_ALGEBRAIC(:,3) = strpad('I_MgATP_1 in component rG6PDH (dimensionless)');
    LEGEND_CONSTANTS(:,5) = strpad('rmax_G6PDH in component rG6PDH (flux)');
    LEGEND_CONSTANTS(:,6) = strpad('K_NADP_2 in component r6PGDH (millimolar)');
    LEGEND_CONSTANTS(:,7) = strpad('Ki_NADPH_2 in component r6PGDH (millimolar)');
    LEGEND_CONSTANTS(:,8) = strpad('Ki_MgATP_2 in component r6PGDH (millimolar)');
    LEGEND_ALGEBRAIC(:,5) = strpad('I_NADPH_2 in component r6PGDH (dimensionless)');
    LEGEND_ALGEBRAIC(:,7) = strpad('I_MgATP_2 in component r6PGDH (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('rmax_6PGDH in component r6PGDH (flux)');
    LEGEND_CONSTANTS(:,10) = strpad('rmax_R5PI in component rR5PI (millimole_per_second)');
    LEGEND_CONSTANTS(:,11) = strpad('rmax_Ru5PE in component rRu5PE (millimole_per_second)');
    LEGEND_CONSTANTS(:,12) = strpad('rmax_TKL1 in component rTKL1 (millimole_per_second)');
    LEGEND_CONSTANTS(:,13) = strpad('C_GAP in component model_constants (millimolar)');
    LEGEND_CONSTANTS(:,14) = strpad('rmax_TAL in component rTAL (millimole_per_second)');
    LEGEND_CONSTANTS(:,15) = strpad('rmax_TKL2 in component rTKL2 (millimole_per_second)');
    LEGEND_CONSTANTS(:,16) = strpad('K_PKDA in component rPKDA (millimolar)');
    LEGEND_CONSTANTS(:,17) = strpad('rmax_PKDA in component rPKDA (millimole_per_second)');
    LEGEND_CONSTANTS(:,18) = strpad('K_RPPK in component rRPPK (millimolar)');
    LEGEND_CONSTANTS(:,19) = strpad('rmax_RPPK in component rRPPK (millimole_per_second)');
    LEGEND_ALGEBRAIC(:,8) = strpad('rHK in component rHK (flux)');
    LEGEND_ALGEBRAIC(:,6) = strpad('qs in component model_constants (flux)');
    LEGEND_ALGEBRAIC(:,9) = strpad('rPGI in component rPGI (flux)');
    LEGEND_RATES(:,1) = strpad('d/dt C_6PG in component C_6PG (millimolar)');
    LEGEND_RATES(:,2) = strpad('d/dt C_Ru5P in component C_Ru5P (millimolar)');
    LEGEND_RATES(:,3) = strpad('d/dt C_R5P in component C_R5P (millimolar)');
    LEGEND_RATES(:,4) = strpad('d/dt C_X5P in component C_X5P (millimolar)');
    LEGEND_RATES(:,5) = strpad('d/dt C_S7P in component C_S7P (millimolar)');
    LEGEND_RATES(:,6) = strpad('d/dt C_E4P in component C_E4P (millimolar)');
    LEGEND_RATES(:,7) = strpad('d/dt C_G6P in component C_G6P (millimolar)');
    LEGEND_RATES(:,8) = strpad('d/dt C_NADP in component C_NADP (millimolar)');
    LEGEND_RATES(:,9) = strpad('d/dt C_NADPH in component C_NADPH (millimolar)');
    LEGEND_RATES(:,10) = strpad('d/dt C_MgATP in component C_MgATP (millimolar)');
    LEGEND_STATES  = LEGEND_STATES';
    LEGEND_ALGEBRAIC = LEGEND_ALGEBRAIC';
    LEGEND_RATES = LEGEND_RATES';
    LEGEND_CONSTANTS = LEGEND_CONSTANTS';
end

function [STATES, CONSTANTS] = initConsts()
    VOI = 0; CONSTANTS = []; STATES = []; ALGEBRAIC = [];
    STATES(:,1) = 0.25;
    CONSTANTS(:,1) = 1.0;
    STATES(:,2) = 0.033;
    STATES(:,3) = 0.118;
    STATES(:,4) = 0.041;
    STATES(:,5) = 0.082;
    STATES(:,6) = 0.029;
    STATES(:,7) = 0.9;
    STATES(:,8) = 0.168;
    STATES(:,9) = 0.168;
    STATES(:,10) = 2.3;
    CONSTANTS(:,2) = 0.116;
    CONSTANTS(:,3) = 1.702;
    CONSTANTS(:,4) = 0.33;
    CONSTANTS(:,5) = 44.19;
    CONSTANTS(:,6) = 1.848;
    CONSTANTS(:,7) = 0.055;
    CONSTANTS(:,8) = 0.109;
    CONSTANTS(:,9) = 0.654;
    CONSTANTS(:,10) = 0.57;
    CONSTANTS(:,11) = 0.85;
    CONSTANTS(:,12) = 3.24;
    CONSTANTS(:,13) = 0.064;
    CONSTANTS(:,14) = 3.0;
    CONSTANTS(:,15) = 10.5;
    CONSTANTS(:,16) = 0.0032;
    CONSTANTS(:,17) = 0.004;
    CONSTANTS(:,18) = 0.0034;
    CONSTANTS(:,19) = 0.003;
    if (isempty(STATES)), warning('Initial values for states not set');, end
end

