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 =4;
end
% There are a total of 17 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_STATES(:,1) = strpad('MPF_n in component MPF_n (dimensionless)');
    LEGEND_CONSTANTS(:,1) = strpad('k_in in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,2) = strpad('k_out in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,3) = strpad('k_dn_ in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,4) = strpad('k_dn__ in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,5) = strpad('k_wee_ in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,6) = strpad('k_wee__ in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,7) = strpad('k_stg_ in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,8) = strpad('k_stg__ in component parameters (first_order_rate_constant)');
    LEGEND_STATES(:,2) = strpad('MPF_c in component MPF_c (dimensionless)');
    LEGEND_STATES(:,3) = strpad('FZY in component FZY (dimensionless)');
    LEGEND_STATES(:,4) = strpad('Wee1_n in component Wee1_n (dimensionless)');
    LEGEND_STATES(:,5) = strpad('StgP_n in component StgP_n (dimensionless)');
    LEGEND_STATES(:,6) = strpad('preMPF_n in component preMPF_n (dimensionless)');
    LEGEND_STATES(:,7) = strpad('preMPF_c in component preMPF_c (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('k_sc in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,10) = strpad('k_dc_ in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,11) = strpad('epsilon in component parameters (dimensionless)');
    LEGEND_STATES(:,8) = strpad('N in component N (dimensionless)');
    LEGEND_STATES(:,9) = strpad('StgP_c in component StgP_c (dimensionless)');
    LEGEND_STATES(:,10) = strpad('Wee1_c in component Wee1_c (dimensionless)');
    LEGEND_STATES(:,11) = strpad('IE in component IE (dimensionless)');
    LEGEND_CONSTANTS(:,12) = strpad('j_aie in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,13) = strpad('j_iie in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,14) = strpad('k_aie in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,15) = strpad('k_iie in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,16) = strpad('j_afz in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,17) = strpad('j_ifz in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,18) = strpad('k_afz in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,19) = strpad('k_ifz in component parameters (first_order_rate_constant)');
    LEGEND_STATES(:,12) = strpad('Stg_m in component Stg_m (dimensionless)');
    LEGEND_CONSTANTS(:,20) = strpad('k_dm_ in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,21) = strpad('k_dm__ in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,22) = strpad('j_m in component parameters (dimensionless)');
    LEGEND_STATES(:,13) = strpad('Xp in component Xp (dimensionless)');
    LEGEND_STATES(:,14) = strpad('Xm in component Xm (dimensionless)');
