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 0 entries in each of the rate and state variable arrays.
% There are a total of 21 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_CONSTANTS(:,17) = strpad('v_cystathionine in component v_cystathionine (flux)');
    LEGEND_CONSTANTS(:,1) = strpad('Cys in component Cys (micromolar)');
    LEGEND_CONSTANTS(:,2) = strpad('CGS in component CGS (micromolar)');
    LEGEND_CONSTANTS(:,3) = strpad('Pi in component Pi (micromolar)');
    LEGEND_CONSTANTS(:,4) = strpad('Phser in component Phser (micromolar)');
    LEGEND_CONSTANTS(:,16) = strpad('Km_CGS_app_Cys in component v_cystathionine (micromolar)');
    LEGEND_CONSTANTS(:,5) = strpad('Km_CGS_Cys in component v_cystathionine (micromolar)');
    LEGEND_CONSTANTS(:,6) = strpad('kcat_CGS in component v_cystathionine (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,15) = strpad('kcat_CGS_app_Cys in component v_cystathionine (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,7) = strpad('Km_CGS_Phser in component v_cystathionine (micromolar)');
    LEGEND_CONSTANTS(:,8) = strpad('Ki_CGS_Pi in component v_cystathionine (micromolar)');
    LEGEND_CONSTANTS(:,20) = strpad('v_Thr in component v_Thr (flux)');
    LEGEND_CONSTANTS(:,9) = strpad('TS in component TS (micromolar)');
    LEGEND_CONSTANTS(:,10) = strpad('AdoMet in component AdoMet (micromolar)');
    LEGEND_CONSTANTS(:,19) = strpad('Km_TS in component v_Thr (micromolar)');
    LEGEND_CONSTANTS(:,11) = strpad('kcat_TS_noAdoMet in component v_Thr (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,12) = strpad('kcat_TS_AdoMet in component v_Thr (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,18) = strpad('kcat_TS in component v_Thr (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,13) = strpad('K1K2 in component v_Thr (micromolar2)');
    LEGEND_CONSTANTS(:,14) = strpad('Ki_TS_Pi in component v_Thr (micromolar)');
    LEGEND_CONSTANTS(:,21) = strpad('J_Phser in component J_Phser (flux)');
    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 = [];
    CONSTANTS(:,1) = 15.0;
    CONSTANTS(:,2) = 0.7;
    CONSTANTS(:,3) = 10000.0;
    CONSTANTS(:,4) = 500.0;
    CONSTANTS(:,5) = 460.0;
    CONSTANTS(:,6) = 30.0;
    CONSTANTS(:,7) = 2500.0;
    CONSTANTS(:,8) = 2500.0;
    CONSTANTS(:,9) = 5.0;
    CONSTANTS(:,10) = 20.0;
    CONSTANTS(:,11) = 0.42;
    CONSTANTS(:,12) = 3.5;
    CONSTANTS(:,13) = 73.0;
    CONSTANTS(:,14) = 1000.0;
    CONSTANTS(:,15) = CONSTANTS(:,6)./(1.00000+ (CONSTANTS(:,7)./CONSTANTS(:,4)).*(1.00000+CONSTANTS(:,3)./CONSTANTS(:,8)));
    CONSTANTS(:,16) = CONSTANTS(:,5)./(1.00000+ (CONSTANTS(:,7)./CONSTANTS(:,4)).*(1.00000+CONSTANTS(:,3)./CONSTANTS(:,8)));
    CONSTANTS(:,17) = ( CONSTANTS(:,15).*CONSTANTS(:,2).*CONSTANTS(:,1))./(CONSTANTS(:,16)+CONSTANTS(:,1));
    CONSTANTS(:,18) = (CONSTANTS(:,11)+ CONSTANTS(:,12).*(power(CONSTANTS(:,10), 2.00000)./CONSTANTS(:,13)))./(1.00000+power(CONSTANTS(:,10), 2.00000)./CONSTANTS(:,13));
    CONSTANTS(:,19) =  (( 250.000.*((1.00000+CONSTANTS(:,10)./0.500000)./(1.00000+CONSTANTS(:,10)./1.10000)))./(1.00000+power(CONSTANTS(:,10), 2.00000)./140.000)).*(1.00000+CONSTANTS(:,3)./CONSTANTS(:,14));
    CONSTANTS(:,20) = ( CONSTANTS(:,9).*CONSTANTS(:,18).*CONSTANTS(:,4))./(CONSTANTS(:,19)+CONSTANTS(:,4));
    CONSTANTS(:,21) = CONSTANTS(:,17)+CONSTANTS(:,20);
    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 = 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