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 =10;
end
% There are a total of 11 entries in each of the rate and state variable arrays.
% There are a total of 45 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_STATES(:,1) = strpad('Cdc13_Cdc2 in component Cdc13_Cdc2 (dimensionless)');
    LEGEND_CONSTANTS(:,1) = strpad('k1 in component Cdc13_Cdc2 (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,4) = strpad('kwee in component kwee (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,2) = strpad('ki in component parameters (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,3) = strpad('kcdc25 in component kcdc25 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,3) = strpad('kir in component parameters (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,1) = strpad('k2 in component k2 (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,6) = strpad('k4 in component k4 (first_order_rate_constant)');
    LEGEND_STATES(:,2) = strpad('mass in component mass (dimensionless)');
    LEGEND_STATES(:,3) = strpad('Cdc13_P_Cdc2 in component Cdc13_P_Cdc2 (dimensionless)');
    LEGEND_STATES(:,4) = strpad('Rum1_Cdc13_Cdc2 in component Rum1_Cdc13_Cdc2 (dimensionless)');
    LEGEND_STATES(:,5) = strpad('Rum1 in component Rum1 (dimensionless)');
    LEGEND_ALGEBRAIC(:,2) = strpad('k2c in component k2c (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,4) = strpad('k3 in component Rum1 (first_order_rate_constant)');
    LEGEND_STATES(:,6) = strpad('Cdc25P in component Cdc25P (dimensionless)');
    LEGEND_CONSTANTS(:,5) = strpad('k25 in component Cdc25P (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,8) = strpad('k25r in component Cdc25P (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,6) = strpad('k25r_ in component Cdc25P (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,7) = strpad('J25 in component Cdc25P (dimensionless)');
    LEGEND_CONSTANTS(:,8) = strpad('J25r in component Cdc25P (dimensionless)');
    LEGEND_ALGEBRAIC(:,7) = strpad('ks in component parameters (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,5) = strpad('MPF in component MPF (dimensionless)');
    LEGEND_STATES(:,7) = strpad('Wee1 in component Wee1 (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('kw in component Wee1 (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,9) = strpad('kwr in component Wee1 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,10) = strpad('kwr_ in component Wee1 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,11) = strpad('Jw in component Wee1 (dimensionless)');
    LEGEND_CONSTANTS(:,12) = strpad('Jwr in component Wee1 (dimensionless)');
    LEGEND_STATES(:,8) = strpad('Mik1 in component Mik1 (dimensionless)');
    LEGEND_CONSTANTS(:,13) = strpad('km in component Mik1 (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,10) = strpad('kmr in component Mik1 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,14) = strpad('kmr_ in component Mik1 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,15) = strpad('Jm in component Mik1 (dimensionless)');
    LEGEND_CONSTANTS(:,16) = strpad('Jmr in component Mik1 (dimensionless)');
    LEGEND_STATES(:,9) = strpad('AAE_total in component AAE_total (dimensionless)');
    LEGEND_CONSTANTS(:,17) = strpad('kas in component AAE_total (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,18) = strpad('kad in component parameters (first_order_rate_constant)');
    LEGEND_STATES(:,10) = strpad('AAE in component AAE (dimensionless)');
    LEGEND_CONSTANTS(:,19) = strpad('kaa in component AAE (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,20) = strpad('kaa_ in component AAE (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,45) = strpad('kai in component AAE (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,21) = strpad('kai_ in component AAE (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,22) = strpad('kx in component AAE (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,23) = strpad('Jaa in component AAE (dimensionless)');
