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 =9;
end
% There are a total of 13 entries in each of the rate and state variable arrays.
% There are a total of 43 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(:,1) = strpad('k1 in component rate_constants (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,2) = strpad('k2 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,2) = strpad('k2_ in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,3) = strpad('k3 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,4) = strpad('k4 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,5) = strpad('k5 in component rate_constants (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,1) = strpad('k6 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,6) = strpad('k6_ in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,7) = strpad('k7 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,8) = strpad('k7r in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,9) = strpad('k8 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,10) = strpad('k8r in component rate_constants (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,6) = strpad('kwee in component rate_constants (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,8) = strpad('k25 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,11) = strpad('ku in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,12) = strpad('kp in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,13) = strpad('kur in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,14) = strpad('ku2 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,15) = strpad('kur2 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,16) = strpad('kc in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,17) = strpad('kcr in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,18) = strpad('kw in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,19) = strpad('kwr in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,20) = strpad('ki in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,21) = strpad('kir in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,22) = strpad('mu in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,23) = strpad('Kmu2 in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,24) = strpad('Kmur2 in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,25) = strpad('Kmi in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,26) = strpad('Kmir in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,27) = strpad('Kmw in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,28) = strpad('Kmwr in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,29) = strpad('Kmu in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,30) = strpad('Kmur in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,31) = strpad('Kmc in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,32) = strpad('Kmcr in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,33) = strpad('Kmp in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,34) = strpad('V2 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,35) = strpad('V2_ in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,36) = strpad('V6 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,37) = strpad('V6_ in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,38) = strpad('V25 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,39) = strpad('V25_ in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,40) = strpad('Vw in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,41) = strpad('Vw_ in component rate_constants (first_order_rate_constant)');
    LEGEND_STATES(:,1) = strpad('Cdc25 in component Cdc25 (dimensionless)');
    LEGEND_STATES(:,2) = strpad('UbE in component UbE (dimensionless)');