    LEGEND_CONSTANTS(:,23) = strpad('k_sxm in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,24) = strpad('k_sxp in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,25) = strpad('k_ins in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,26) = strpad('k_outs in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,27) = strpad('k_astg_ in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,28) = strpad('k_astg__ in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,29) = strpad('k_istg in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,30) = strpad('k_dstg in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,31) = strpad('j_astg in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,32) = strpad('j_istg in component parameters (dimensionless)');
    LEGEND_STATES(:,15) = strpad('Stg_n in component Stg_n (dimensionless)');
    LEGEND_STATES(:,16) = strpad('Stg_c in component Stg_c (dimensionless)');
    LEGEND_CONSTANTS(:,33) = strpad('k_sstg in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,34) = strpad('k_inw in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,35) = strpad('k_outw in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,36) = strpad('k_awee in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,37) = strpad('k_iwee_ in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,38) = strpad('k_iwee__ in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,39) = strpad('j_awee in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,40) = strpad('j_iwee in component parameters (dimensionless)');
    LEGEND_STATES(:,17) = strpad('Wee1P_n in component Wee1P_n (dimensionless)');
    LEGEND_ALGEBRAIC(:,1) = strpad('Wee1P_c in component Wee1P_c (dimensionless)');
    LEGEND_CONSTANTS(:,41) = strpad('Wee1_T in component Wee1P_c (dimensionless)');
    LEGEND_ALGEBRAIC(:,2) = strpad('CycB_T in component CycB_T (dimensionless)');
    LEGEND_ALGEBRAIC(:,3) = strpad('Stg_T in component Stg_T (dimensionless)');
    LEGEND_ALGEBRAIC(:,4) = strpad('StgP_T in component StgP_T (dimensionless)');
    LEGEND_CONSTANTS(:,42) = strpad('k_ez in component parameters (first_order_rate_constant)');
    LEGEND_RATES(:,1) = strpad('d/dt MPF_n in component MPF_n (dimensionless)');
    LEGEND_RATES(:,6) = strpad('d/dt preMPF_n in component preMPF_n (dimensionless)');
    LEGEND_RATES(:,2) = strpad('d/dt MPF_c in component MPF_c (dimensionless)');
    LEGEND_RATES(:,7) = strpad('d/dt preMPF_c in component preMPF_c (dimensionless)');
    LEGEND_RATES(:,11) = strpad('d/dt IE in component IE (dimensionless)');
    LEGEND_RATES(:,3) = strpad('d/dt FZY in component FZY (dimensionless)');
    LEGEND_RATES(:,12) = strpad('d/dt Stg_m in component Stg_m (dimensionless)');
    LEGEND_RATES(:,14) = strpad('d/dt Xm in component Xm (dimensionless)');
    LEGEND_RATES(:,13) = strpad('d/dt Xp in component Xp (dimensionless)');
    LEGEND_RATES(:,5) = strpad('d/dt StgP_n in component StgP_n (dimensionless)');
    LEGEND_RATES(:,15) = strpad('d/dt Stg_n in component Stg_n (dimensionless)');
    LEGEND_RATES(:,9) = strpad('d/dt StgP_c in component StgP_c (dimensionless)');
    LEGEND_RATES(:,16) = strpad('d/dt Stg_c in component Stg_c (dimensionless)');
    LEGEND_RATES(:,4) = strpad('d/dt Wee1_n in component Wee1_n (dimensionless)');
    LEGEND_RATES(:,10) = strpad('d/dt Wee1_c in component Wee1_c (dimensionless)');
    LEGEND_RATES(:,17) = strpad('d/dt Wee1P_n in component Wee1P_n (dimensionless)');
