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 =5;
end
% There are a total of 9 entries in each of the rate and state variable arrays.
% There are a total of 31 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('k1AA in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,2) = strpad('k3 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,3) = strpad('kinh in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,4) = strpad('kcak in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,5) = strpad('kbPPase in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,6) = strpad('kfPPase in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,7) = strpad('khPPase in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,8) = strpad('kd_antiIE in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,9) = strpad('ka in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,10) = strpad('kc in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,11) = strpad('ke in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,12) = strpad('kg in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,13) = strpad('V2_ in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,14) = strpad('V2__ in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,15) = strpad('V25_ in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,16) = strpad('V25__ in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,17) = strpad('Vwee_ in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,18) = strpad('Vwee__ in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,19) = strpad('K_a in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,20) = strpad('K_b in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,21) = strpad('K_c in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,22) = strpad('K_d in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,23) = strpad('K_e in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,24) = strpad('K_f in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,25) = strpad('K_g in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,26) = strpad('K_h in component rate_constants (dimensionless)');
    LEGEND_CONSTANTS(:,27) = strpad('Cdc25_T in component concentration_variables (dimensionless)');
    LEGEND_STATES(:,1) = strpad('Cdc25_P in component Cdc25_P (dimensionless)');
    LEGEND_STATES(:,2) = strpad('Wee1_P in component Wee1_P (dimensionless)');
    LEGEND_CONSTANTS(:,28) = strpad('Wee1_T in component concentration_variables (dimensionless)');
    LEGEND_CONSTANTS(:,29) = strpad('UbE_T in component concentration_variables (dimensionless)');
    LEGEND_STATES(:,3) = strpad('UbE in component UbE (dimensionless)');
    LEGEND_ALGEBRAIC(:,1) = strpad('k25 in component rate_constants (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,3) = strpad('kwee in component rate_constants (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,4) = strpad('k2 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,30) = strpad('Cdc2_T in component concentration_variables (dimensionless)');
    LEGEND_CONSTANTS(:,31) = strpad('IE_T in component concentration_variables (dimensionless)');
    LEGEND_STATES(:,4) = strpad('cyclin in component cyclin (dimensionless)');
    LEGEND_ALGEBRAIC(:,5) = strpad('Cdc2 in component Cdc2 (dimensionless)');
    LEGEND_STATES(:,5) = strpad('cyclin_Cdc2 in component cyclin_Cdc2 (dimensionless)');
    LEGEND_STATES(:,6) = strpad('MPF_active in component MPF_active (dimensionless)');
    LEGEND_STATES(:,7) = strpad('Tyr15P_dimer in component Tyr15P_dimer (dimensionless)');
    LEGEND_STATES(:,8) = strpad('MPF_pre in component MPF_pre (dimensionless)');
    LEGEND_ALGEBRAIC(:,2) = strpad('cyclin_T in component cyclin_T (dimensionless)');
    LEGEND_STATES(:,9) = strpad('IE_P in component IE_P (dimensionless)');
    LEGEND_RATES(:,4) = strpad('d/dt cyclin in component cyclin (dimensionless)');
    LEGEND_RATES(:,5) = strpad('d/dt cyclin_Cdc2 in component cyclin_Cdc2 (dimensionless)');
    LEGEND_RATES(:,7) = strpad('d/dt Tyr15P_dimer in component Tyr15P_dimer (dimensionless)');