    LEGEND_STATES(:,3) = strpad('UbE2 in component UbE2 (dimensionless)');
    LEGEND_STATES(:,4) = strpad('Wee1 in component Wee1 (dimensionless)');
    LEGEND_ALGEBRAIC(:,9) = strpad('SPF in component concentration_variables (dimensionless)');
    LEGEND_ALGEBRAIC(:,7) = strpad('MPF in component concentration_variables (dimensionless)');
    LEGEND_CONSTANTS(:,42) = strpad('alpha in component concentration_variables (dimensionless)');
    LEGEND_CONSTANTS(:,43) = strpad('beta in component concentration_variables (dimensionless)');
    LEGEND_STATES(:,5) = strpad('G1K in component G1K (dimensionless)');
    LEGEND_STATES(:,6) = strpad('G2K in component G2K (dimensionless)');
    LEGEND_STATES(:,7) = strpad('PG2 in component PG2 (dimensionless)');
    LEGEND_STATES(:,8) = strpad('G2R in component G2R (dimensionless)');
    LEGEND_STATES(:,9) = strpad('R in component R (dimensionless)');
    LEGEND_STATES(:,10) = strpad('G1R in component G1R (dimensionless)');
    LEGEND_STATES(:,11) = strpad('PG2R in component PG2R (dimensionless)');
    LEGEND_STATES(:,12) = strpad('mass in component mass (dimensionless)');
    LEGEND_STATES(:,13) = strpad('IE in component IE (dimensionless)');
    LEGEND_ALGEBRAIC(:,3) = strpad('Cig2_total in component Cig2_total (dimensionless)');
    LEGEND_ALGEBRAIC(:,4) = strpad('Rum1_total in component Rum1_total (dimensionless)');
    LEGEND_ALGEBRAIC(:,5) = strpad('Cdc13_total in component Cdc13_total (dimensionless)');
    LEGEND_RATES(:,6) = strpad('d/dt G2K in component G2K (dimensionless)');
    LEGEND_RATES(:,9) = strpad('d/dt R in component R (dimensionless)');
    LEGEND_RATES(:,5) = strpad('d/dt G1K in component G1K (dimensionless)');
    LEGEND_RATES(:,8) = strpad('d/dt G2R in component G2R (dimensionless)');
    LEGEND_RATES(:,13) = strpad('d/dt IE in component IE (dimensionless)');
    LEGEND_RATES(:,3) = strpad('d/dt UbE2 in component UbE2 (dimensionless)');
    LEGEND_RATES(:,4) = strpad('d/dt Wee1 in component Wee1 (dimensionless)');
    LEGEND_RATES(:,7) = strpad('d/dt PG2 in component PG2 (dimensionless)');
    LEGEND_RATES(:,10) = strpad('d/dt G1R in component G1R (dimensionless)');
    LEGEND_RATES(:,11) = strpad('d/dt PG2R in component PG2R (dimensionless)');
    LEGEND_RATES(:,2) = strpad('d/dt UbE in component UbE (dimensionless)');
    LEGEND_RATES(:,12) = strpad('d/dt mass in component mass (dimensionless)');
    LEGEND_RATES(:,1) = strpad('d/dt Cdc25 in component Cdc25 (dimensionless)');
    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) = 0.015;
    CONSTANTS(:,2) = 0.05;
    CONSTANTS(:,3) = 0.09375;
    CONSTANTS(:,4) = 0.1875;
    CONSTANTS(:,5) = 0.00175;
    CONSTANTS(:,6) = 0;
    CONSTANTS(:,7) = 100;
    CONSTANTS(:,8) = 0.1;
    CONSTANTS(:,9) = 10;
    CONSTANTS(:,10) = 0.1;
    CONSTANTS(:,11) = 0.2;
    CONSTANTS(:,12) = 3.25;
    CONSTANTS(:,13) = 0.1;
    CONSTANTS(:,14) = 1;
    CONSTANTS(:,15) = 0.3;
    CONSTANTS(:,16) = 1;
    CONSTANTS(:,17) = 0.25;
    CONSTANTS(:,18) = 1;
    CONSTANTS(:,19) = 0.25;
    CONSTANTS(:,20) = 0.4;
    CONSTANTS(:,21) = 0.1;
    CONSTANTS(:,22) = 0.00495;
    CONSTANTS(:,23) = 0.05;
    CONSTANTS(:,24) = 0.05;
    CONSTANTS(:,25) = 0.01;
    CONSTANTS(:,26) = 0.01;
    CONSTANTS(:,27) = 0.1;
    CONSTANTS(:,28) = 0.1;
    CONSTANTS(:,29) = 0.01;
    CONSTANTS(:,30) = 0.01;
    CONSTANTS(:,31) = 0.1;
    CONSTANTS(:,32) = 0.1;
    CONSTANTS(:,33) = 0.001;
    CONSTANTS(:,34) = 0.25;
    CONSTANTS(:,35) = 0.0075;
    CONSTANTS(:,36) = 7.5;
    CONSTANTS(:,37) = 0.0375;
    CONSTANTS(:,38) = 0.5;
    CONSTANTS(:,39) = 0.025;
    CONSTANTS(:,40) = 0.35;
    CONSTANTS(:,41) = 0.035;
    STATES(:,1) = 0;
    STATES(:,2) = 1;
    STATES(:,3) = 0;
    STATES(:,4) = 0;
    CONSTANTS(:,42) = 0.25;
    CONSTANTS(:,43) = 0.05;
    STATES(:,5) = 0;