    LEGEND_RATES(:,8) = strpad('d/dt N in component N (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) = 0;
    CONSTANTS(:,1) = 0.15;
    CONSTANTS(:,2) = 0;
    CONSTANTS(:,3) = 0.01;
    CONSTANTS(:,4) = 1.5;
    CONSTANTS(:,5) = 0.005;
    CONSTANTS(:,6) = 1;
    CONSTANTS(:,7) = 0.2;
    CONSTANTS(:,8) = 2;
    STATES(:,2) = 1;
    STATES(:,3) = 0;
    STATES(:,4) = 0;
    STATES(:,5) = 0;
    STATES(:,6) = 0;
    STATES(:,7) = 0;
    CONSTANTS(:,9) = 0.01;
    CONSTANTS(:,10) = 0.01;
    CONSTANTS(:,11) = 0.00007;
    STATES(:,8) = 1;
    STATES(:,9) = 0;
    STATES(:,10) = 0;
    STATES(:,11) = 0;
    CONSTANTS(:,12) = 0.01;
    CONSTANTS(:,13) = 0.01;
    CONSTANTS(:,14) = 1;
    CONSTANTS(:,15) = 0.4;
    CONSTANTS(:,16) = 0.01;
    CONSTANTS(:,17) = 0.01;
    CONSTANTS(:,18) = 1;
    CONSTANTS(:,19) = 0.2;
    STATES(:,12) = 1;
    CONSTANTS(:,20) = 0.002;
    CONSTANTS(:,21) = 0.2;
    CONSTANTS(:,22) = 0.05;
    STATES(:,13) = 0;
    STATES(:,14) = 0;
    CONSTANTS(:,23) = 0.0005;
    CONSTANTS(:,24) = 0.001;
    CONSTANTS(:,25) = 0.08;
    CONSTANTS(:,26) = 0.02;
    CONSTANTS(:,27) = 0;
    CONSTANTS(:,28) = 1;
    CONSTANTS(:,29) = 0.3;
    CONSTANTS(:,30) = 0.015;
    CONSTANTS(:,31) = 0.05;
    CONSTANTS(:,32) = 0.05;
    STATES(:,15) = 0;
    STATES(:,16) = 1;
    CONSTANTS(:,33) = 0.02;
    CONSTANTS(:,34) = 0.04;
    CONSTANTS(:,35) = 0.01;
    CONSTANTS(:,36) = 0.3;
    CONSTANTS(:,37) = 0.01;
    CONSTANTS(:,38) = 1;
    CONSTANTS(:,39) = 0.05;
    CONSTANTS(:,40) = 0.05;
    STATES(:,17) = 0;
    CONSTANTS(:,41) = 0.8;
    CONSTANTS(:,42) = 0.5;
    CONSTANTS(:,42) = 0.00000;
    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(:,8) = CONSTANTS(:,42);
    RATES(:,1) = ((( CONSTANTS(:,1).*STATES(:,2) -  CONSTANTS(:,2).*STATES(:,1)) -  (CONSTANTS(:,3)+ CONSTANTS(:,4).*STATES(:,3)).*STATES(:,1)) -  (CONSTANTS(:,5)+ CONSTANTS(:,6).*STATES(:,4)).*STATES(:,1))+ (CONSTANTS(:,7)+ CONSTANTS(:,8).*STATES(:,5)).*STATES(:,6);
    RATES(:,6) = ((( CONSTANTS(:,1).*STATES(:,7) -  CONSTANTS(:,2).*STATES(:,6)) -  (CONSTANTS(:,3)+ CONSTANTS(:,4).*STATES(:,3)).*STATES(:,6))+ (CONSTANTS(:,5)+ CONSTANTS(:,6).*STATES(:,4)).*STATES(:,1)) -  (CONSTANTS(:,5)+ CONSTANTS(:,8).*STATES(:,5)).*STATES(:,6);
    RATES(:,2) = (((CONSTANTS(:,9) - ( CONSTANTS(:,11).*STATES(:,8).*( CONSTANTS(:,1).*STATES(:,2) -  CONSTANTS(:,2).*STATES(:,1)))./(1.00000 -  STATES(:,8).*CONSTANTS(:,11))) -  CONSTANTS(:,10).*STATES(:,2))+ (CONSTANTS(:,7)+ CONSTANTS(:,8).*STATES(:,9)).*STATES(:,7)) -  (CONSTANTS(:,5)+ CONSTANTS(:,6).*STATES(:,10)).*STATES(:,2);
    RATES(:,7) = (((  - CONSTANTS(:,11).*STATES(:,8).*( CONSTANTS(:,1).*STATES(:,7) -  CONSTANTS(:,2).*STATES(:,6)))./(1.00000 -  STATES(:,8).*CONSTANTS(:,11)) -  CONSTANTS(:,10).*STATES(:,7)) -  (CONSTANTS(:,7)+ CONSTANTS(:,8).*STATES(:,9)).*STATES(:,7))+ (CONSTANTS(:,5)+ CONSTANTS(:,6).*STATES(:,10)).*STATES(:,2);
    RATES(:,11) = ( CONSTANTS(:,14).*(1.00000 - STATES(:,11)).*STATES(:,1))./((CONSTANTS(:,12)+1.00000) - STATES(:,11)) - ( CONSTANTS(:,15).*STATES(:,11))./(CONSTANTS(:,13)+STATES(:,11));
    RATES(:,3) = ( CONSTANTS(:,18).*STATES(:,11).*(1.00000 - STATES(:,3)))./((CONSTANTS(:,16)+1.00000) - STATES(:,3)) - ( CONSTANTS(:,19).*STATES(:,3))./(CONSTANTS(:,17)+STATES(:,3));