    LEGEND_CONSTANTS(:,24) = strpad('Jai in component AAE (dimensionless)');
    LEGEND_STATES(:,11) = strpad('APC in component APC (dimensionless)');
    LEGEND_CONSTANTS(:,25) = strpad('kapr in component APC (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,26) = strpad('kapr_ in component APC (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,27) = strpad('kap in component APC (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,28) = strpad('Japr in component APC (dimensionless)');
    LEGEND_CONSTANTS(:,29) = strpad('Jap in component APC (dimensionless)');
    LEGEND_CONSTANTS(:,30) = strpad('Puc1 in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,31) = strpad('mu in component mass (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,32) = strpad('V2 in component k2 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,33) = strpad('V2_ in component k2 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,34) = strpad('V2c in component k2c (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,35) = strpad('V2c_ in component k2c (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,36) = strpad('k4_ in component k4 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,37) = strpad('k4__ in component k4 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,38) = strpad('V25 in component kcdc25 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,39) = strpad('V25_ in component kcdc25 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,40) = strpad('Vwee in component kwee (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,41) = strpad('Vwee_ in component kwee (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,42) = strpad('Vmik in component kwee (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,43) = strpad('Vmik_ in component kwee (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,44) = strpad('alpha in component MPF (dimensionless)');
    LEGEND_RATES(:,1) = strpad('d/dt Cdc13_Cdc2 in component Cdc13_Cdc2 (dimensionless)');
    LEGEND_RATES(:,3) = strpad('d/dt Cdc13_P_Cdc2 in component Cdc13_P_Cdc2 (dimensionless)');
    LEGEND_RATES(:,4) = strpad('d/dt Rum1_Cdc13_Cdc2 in component Rum1_Cdc13_Cdc2 (dimensionless)');
    LEGEND_RATES(:,5) = strpad('d/dt Rum1 in component Rum1 (dimensionless)');
    LEGEND_RATES(:,6) = strpad('d/dt Cdc25P in component Cdc25P (dimensionless)');
    LEGEND_RATES(:,7) = strpad('d/dt Wee1 in component Wee1 (dimensionless)');
    LEGEND_RATES(:,8) = strpad('d/dt Mik1 in component Mik1 (dimensionless)');
    LEGEND_RATES(:,9) = strpad('d/dt AAE_total in component AAE_total (dimensionless)');
    LEGEND_RATES(:,10) = strpad('d/dt AAE in component AAE (dimensionless)');
    LEGEND_RATES(:,11) = strpad('d/dt APC in component APC (dimensionless)');
    LEGEND_RATES(:,2) = strpad('d/dt mass in component mass (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 = [];
    STATES(:,1) = 1;
    CONSTANTS(:,1) = 0.03;
    CONSTANTS(:,2) = 200;
    CONSTANTS(:,3) = 1;
    STATES(:,2) = 1;
    STATES(:,3) = 0;
    STATES(:,4) = 0;
    STATES(:,5) = 0;
    CONSTANTS(:,4) = 0.15;
    STATES(:,6) = 0;
    CONSTANTS(:,5) = 0.5;
    CONSTANTS(:,6) = 0.2;
    CONSTANTS(:,7) = 0.2;
    CONSTANTS(:,8) = 0.2;
    STATES(:,7) = 0;
    CONSTANTS(:,9) = 0.5;
    CONSTANTS(:,10) = 0.2;
    CONSTANTS(:,11) = 0.2;
    CONSTANTS(:,12) = 0.2;
    STATES(:,8) = 0;
    CONSTANTS(:,13) = 0.1;
    CONSTANTS(:,14) = 0;
    CONSTANTS(:,15) = 0.2;
    CONSTANTS(:,16) = 0.2;
    STATES(:,9) = 2;
    CONSTANTS(:,17) = 0.25;
    CONSTANTS(:,18) = 0.1;
    STATES(:,10) = 2;
    CONSTANTS(:,19) = 0.001;
    CONSTANTS(:,20) = 1;
    CONSTANTS(:,21) = 0.25;
    CONSTANTS(:,22) = 0;
    CONSTANTS(:,23) = 0.1;
    CONSTANTS(:,24) = 0.1;
    STATES(:,11) = 0;
    CONSTANTS(:,25) = 0.04;
    CONSTANTS(:,26) = 3;
    CONSTANTS(:,27) = 4;
    CONSTANTS(:,28) = 0.01;
    CONSTANTS(:,29) = 0.01;
    CONSTANTS(:,30) = 0.013;
    CONSTANTS(:,31) = 0.005776;
    CONSTANTS(:,32) = 0.03;
    CONSTANTS(:,33) = 1;
    CONSTANTS(:,34) = 0.03;