    STATES(:,6) = 0;
    STATES(:,7) = 0;
    STATES(:,8) = 0;
    STATES(:,9) = 0.4;
    STATES(:,10) = 0;
    STATES(:,11) = 0;
    STATES(:,12) = 0.5;
    STATES(:,13) = 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(:,10) =  CONSTANTS(:,9).*STATES(:,9).*STATES(:,5) -  (CONSTANTS(:,10)+CONSTANTS(:,4)+CONSTANTS(:,6)).*STATES(:,10);
    RATES(:,2) = ( CONSTANTS(:,11).*STATES(:,13).*(1.00000 - STATES(:,2)))./((CONSTANTS(:,29)+1.00000) - STATES(:,2)) - ( CONSTANTS(:,13).*STATES(:,2))./(CONSTANTS(:,30)+STATES(:,2));
    RATES(:,12) =  CONSTANTS(:,22).*STATES(:,12);
    ALGEBRAIC(:,1) =  CONSTANTS(:,37).*(1.00000 - STATES(:,3))+ CONSTANTS(:,36).*STATES(:,3);
    RATES(:,5) = (CONSTANTS(:,5)+ (CONSTANTS(:,10)+CONSTANTS(:,4)).*STATES(:,10)) -  (ALGEBRAIC(:,1)+ CONSTANTS(:,9).*STATES(:,9)).*STATES(:,5);
    ALGEBRAIC(:,2) =  CONSTANTS(:,35).*(1.00000 - STATES(:,2))+ CONSTANTS(:,34).*STATES(:,2);
    RATES(:,8) =  CONSTANTS(:,7).*STATES(:,9).*STATES(:,6) -  (CONSTANTS(:,8)+CONSTANTS(:,4)+ALGEBRAIC(:,2)+CONSTANTS(:,2)).*STATES(:,8);
    RATES(:,11) =  CONSTANTS(:,7).*STATES(:,9).*STATES(:,7) -  (CONSTANTS(:,8)+CONSTANTS(:,4)+ALGEBRAIC(:,2)+CONSTANTS(:,2)).*STATES(:,11);
    ALGEBRAIC(:,7) = STATES(:,6)+ CONSTANTS(:,43).*STATES(:,7);
    RATES(:,13) = ( CONSTANTS(:,20).*ALGEBRAIC(:,7).*(1.00000 - STATES(:,13)))./((CONSTANTS(:,25)+1.00000) - STATES(:,13)) - ( CONSTANTS(:,21).*STATES(:,13))./(CONSTANTS(:,26)+STATES(:,13));
    RATES(:,3) = ( CONSTANTS(:,14).*ALGEBRAIC(:,7).*(1.00000 - STATES(:,3)))./((CONSTANTS(:,23)+1.00000) - STATES(:,3)) - ( CONSTANTS(:,15).*STATES(:,3))./(CONSTANTS(:,24)+STATES(:,3));
    RATES(:,4) = ( CONSTANTS(:,19).*(1.00000 - STATES(:,4)))./((CONSTANTS(:,28)+1.00000) - STATES(:,4)) - ( CONSTANTS(:,18).*ALGEBRAIC(:,7).*STATES(:,4))./(CONSTANTS(:,27)+STATES(:,4));
    RATES(:,1) = ( CONSTANTS(:,16).*ALGEBRAIC(:,7).*(1.00000 - STATES(:,1)))./((CONSTANTS(:,31)+1.00000) - STATES(:,1)) - ( CONSTANTS(:,17).*STATES(:,1))./(CONSTANTS(:,32)+STATES(:,1));
    ALGEBRAIC(:,6) =  CONSTANTS(:,41).*(1.00000 - STATES(:,4))+ CONSTANTS(:,40).*STATES(:,4);
    ALGEBRAIC(:,8) =  CONSTANTS(:,39).*(1.00000 - STATES(:,1))+ CONSTANTS(:,38).*STATES(:,1);
    RATES(:,6) = (CONSTANTS(:,1)+ ALGEBRAIC(:,8).*STATES(:,7)+ (CONSTANTS(:,8)+CONSTANTS(:,4)).*STATES(:,8)) -  (ALGEBRAIC(:,2)+ALGEBRAIC(:,6)+ CONSTANTS(:,7).*STATES(:,9)).*STATES(:,6);
    ALGEBRAIC(:,9) = ALGEBRAIC(:,7)+ CONSTANTS(:,42).*STATES(:,5);
    RATES(:,9) = (CONSTANTS(:,3)+ (CONSTANTS(:,8)+ALGEBRAIC(:,2)+CONSTANTS(:,2)).*(STATES(:,8)+STATES(:,11))+ (CONSTANTS(:,10)+CONSTANTS(:,6)).*STATES(:,10)) - ( CONSTANTS(:,4).*STATES(:,9)+ CONSTANTS(:,7).*STATES(:,9).*(STATES(:,6)+STATES(:,7))+ CONSTANTS(:,9).*STATES(:,9).*STATES(:,5)+( CONSTANTS(:,12).*STATES(:,9).*ALGEBRAIC(:,9).*STATES(:,12))./(CONSTANTS(:,33)+STATES(:,9)));
    RATES(:,7) = ( ALGEBRAIC(:,6).*STATES(:,6)+ (CONSTANTS(:,8)+CONSTANTS(:,4)).*STATES(:,11)) -  (ALGEBRAIC(:,8)+ALGEBRAIC(:,2)+ CONSTANTS(:,7).*STATES(:,9)).*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
    ALGEBRAIC(:,1) =  CONSTANTS(:,37).*(1.00000 - STATES(:,3))+ CONSTANTS(:,36).*STATES(:,3);
    ALGEBRAIC(:,2) =  CONSTANTS(:,35).*(1.00000 - STATES(:,2))+ CONSTANTS(:,34).*STATES(:,2);
    ALGEBRAIC(:,7) = STATES(:,6)+ CONSTANTS(:,43).*STATES(:,7);
    ALGEBRAIC(:,6) =  CONSTANTS(:,41).*(1.00000 - STATES(:,4))+ CONSTANTS(:,40).*STATES(:,4);
    ALGEBRAIC(:,8) =  CONSTANTS(:,39).*(1.00000 - STATES(:,1))+ CONSTANTS(:,38).*STATES(:,1);
    ALGEBRAIC(:,9) = ALGEBRAIC(:,7)+ CONSTANTS(:,42).*STATES(:,5);
    ALGEBRAIC(:,3) = STATES(:,5)+STATES(:,10);
    ALGEBRAIC(:,4) = STATES(:,9)+STATES(:,10)+STATES(:,8)+STATES(:,11);
    ALGEBRAIC(:,5) = STATES(:,6)+STATES(:,8)+STATES(:,7)+STATES(:,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