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 =6;
end
% There are a total of 13 entries in each of the rate and state variable arrays.
% There are a total of 23 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('Cdk2_CycE in component Cdk2_CycE (dimensionless)');
    LEGEND_CONSTANTS(:,1) = strpad('kwee in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,2) = strpad('kon in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,3) = strpad('k25A in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,4) = strpad('koff in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,5) = strpad('kassoc in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,6) = strpad('kdissoc in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,5) = strpad('phi in component kinetic_parameters (dimensionless)');
    LEGEND_STATES(:,2) = strpad('Wee1_a in component Wee1_a (dimensionless)');
    LEGEND_STATES(:,3) = strpad('PCdk2_CycE in component PCdk2_CycE (dimensionless)');
    LEGEND_STATES(:,4) = strpad('Xic in component Xic (dimensionless)');
    LEGEND_STATES(:,5) = strpad('Cdk2_CycErem in component Cdk2_CycErem (dimensionless)');
    LEGEND_STATES(:,6) = strpad('Xic_Cdk2_CycE in component Xic_Cdk2_CycE (dimensionless)');
    LEGEND_STATES(:,7) = strpad('PCdk2_CycErem in component PCdk2_CycErem (dimensionless)');
    LEGEND_STATES(:,8) = strpad('Xic_PCdk2_CycE in component Xic_PCdk2_CycE (dimensionless)');
    LEGEND_CONSTANTS(:,7) = strpad('Jwact in component Wee1_a (dimensionless)');
    LEGEND_CONSTANTS(:,8) = strpad('Jwinact in component Wee1_a (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('Wee1_total in component Wee1_a (dimensionless)');
    LEGEND_CONSTANTS(:,10) = strpad('kwact in component Wee1_a (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,11) = strpad('kwinact in component Wee1_a (first_order_rate_constant)');
    LEGEND_STATES(:,9) = strpad('Kin_a in component Kin_a (dimensionless)');
    LEGEND_CONSTANTS(:,12) = strpad('Jiact in component Kin_a (dimensionless)');
    LEGEND_CONSTANTS(:,13) = strpad('Jiinact in component Kin_a (dimensionless)');
    LEGEND_CONSTANTS(:,14) = strpad('kiact in component Kin_a (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,15) = strpad('kiinact in component Kin_a (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,16) = strpad('kedeg in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,17) = strpad('kxdeg in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_STATES(:,10) = strpad('Deg_a in component Deg_a (dimensionless)');
    LEGEND_STATES(:,11) = strpad('Xic_Cdk2_CycErem in component Xic_Cdk2_CycErem (dimensionless)');
    LEGEND_STATES(:,12) = strpad('Xic_PCdk2_CycErem in component Xic_PCdk2_CycErem (dimensionless)');
    LEGEND_ALGEBRAIC(:,6) = strpad('Heav in component Deg_a (dimensionless)');
    LEGEND_CONSTANTS(:,18) = strpad('kdact in component Deg_a (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,19) = strpad('theta in component Deg_a (dimensionless)');
    LEGEND_ALGEBRAIC(:,2) = strpad('x in component Deg_a (dimensionless)');
    LEGEND_CONSTANTS(:,20) = strpad('Deg in component kinetic_parameters (dimensionless)');
    LEGEND_STATES(:,13) = strpad('Xicrem in component Xicrem (dimensionless)');
    LEGEND_ALGEBRAIC(:,3) = strpad('Cyc_total in component Cyc_total (dimensionless)');
    LEGEND_ALGEBRAIC(:,4) = strpad('Xic_total in component Xic_total (dimensionless)');
    LEGEND_CONSTANTS(:,21) = strpad('epsilon in component kinetic_parameters (dimensionless)');
    LEGEND_ALGEBRAIC(:,1) = strpad('pool in component kinetic_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,22) = strpad('n in component kinetic_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,23) = strpad('L in component kinetic_parameters (dimensionless)');
    LEGEND_RATES(:,1) = strpad('d/dt Cdk2_CycE in component Cdk2_CycE (dimensionless)');