    RATES(:,12) =   - (CONSTANTS(:,20)./(CONSTANTS(:,22)+STATES(:,12))+ CONSTANTS(:,21).*STATES(:,13)).*STATES(:,12);
    RATES(:,14) =  CONSTANTS(:,23).*STATES(:,8);
    RATES(:,13) =  CONSTANTS(:,24).*STATES(:,14);
    RATES(:,5) = ((( CONSTANTS(:,25).*STATES(:,9) -  CONSTANTS(:,26).*STATES(:,5))+( (CONSTANTS(:,27)+ CONSTANTS(:,28).*STATES(:,1)).*STATES(:,15))./(CONSTANTS(:,31)+STATES(:,15))) - ( CONSTANTS(:,29).*STATES(:,5))./(CONSTANTS(:,32)+STATES(:,5))) -  CONSTANTS(:,30).*STATES(:,5);
    RATES(:,15) = ((( CONSTANTS(:,25).*STATES(:,16) -  CONSTANTS(:,26).*STATES(:,15)) - ( (CONSTANTS(:,27)+ CONSTANTS(:,28).*STATES(:,1)).*STATES(:,15))./(CONSTANTS(:,31)+STATES(:,15)))+( CONSTANTS(:,29).*STATES(:,5))./(CONSTANTS(:,32)+STATES(:,5))) -  CONSTANTS(:,30).*STATES(:,15);
    RATES(:,9) = ((  - CONSTANTS(:,30).*STATES(:,9) - ( CONSTANTS(:,11).*STATES(:,8).*( CONSTANTS(:,25).*STATES(:,9) -  CONSTANTS(:,26).*STATES(:,5)))./(1.00000 -  STATES(:,8).*CONSTANTS(:,11)))+( (CONSTANTS(:,27)+ CONSTANTS(:,28).*STATES(:,2)).*STATES(:,16))./(CONSTANTS(:,31)+STATES(:,16))) - ( CONSTANTS(:,29).*STATES(:,9))./(CONSTANTS(:,32)+STATES(:,9));
    RATES(:,16) = ((( CONSTANTS(:,33).*STATES(:,12) -  CONSTANTS(:,30).*STATES(:,16)) - ( CONSTANTS(:,11).*STATES(:,8).*( CONSTANTS(:,25).*STATES(:,16) -  CONSTANTS(:,26).*STATES(:,15)))./(1.00000 -  STATES(:,8).*CONSTANTS(:,11))) - ( (CONSTANTS(:,27)+ CONSTANTS(:,28).*STATES(:,2)).*STATES(:,16))./(CONSTANTS(:,31)+STATES(:,16)))+( CONSTANTS(:,29).*STATES(:,9))./(CONSTANTS(:,32)+STATES(:,9));
    RATES(:,4) = (( CONSTANTS(:,34).*STATES(:,10) -  CONSTANTS(:,35).*STATES(:,4))+( CONSTANTS(:,36).*STATES(:,17))./(CONSTANTS(:,39)+STATES(:,17))) - ( (CONSTANTS(:,37)+ CONSTANTS(:,38).*STATES(:,1)).*STATES(:,4))./(CONSTANTS(:,40)+STATES(:,4));
    ALGEBRAIC(:,1) = (CONSTANTS(:,41) -  STATES(:,8).*CONSTANTS(:,11).*(STATES(:,4)+STATES(:,17)))./(1.00000 -  STATES(:,8).*CONSTANTS(:,11)) - STATES(:,10);
    RATES(:,10) = ((  - ( CONSTANTS(:,34).*STATES(:,10) -  CONSTANTS(:,35).*STATES(:,4)).*STATES(:,8).*CONSTANTS(:,11))./(1.00000 -  STATES(:,8).*CONSTANTS(:,11))+( CONSTANTS(:,36).*ALGEBRAIC(:,1))./(CONSTANTS(:,39)+ALGEBRAIC(:,1))) - ( (CONSTANTS(:,37)+ CONSTANTS(:,38).*STATES(:,2)).*STATES(:,10))./(CONSTANTS(:,40)+STATES(:,10));
    RATES(:,17) = (( CONSTANTS(:,34).*ALGEBRAIC(:,1) -  CONSTANTS(:,35).*STATES(:,17)) - ( CONSTANTS(:,36).*STATES(:,17))./(CONSTANTS(:,39)+STATES(:,17)))+( (CONSTANTS(:,37)+ CONSTANTS(:,38).*STATES(:,1)).*STATES(:,4))./(CONSTANTS(:,40)+STATES(:,4));
   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(:,41) -  STATES(:,8).*CONSTANTS(:,11).*(STATES(:,4)+STATES(:,17)))./(1.00000 -  STATES(:,8).*CONSTANTS(:,11)) - STATES(:,10);
    ALGEBRAIC(:,2) =  (1.00000 -  STATES(:,8).*CONSTANTS(:,11)).*(STATES(:,2)+STATES(:,7))+ STATES(:,8).*CONSTANTS(:,11).*(STATES(:,1)+STATES(:,6));
    ALGEBRAIC(:,3) =  (1.00000 -  STATES(:,8).*CONSTANTS(:,11)).*(STATES(:,16)+STATES(:,9))+ STATES(:,8).*CONSTANTS(:,11).*(STATES(:,15)+STATES(:,5));
    ALGEBRAIC(:,4) =  (1.00000 -  STATES(:,8).*CONSTANTS(:,11)).*STATES(:,9)+ STATES(:,8).*CONSTANTS(:,11).*STATES(:,5);
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