    CONSTANTS(:,35) = 0.16;
    CONSTANTS(:,36) = 0.15;
    CONSTANTS(:,37) = 20;
    CONSTANTS(:,38) = 0.01;
    CONSTANTS(:,39) = 0.4;
    CONSTANTS(:,40) = 0.01;
    CONSTANTS(:,41) = 0.93;
    CONSTANTS(:,42) = 0.002;
    CONSTANTS(:,43) = 0.2;
    CONSTANTS(:,44) = 0.1;
    CONSTANTS(:,45) = CONSTANTS(:,21)+CONSTANTS(:,22);
    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(:,2) =  CONSTANTS(:,31).*STATES(:,2);
    ALGEBRAIC(:,4) =  CONSTANTS(:,40).*( (1.00000 - STATES(:,7)).*1.00000+ CONSTANTS(:,41).*STATES(:,7)+ CONSTANTS(:,42).*(1.00000 - STATES(:,8))).*1.00000+ CONSTANTS(:,43).*STATES(:,8);
    ALGEBRAIC(:,3) =  CONSTANTS(:,38).*(1.00000 - STATES(:,6))+ CONSTANTS(:,39).*STATES(:,6);
    ALGEBRAIC(:,1) =  CONSTANTS(:,32).*(1.00000 - STATES(:,11))+ CONSTANTS(:,33).*STATES(:,11);
    RATES(:,3) =  ALGEBRAIC(:,4).*STATES(:,1) - ( ALGEBRAIC(:,3).*STATES(:,3)+ ALGEBRAIC(:,1).*STATES(:,3));
    ALGEBRAIC(:,5) = STATES(:,1)+ CONSTANTS(:,44).*STATES(:,3);
    RATES(:,9) =  CONSTANTS(:,17).*ALGEBRAIC(:,5) -  CONSTANTS(:,18).*STATES(:,9);
    RATES(:,10) = ( (CONSTANTS(:,19)+ CONSTANTS(:,20).*ALGEBRAIC(:,5)).*(STATES(:,9) - STATES(:,10)))./((CONSTANTS(:,23)+STATES(:,9)) - STATES(:,10)) - (( CONSTANTS(:,45).*STATES(:,10))./(CONSTANTS(:,24)+STATES(:,10))+ CONSTANTS(:,18).*STATES(:,10));
    RATES(:,11) = ( (CONSTANTS(:,25)+ CONSTANTS(:,26).*STATES(:,10)).*(1.00000 - STATES(:,11)))./((CONSTANTS(:,28)+1.00000) - STATES(:,11)) - ( CONSTANTS(:,27).*( CONSTANTS(:,30).*STATES(:,2)+ALGEBRAIC(:,5)).*STATES(:,11))./(CONSTANTS(:,29)+STATES(:,11));
    ALGEBRAIC(:,6) = CONSTANTS(:,36)+ CONSTANTS(:,37).*( CONSTANTS(:,30).*STATES(:,2)+ALGEBRAIC(:,5));
    RATES(:,1) = ( CONSTANTS(:,1).*STATES(:,2)+ ALGEBRAIC(:,3).*STATES(:,3)+ STATES(:,4).*(CONSTANTS(:,3)+ALGEBRAIC(:,6))) - ( ALGEBRAIC(:,4).*STATES(:,1)+ CONSTANTS(:,2).*STATES(:,1).*STATES(:,5)+ ALGEBRAIC(:,1).*STATES(:,1));
    ALGEBRAIC(:,2) =  CONSTANTS(:,34).*(1.00000 - STATES(:,11))+ CONSTANTS(:,35).*STATES(:,11);
    RATES(:,4) =  CONSTANTS(:,2).*STATES(:,5).*STATES(:,1) -  STATES(:,4).*(ALGEBRAIC(:,6)+ALGEBRAIC(:,2)+CONSTANTS(:,3));
    RATES(:,5) = (CONSTANTS(:,4)+ STATES(:,4).*(CONSTANTS(:,3)+ALGEBRAIC(:,2))) - ( ALGEBRAIC(:,6).*STATES(:,5)+ CONSTANTS(:,2).*STATES(:,1).*STATES(:,5));
    ALGEBRAIC(:,7) = piecewise({STATES(:,11)<=0.200000, 0.500000 }, 0.00000);
    ALGEBRAIC(:,8) = CONSTANTS(:,6)+ALGEBRAIC(:,7);
    RATES(:,6) = ( CONSTANTS(:,5).*ALGEBRAIC(:,5).*(1.00000 - STATES(:,6)))./((CONSTANTS(:,7)+1.00000) - STATES(:,6)) - ( ALGEBRAIC(:,8).*STATES(:,6))./(CONSTANTS(:,8)+STATES(:,6));
    ALGEBRAIC(:,9) = CONSTANTS(:,10)+ALGEBRAIC(:,7);
    RATES(:,7) = ( ALGEBRAIC(:,9).*(1.00000 - STATES(:,7)))./((CONSTANTS(:,12)+1.00000) - STATES(:,7)) - ( CONSTANTS(:,9).*ALGEBRAIC(:,5).*STATES(:,7))./(CONSTANTS(:,11)+STATES(:,7));
    ALGEBRAIC(:,10) = CONSTANTS(:,14)+ALGEBRAIC(:,7);
    RATES(:,8) = ( ALGEBRAIC(:,10).*(1.00000 - STATES(:,8)))./((CONSTANTS(:,16)+1.00000) - STATES(:,8)) - ( CONSTANTS(:,13).*STATES(:,8))./(CONSTANTS(:,15)+STATES(:,8));
   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(:,4) =  CONSTANTS(:,40).*( (1.00000 - STATES(:,7)).*1.00000+ CONSTANTS(:,41).*STATES(:,7)+ CONSTANTS(:,42).*(1.00000 - STATES(:,8))).*1.00000+ CONSTANTS(:,43).*STATES(:,8);
    ALGEBRAIC(:,3) =  CONSTANTS(:,38).*(1.00000 - STATES(:,6))+ CONSTANTS(:,39).*STATES(:,6);
    ALGEBRAIC(:,1) =  CONSTANTS(:,32).*(1.00000 - STATES(:,11))+ CONSTANTS(:,33).*STATES(:,11);
    ALGEBRAIC(:,5) = STATES(:,1)+ CONSTANTS(:,44).*STATES(:,3);
    ALGEBRAIC(:,6) = CONSTANTS(:,36)+ CONSTANTS(:,37).*( CONSTANTS(:,30).*STATES(:,2)+ALGEBRAIC(:,5));
    ALGEBRAIC(:,2) =  CONSTANTS(:,34).*(1.00000 - STATES(:,11))+ CONSTANTS(:,35).*STATES(:,11);
    ALGEBRAIC(:,7) = piecewise({STATES(:,11)<=0.200000, 0.500000 }, 0.00000);
    ALGEBRAIC(:,8) = CONSTANTS(:,6)+ALGEBRAIC(:,7);
    ALGEBRAIC(:,9) = CONSTANTS(:,10)+ALGEBRAIC(:,7);
    ALGEBRAIC(:,10) = CONSTANTS(:,14)+ALGEBRAIC(:,7);
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