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 =2;
end
% There are a total of 1 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 (minute)');
    LEGEND_CONSTANTS(:,13) = strpad('F16BP in component F16BP (millimolar)');
    LEGEND_STATES(:,1) = strpad('G3P in component G3P (millimolar)');
    LEGEND_ALGEBRAIC(:,1) = strpad('V_Gpd_p in component V_Gpd_p (flux)');
    LEGEND_ALGEBRAIC(:,2) = strpad('V_Gpp_p in component V_Gpp_p (flux)');
    LEGEND_CONSTANTS(:,14) = strpad('DHAP in component DHAP (millimolar)');
    LEGEND_CONSTANTS(:,15) = strpad('ATP in component ATP (millimolar)');
    LEGEND_CONSTANTS(:,16) = strpad('ADP in component ADP (millimolar)');
    LEGEND_CONSTANTS(:,17) = strpad('NADH in component NADH (millimolar)');
    LEGEND_CONSTANTS(:,18) = strpad('NAD in component NAD (millimolar)');
    LEGEND_CONSTANTS(:,19) = strpad('Pi_ in component Pi (millimolar)');
    LEGEND_CONSTANTS(:,1) = strpad('K_F16BP in component V_Gpd_p (millimolar)');
    LEGEND_CONSTANTS(:,2) = strpad('K_ATP in component V_Gpd_p (millimolar)');
    LEGEND_CONSTANTS(:,3) = strpad('K_ADP in component V_Gpd_p (millimolar)');
    LEGEND_CONSTANTS(:,4) = strpad('K_NAD in component V_Gpd_p (millimolar)');
    LEGEND_CONSTANTS(:,5) = strpad('K_NADH in component V_Gpd_p (millimolar)');
    LEGEND_CONSTANTS(:,6) = strpad('K_G3P in component V_Gpd_p (millimolar)');
    LEGEND_CONSTANTS(:,7) = strpad('K_DHAP in component V_Gpd_p (millimolar)');
    LEGEND_CONSTANTS(:,8) = strpad('K_eq in component V_Gpd_p (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('Vf in component V_Gpd_p (flux)');
    LEGEND_CONSTANTS(:,10) = strpad('K_G3P in component V_Gpp_p (millimolar)');
    LEGEND_CONSTANTS(:,11) = strpad('K_Pi in component V_Gpp_p (millimolar)');
    LEGEND_CONSTANTS(:,12) = strpad('V in component V_Gpp_p (flux)');
    LEGEND_RATES(:,1) = strpad('d/dt G3P in component G3P (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) = 24;
    CONSTANTS(:,1) = 4.8;
    CONSTANTS(:,2) = 0.73;
    CONSTANTS(:,3) = 2;
    CONSTANTS(:,4) = 0.93;
    CONSTANTS(:,5) = 0.023;
    CONSTANTS(:,6) = 1.2;
    CONSTANTS(:,7) = 0.54;
    CONSTANTS(:,8) = 1e4;
    CONSTANTS(:,9) = 36;
    CONSTANTS(:,10) = 3.5;
    CONSTANTS(:,11) = 1;
    CONSTANTS(:,12) = 18;
    CONSTANTS(:,13) = 0.00000;
    CONSTANTS(:,14) = 0.590000;
    CONSTANTS(:,15) = 2.37000;
    CONSTANTS(:,16) = 2.17000;
    CONSTANTS(:,17) = 1.87000;
    CONSTANTS(:,18) = 1.45000;
    CONSTANTS(:,19) = 2.17000;
    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
    ALGEBRAIC(:,1) = ( (CONSTANTS(:,9)./( CONSTANTS(:,5).*CONSTANTS(:,7))).*( CONSTANTS(:,17).*CONSTANTS(:,14) - ( CONSTANTS(:,18).*STATES(:,1))./CONSTANTS(:,8)))./( (1.00000+CONSTANTS(:,13)./CONSTANTS(:,1)+CONSTANTS(:,15)./CONSTANTS(:,2)+CONSTANTS(:,16)./CONSTANTS(:,3)).*(1.00000+CONSTANTS(:,17)./CONSTANTS(:,5)+CONSTANTS(:,18)./CONSTANTS(:,4)).*(1.00000+CONSTANTS(:,14)./CONSTANTS(:,7)+STATES(:,1)./CONSTANTS(:,6)));
    ALGEBRAIC(:,2) = (( CONSTANTS(:,12).*STATES(:,1))./CONSTANTS(:,10))./( (1.00000+STATES(:,1)./CONSTANTS(:,10)).*(1.00000+CONSTANTS(:,19)./CONSTANTS(:,11)));
    RATES(:,1) =  - ALGEBRAIC(:,2)+ALGEBRAIC(:,1);
   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) = ( (CONSTANTS(:,9)./( CONSTANTS(:,5).*CONSTANTS(:,7))).*( CONSTANTS(:,17).*CONSTANTS(:,14) - ( CONSTANTS(:,18).*STATES(:,1))./CONSTANTS(:,8)))./( (1.00000+CONSTANTS(:,13)./CONSTANTS(:,1)+CONSTANTS(:,15)./CONSTANTS(:,2)+CONSTANTS(:,16)./CONSTANTS(:,3)).*(1.00000+CONSTANTS(:,17)./CONSTANTS(:,5)+CONSTANTS(:,18)./CONSTANTS(:,4)).*(1.00000+CONSTANTS(:,14)./CONSTANTS(:,7)+STATES(:,1)./CONSTANTS(:,6)));
    ALGEBRAIC(:,2) = (( CONSTANTS(:,12).*STATES(:,1))./CONSTANTS(:,10))./( (1.00000+STATES(:,1)./CONSTANTS(:,10)).*(1.00000+CONSTANTS(:,19)./CONSTANTS(:,11)));
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