Generated Code

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 =0;
end
% There are a total of 9 entries in each of the rate and state variable arrays.
% There are a total of 11 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 (hour)');
    LEGEND_STATES(:,1) = strpad('Pfr in component Pfr (micromolar)');
    LEGEND_STATES(:,2) = strpad('Pr in component Pr (micromolar)');
    LEGEND_CONSTANTS(:,1) = strpad('Ifr_sigma_fr_phi_fr in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,2) = strpad('Ir_sigma_r_phi_r in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,3) = strpad('kd in component Pr (first_order_rate_constant)');
    LEGEND_STATES(:,3) = strpad('Xi in component Xi (micromolar)');
    LEGEND_STATES(:,4) = strpad('Xa in component Xa (micromolar)');
    LEGEND_CONSTANTS(:,4) = strpad('kia in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,5) = strpad('kai in component model_parameters (first_order_rate_constant)');
    LEGEND_STATES(:,5) = strpad('prepreS in component prepreS (micromolar)');
    LEGEND_CONSTANTS(:,6) = strpad('kx in component model_parameters (second_order_rate_constant)');
    LEGEND_STATES(:,6) = strpad('preS in component preS (micromolar)');
    LEGEND_STATES(:,7) = strpad('Ya in component Ya (micromolar)');
    LEGEND_CONSTANTS(:,7) = strpad('ky in component model_parameters (second_order_rate_constant)');
    LEGEND_STATES(:,8) = strpad('S in component S (micromolar)');
    LEGEND_CONSTANTS(:,8) = strpad('alpha1 in component S (micromolar)');
    LEGEND_STATES(:,9) = strpad('V in component V (micromolar)');
    LEGEND_CONSTANTS(:,9) = strpad('alpha2 in component V (micromolar)');
    LEGEND_CONSTANTS(:,10) = strpad('kG in component Ya (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,11) = strpad('glucose in component model_parameters (micromolar)');
    LEGEND_RATES(:,1) = strpad('d/dt Pfr in component Pfr (micromolar)');
    LEGEND_RATES(:,2) = strpad('d/dt Pr in component Pr (micromolar)');
    LEGEND_RATES(:,3) = strpad('d/dt Xi in component Xi (micromolar)');
    LEGEND_RATES(:,4) = strpad('d/dt Xa in component Xa (micromolar)');
    LEGEND_RATES(:,5) = strpad('d/dt prepreS in component prepreS (micromolar)');
    LEGEND_RATES(:,6) = strpad('d/dt preS in component preS (micromolar)');
    LEGEND_RATES(:,8) = strpad('d/dt S in component S (micromolar)');
    LEGEND_RATES(:,9) = strpad('d/dt V in component V (micromolar)');
    LEGEND_RATES(:,7) = strpad('d/dt Ya in component Ya (micromolar)');
    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) = 10.0;
    STATES(:,2) = 0.0;
    CONSTANTS(:,1) = 0.1;
    CONSTANTS(:,2) = 0.0;
    CONSTANTS(:,3) = 0.1;
    STATES(:,3) = 6.0;
    STATES(:,4) = 0.0;
    CONSTANTS(:,4) = 0.1;
    CONSTANTS(:,5) = 0.8;
    STATES(:,5) = 200.0;
    CONSTANTS(:,6) = 0.2;
    STATES(:,6) = 0.0;
    STATES(:,7) = 0.9;
    CONSTANTS(:,7) = 1.0;
    STATES(:,8) = 0.0;
    CONSTANTS(:,8) = 30.0;
    STATES(:,9) = 50.0;
    CONSTANTS(:,9) = 50.0;
    CONSTANTS(:,10) = 0.1;
    CONSTANTS(:,11) = 1.0;
    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(:,1) =  CONSTANTS(:,2).*STATES(:,2) -  CONSTANTS(:,1).*STATES(:,1);
    RATES(:,2) =  CONSTANTS(:,1).*STATES(:,2) - ( CONSTANTS(:,2).*STATES(:,2)+ CONSTANTS(:,3).*STATES(:,2));
    RATES(:,3) =  CONSTANTS(:,5).*STATES(:,4) -  CONSTANTS(:,4).*STATES(:,2).*STATES(:,3);
    RATES(:,4) =  CONSTANTS(:,4).*STATES(:,2).*STATES(:,3) -  CONSTANTS(:,5).*STATES(:,4);
    RATES(:,5) =  - ( CONSTANTS(:,6).*STATES(:,4).*STATES(:,5));
    RATES(:,6) =  CONSTANTS(:,6).*STATES(:,4).*STATES(:,5) -  CONSTANTS(:,7).*STATES(:,7).*STATES(:,6);
    RATES(:,8) = ( CONSTANTS(:,7).*STATES(:,7).*STATES(:,6)+CONSTANTS(:,8)./(1.00000+power(STATES(:,9), 3.00000))) - STATES(:,8);
    RATES(:,9) = CONSTANTS(:,9)./(1.00000+power(STATES(:,8), 3.00000)) - STATES(:,9);
    RATES(:,7) =  - ( CONSTANTS(:,10).*CONSTANTS(:,11).*STATES(:,7));
   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
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