function [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS)
    global algebraicVariableCount;
    statesSize = size(STATES);
    statesColumnCount = statesSize(2);
    if ( statesColumnCount == 1)
        STATES = STATES';
        ALGEBRAIC = zeros(1, algebraicVariableCount);
        utilOnes = 1;
    else
        statesRowCount = statesSize(1);
        ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
        RATES = zeros(statesRowCount, statesColumnCount);
        utilOnes = ones(statesRowCount, 1);
    end
    RATES(:,8) = -1.48000./(9.17000+ 16.1000.*VOI+ 0.480000.*power(VOI, 2.00000))+ (( 1.48000.*VOI)./( (9.17000+ 16.1000.*VOI+ 0.480000.*power(VOI, 2.00000)).*(9.17000+ 16.1000.*VOI+ 0.480000.*power(VOI, 2.00000)))).*(16.1000+ 0.960000.*VOI);
    RATES(:,9) = 0.516000./(25.3900+ 0.370000.*VOI+ 0.500000.*power(VOI, 2.00000)) -  (( 0.516000.*VOI)./( (25.3900+ 0.370000.*VOI+ 0.500000.*power(VOI, 2.00000)).*(25.3900+ 0.370000.*VOI+ 0.500000.*power(VOI, 2.00000)))).*(0.370000+ 1.00000.*VOI);
    RATES(:,10) = 29.8300./(29.7700+ 13.4200.*VOI+ 0.0500000.*power(VOI, 2.00000)) -  (( 29.8300.*VOI)./( (29.7700+ 13.4200.*VOI+ 0.0500000.*power(VOI, 2.00000)).*(29.7700+ 13.4200.*VOI+ 0.0500000.*power(VOI, 2.00000)))).*(13.4200+ 0.100000.*VOI);
    ALGEBRAIC(:,1) = 44.1000./(48.0000+ 1.00000.*VOI+ 0.450000.*power(VOI, 2.00000))+ (( 44.1000.*VOI)./( (48.0000+ 1.00000.*VOI+ 0.450000.*power(VOI, 2.00000)).*(48.0000+ 1.00000.*VOI+ 0.450000.*power(VOI, 2.00000)))).*(1.00000+ 0.900000.*VOI);
    RATES(:,7) = ALGEBRAIC(:,1);
    ALGEBRAIC(:,2) = 1.00000+STATES(:,9)./CONSTANTS(:,3);
    ALGEBRAIC(:,3) = 1.00000+STATES(:,10)./CONSTANTS(:,4);
    ALGEBRAIC(:,4) =  CONSTANTS(:,5).*(STATES(:,8)./( (STATES(:,8)+ CONSTANTS(:,2).*ALGEBRAIC(:,2)).*ALGEBRAIC(:,3)));
    ALGEBRAIC(:,5) = 1.00000+STATES(:,9)./CONSTANTS(:,7);
    ALGEBRAIC(:,7) = 1.00000+STATES(:,10)./CONSTANTS(:,8);
    ALGEBRAIC(:,10) =  CONSTANTS(:,9).*(STATES(:,8)./( (STATES(:,8)+ CONSTANTS(:,6).*ALGEBRAIC(:,5)).*ALGEBRAIC(:,7)));
    RATES(:,1) = ALGEBRAIC(:,4) - (ALGEBRAIC(:,10)+ CONSTANTS(:,1).*STATES(:,1));
    ALGEBRAIC(:,12) =  1.00000.*CONSTANTS(:,11).*STATES(:,2);
    ALGEBRAIC(:,11) =  1.00000.*CONSTANTS(:,10).*STATES(:,2);
    RATES(:,2) = ALGEBRAIC(:,10) - (ALGEBRAIC(:,11)+ALGEBRAIC(:,12)+ CONSTANTS(:,1).*STATES(:,2));
    ALGEBRAIC(:,13) =  1.00000.*CONSTANTS(:,12).*STATES(:,4).*STATES(:,3);
    ALGEBRAIC(:,14) =  1.00000.*CONSTANTS(:,19).*(STATES(:,3)./(STATES(:,3)+CONSTANTS(:,18)));
    RATES(:,3) = ALGEBRAIC(:,11) - (ALGEBRAIC(:,13)+ALGEBRAIC(:,14)+ CONSTANTS(:,1).*STATES(:,3));
    ALGEBRAIC(:,15) =  1.00000.*CONSTANTS(:,14).*CONSTANTS(:,13).*STATES(:,5);
    RATES(:,5) = ALGEBRAIC(:,13) - (ALGEBRAIC(:,15)+ CONSTANTS(:,1).*STATES(:,5));
    ALGEBRAIC(:,16) =  1.00000.*CONSTANTS(:,15).*STATES(:,6).*STATES(:,4);
    RATES(:,4) = ALGEBRAIC(:,12) - (ALGEBRAIC(:,13)+ALGEBRAIC(:,16)+ CONSTANTS(:,1).*STATES(:,4));
    ALGEBRAIC(:,17) =  1.00000.*CONSTANTS(:,17).*(STATES(:,6)./(STATES(:,6)+CONSTANTS(:,16)));
    RATES(:,6) = ALGEBRAIC(:,15) - (ALGEBRAIC(:,16)+ALGEBRAIC(:,17)+ CONSTANTS(:,1).*STATES(:,6));
   RATES = RATES';
end

% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
    statesSize = size(STATES);
    statesColumnCount = statesSize(2);
    if ( statesColumnCount == 1)
        STATES = STATES';
        utilOnes = 1;
    else
        statesRowCount = statesSize(1);
        utilOnes = ones(statesRowCount, 1);
    end
    ALGEBRAIC(:,1) = 44.1000./(48.0000+ 1.00000.*VOI+ 0.450000.*power(VOI, 2.00000))+ (( 44.1000.*VOI)./( (48.0000+ 1.00000.*VOI+ 0.450000.*power(VOI, 2.00000)).*(48.0000+ 1.00000.*VOI+ 0.450000.*power(VOI, 2.00000)))).*(1.00000+ 0.900000.*VOI);
    ALGEBRAIC(:,2) = 1.00000+STATES(:,9)./CONSTANTS(:,3);
    ALGEBRAIC(:,3) = 1.00000+STATES(:,10)./CONSTANTS(:,4);
    ALGEBRAIC(:,4) =  CONSTANTS(:,5).*(STATES(:,8)./( (STATES(:,8)+ CONSTANTS(:,2).*ALGEBRAIC(:,2)).*ALGEBRAIC(:,3)));
    ALGEBRAIC(:,5) = 1.00000+STATES(:,9)./CONSTANTS(:,7);
    ALGEBRAIC(:,7) = 1.00000+STATES(:,10)./CONSTANTS(:,8);
    ALGEBRAIC(:,10) =  CONSTANTS(:,9).*(STATES(:,8)./( (STATES(:,8)+ CONSTANTS(:,6).*ALGEBRAIC(:,5)).*ALGEBRAIC(:,7)));
    ALGEBRAIC(:,12) =  1.00000.*CONSTANTS(:,11).*STATES(:,2);
    ALGEBRAIC(:,11) =  1.00000.*CONSTANTS(:,10).*STATES(:,2);
    ALGEBRAIC(:,13) =  1.00000.*CONSTANTS(:,12).*STATES(:,4).*STATES(:,3);
    ALGEBRAIC(:,14) =  1.00000.*CONSTANTS(:,19).*(STATES(:,3)./(STATES(:,3)+CONSTANTS(:,18)));
    ALGEBRAIC(:,15) =  1.00000.*CONSTANTS(:,14).*CONSTANTS(:,13).*STATES(:,5);
    ALGEBRAIC(:,16) =  1.00000.*CONSTANTS(:,15).*STATES(:,6).*STATES(:,4);
    ALGEBRAIC(:,17) =  1.00000.*CONSTANTS(:,17).*(STATES(:,6)./(STATES(:,6)+CONSTANTS(:,16)));
    ALGEBRAIC(:,6) = piecewise({VOI<0.00000, 0.131000 }, 0.546000);
    ALGEBRAIC(:,8) = ALGEBRAIC(:,6);
    ALGEBRAIC(:,9) = ALGEBRAIC(:,6) - (ALGEBRAIC(:,4)+ CONSTANTS(:,1).*STATES(:,7)+ALGEBRAIC(:,1));
end

% Compute result of a piecewise function
function x = piecewise(cases, default)
    set = [0];
    for i = 1:2:length(cases)
        if (length(cases{i+1}) == 1)
            x(cases{i} & ~set,:) = cases{i+1};
        else
            x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set);
        end
        set = set | cases{i};
        if(set), break, end
    end
    if (length(default) == 1)
        x(~set,:) = default;
    else
        x(~set,:) = default(~set);
    end
end

% Pad out or shorten strings to a set length
function strout = strpad(strin)
    req_length = 160;
    insize = size(strin,2);
    if insize > req_length
        strout = strin(1:req_length);
    else
        strout = [strin, blanks(req_length - insize)];
    end
end