    LEGEND_RATES(:,8) = strpad('d/dt MPF_pre in component MPF_pre (dimensionless)');
    LEGEND_RATES(:,6) = strpad('d/dt MPF_active in component MPF_active (dimensionless)');
    LEGEND_RATES(:,1) = strpad('d/dt Cdc25_P in component Cdc25_P (dimensionless)');
    LEGEND_RATES(:,2) = strpad('d/dt Wee1_P in component Wee1_P (dimensionless)');
    LEGEND_RATES(:,9) = strpad('d/dt IE_P in component IE_P (dimensionless)');
    LEGEND_RATES(:,3) = strpad('d/dt UbE in component UbE (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) = 1;
    CONSTANTS(:,2) = 0.01;
    CONSTANTS(:,3) = 0.025;
    CONSTANTS(:,4) = 0.25;
    CONSTANTS(:,5) = 0.125;
    CONSTANTS(:,6) = 0.1;
    CONSTANTS(:,7) = 0.087;
    CONSTANTS(:,8) = 0.095;
    CONSTANTS(:,9) = 0.01;
    CONSTANTS(:,10) = 0.1;
    CONSTANTS(:,11) = 0.0133;
    CONSTANTS(:,12) = 0.0065;
    CONSTANTS(:,13) = 0.015;
    CONSTANTS(:,14) = 1;
    CONSTANTS(:,15) = 0.1;
    CONSTANTS(:,16) = 2;
    CONSTANTS(:,17) = 0.1;
    CONSTANTS(:,18) = 1;
    CONSTANTS(:,19) = 0.1;
    CONSTANTS(:,20) = 0.1;
    CONSTANTS(:,21) = 0.01;
    CONSTANTS(:,22) = 0.01;
    CONSTANTS(:,23) = 0.3;
    CONSTANTS(:,24) = 0.3;
    CONSTANTS(:,25) = 0.01;
    CONSTANTS(:,26) = 0.01;
    CONSTANTS(:,27) = 1;
    STATES(:,1) = 0;
    STATES(:,2) = 0;
    CONSTANTS(:,28) = 1;
    CONSTANTS(:,29) = 1;
    STATES(:,3) = 0;
    CONSTANTS(:,30) = 100;
    CONSTANTS(:,31) = 1;
    STATES(:,4) = 1;
    STATES(:,5) = 0;
    STATES(:,6) = 0;
    STATES(:,7) = 0;
    STATES(:,8) = 0;
    STATES(:,9) = 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(:,9).*STATES(:,6).*(CONSTANTS(:,27) - STATES(:,1)))./((CONSTANTS(:,19)+CONSTANTS(:,27)) - STATES(:,1)) - ( CONSTANTS(:,5).*STATES(:,1))./(CONSTANTS(:,20)+STATES(:,1));
    RATES(:,2) = ( CONSTANTS(:,11).*STATES(:,6).*(CONSTANTS(:,28) - STATES(:,2)))./((CONSTANTS(:,23)+CONSTANTS(:,28)) - STATES(:,2)) - ( CONSTANTS(:,6).*STATES(:,2))./(CONSTANTS(:,24)+STATES(:,2));
    RATES(:,9) = ( CONSTANTS(:,12).*STATES(:,6).*(CONSTANTS(:,31) - STATES(:,9)))./((CONSTANTS(:,25)+CONSTANTS(:,31)) - STATES(:,9)) - ( CONSTANTS(:,7).*STATES(:,9))./(CONSTANTS(:,26)+STATES(:,9));
    RATES(:,3) = ( CONSTANTS(:,10).*STATES(:,9).*(CONSTANTS(:,29) - STATES(:,3)))./((CONSTANTS(:,21)+CONSTANTS(:,29)) - STATES(:,3)) - ( CONSTANTS(:,8).*STATES(:,3))./(CONSTANTS(:,22)+STATES(:,3));
    ALGEBRAIC(:,1) =  CONSTANTS(:,15).*(CONSTANTS(:,27) - STATES(:,1))+ CONSTANTS(:,16).*STATES(:,1);
    ALGEBRAIC(:,3) =  CONSTANTS(:,17).*STATES(:,2)+ CONSTANTS(:,18).*(CONSTANTS(:,28) - STATES(:,2));
    ALGEBRAIC(:,4) =  CONSTANTS(:,13).*(CONSTANTS(:,29) - STATES(:,3))+ CONSTANTS(:,14).*STATES(:,3);
    RATES(:,7) = ( ALGEBRAIC(:,3).*STATES(:,5) -  (ALGEBRAIC(:,1)+CONSTANTS(:,4)+ALGEBRAIC(:,4)).*STATES(:,7))+ CONSTANTS(:,3).*STATES(:,8);
    RATES(:,8) = ( ALGEBRAIC(:,3).*STATES(:,6) -  (CONSTANTS(:,3)+ALGEBRAIC(:,1)+ALGEBRAIC(:,4)).*STATES(:,8))+ CONSTANTS(:,4).*STATES(:,7);
    RATES(:,6) = ( CONSTANTS(:,4).*STATES(:,5) -  (CONSTANTS(:,3)+ALGEBRAIC(:,3)+ALGEBRAIC(:,4)).*STATES(:,6))+ ALGEBRAIC(:,1).*STATES(:,8);
    ALGEBRAIC(:,5) = CONSTANTS(:,30) - (STATES(:,5)+STATES(:,6)+STATES(:,8)+STATES(:,7));
    RATES(:,4) = (CONSTANTS(:,1) -  ALGEBRAIC(:,4).*STATES(:,4)) -  CONSTANTS(:,2).*STATES(:,4).*ALGEBRAIC(:,5);
    RATES(:,5) = ( CONSTANTS(:,3).*STATES(:,6) -  (ALGEBRAIC(:,3)+CONSTANTS(:,4)+ALGEBRAIC(:,4)).*STATES(:,5))+ ALGEBRAIC(:,1).*STATES(:,7)+ CONSTANTS(:,2).*STATES(:,4).*ALGEBRAIC(:,5);
   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(:,15).*(CONSTANTS(:,27) - STATES(:,1))+ CONSTANTS(:,16).*STATES(:,1);
    ALGEBRAIC(:,3) =  CONSTANTS(:,17).*STATES(:,2)+ CONSTANTS(:,18).*(CONSTANTS(:,28) - STATES(:,2));
    ALGEBRAIC(:,4) =  CONSTANTS(:,13).*(CONSTANTS(:,29) - STATES(:,3))+ CONSTANTS(:,14).*STATES(:,3);
    ALGEBRAIC(:,5) = CONSTANTS(:,30) - (STATES(:,5)+STATES(:,6)+STATES(:,8)+STATES(:,7));
    ALGEBRAIC(:,2) = STATES(:,4)+STATES(:,5)+STATES(:,6)+STATES(:,8)+STATES(:,7);
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