    LEGEND_RATES(:,3) = strpad('d/dt PCdk2_CycE in component PCdk2_CycE (dimensionless)');
    LEGEND_RATES(:,2) = strpad('d/dt Wee1_a in component Wee1_a (dimensionless)');
    LEGEND_RATES(:,9) = strpad('d/dt Kin_a in component Kin_a (dimensionless)');
    LEGEND_RATES(:,5) = strpad('d/dt Cdk2_CycErem in component Cdk2_CycErem (dimensionless)');
    LEGEND_RATES(:,7) = strpad('d/dt PCdk2_CycErem in component PCdk2_CycErem (dimensionless)');
    LEGEND_RATES(:,10) = strpad('d/dt Deg_a in component Deg_a (dimensionless)');
    LEGEND_RATES(:,4) = strpad('d/dt Xic in component Xic (dimensionless)');
    LEGEND_RATES(:,6) = strpad('d/dt Xic_Cdk2_CycE in component Xic_Cdk2_CycE (dimensionless)');
    LEGEND_RATES(:,8) = strpad('d/dt Xic_PCdk2_CycE in component Xic_PCdk2_CycE (dimensionless)');
    LEGEND_RATES(:,11) = strpad('d/dt Xic_Cdk2_CycErem in component Xic_Cdk2_CycErem (dimensionless)');
    LEGEND_RATES(:,12) = strpad('d/dt Xic_PCdk2_CycErem in component Xic_PCdk2_CycErem (dimensionless)');
    LEGEND_RATES(:,13) = strpad('d/dt Xicrem in component Xicrem (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) = 0.06;
    CONSTANTS(:,1) = 1.5;
    CONSTANTS(:,2) = 0.02;
    CONSTANTS(:,3) = 0.1;
    CONSTANTS(:,4) = 0.0001;
    CONSTANTS(:,5) = 0.1;
    CONSTANTS(:,6) = 0.001;
    STATES(:,2) = 1.02;
    STATES(:,3) = 0.94;
    STATES(:,4) = 3;
    STATES(:,5) = 0;
    STATES(:,6) = 0;
    STATES(:,7) = 0;
    STATES(:,8) = 0;
    CONSTANTS(:,7) = 0.01;
    CONSTANTS(:,8) = 0.01;
    CONSTANTS(:,9) = 8;
    CONSTANTS(:,10) = 0.75;
    CONSTANTS(:,11) = 1.5;
    STATES(:,9) = 0.6;
    CONSTANTS(:,12) = 0.01;
    CONSTANTS(:,13) = 0.01;
    CONSTANTS(:,14) = 0.15;
    CONSTANTS(:,15) = 0.6;
    CONSTANTS(:,16) = 0.017;
    CONSTANTS(:,17) = 0.01;
    STATES(:,10) = 0;
    STATES(:,11) = 0;
    STATES(:,12) = 0;
    CONSTANTS(:,18) = 0.023;
    CONSTANTS(:,19) = 0.3;
    CONSTANTS(:,20) = 0;
    STATES(:,13) = 0;
    CONSTANTS(:,21) = 0.001;
    CONSTANTS(:,22) = 4;
    CONSTANTS(:,23) = 0.4;
    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(:,10).*(CONSTANTS(:,9) - STATES(:,2)))./((CONSTANTS(:,7)+CONSTANTS(:,9)) - STATES(:,2)) - ( CONSTANTS(:,11).*STATES(:,9).*STATES(:,2))./(CONSTANTS(:,8)+STATES(:,2));
    RATES(:,9) = ( CONSTANTS(:,14).*(1.00000 - STATES(:,9)))./((CONSTANTS(:,12)+1.00000) - STATES(:,9)) - ( CONSTANTS(:,15).*STATES(:,1).*STATES(:,9))./(CONSTANTS(:,13)+STATES(:,9));
    RATES(:,4) =  CONSTANTS(:,6).*(STATES(:,6)+STATES(:,8)+STATES(:,11)+STATES(:,12)) -  CONSTANTS(:,5).*STATES(:,4).*(STATES(:,1)+STATES(:,3)+STATES(:,5)+STATES(:,7));
    RATES(:,13) = ( CONSTANTS(:,16).*STATES(:,10).*STATES(:,11)+ CONSTANTS(:,16).*STATES(:,10).*STATES(:,12)) -  CONSTANTS(:,17).*STATES(:,13);
    ALGEBRAIC(:,1) = STATES(:,5)+STATES(:,7)+STATES(:,11)+STATES(:,12);
    ALGEBRAIC(:,5) = (CONSTANTS(:,21)+power(ALGEBRAIC(:,1), CONSTANTS(:,22)))./(power(CONSTANTS(:,23), CONSTANTS(:,22))+power(ALGEBRAIC(:,1), CONSTANTS(:,22)));
    RATES(:,1) = ( CONSTANTS(:,3).*STATES(:,3)+ CONSTANTS(:,4).*STATES(:,5)+ CONSTANTS(:,6).*STATES(:,6)) - ( CONSTANTS(:,1).*STATES(:,2).*STATES(:,1)+ CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,1)+ CONSTANTS(:,5).*STATES(:,4).*STATES(:,1));
    RATES(:,3) = ( CONSTANTS(:,1).*STATES(:,2).*STATES(:,1)+ CONSTANTS(:,4).*STATES(:,7)+ CONSTANTS(:,6).*STATES(:,8)) - ( CONSTANTS(:,3).*STATES(:,3)+ CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,3)+ CONSTANTS(:,5).*STATES(:,4).*STATES(:,3));
    RATES(:,5) = ( CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,1)+ CONSTANTS(:,17).*STATES(:,11)+ CONSTANTS(:,6).*STATES(:,11)) - ( CONSTANTS(:,4).*STATES(:,5)+ CONSTANTS(:,16).*STATES(:,10).*STATES(:,5)+ CONSTANTS(:,5).*STATES(:,4).*STATES(:,5));
    RATES(:,7) = ( CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,3)+ CONSTANTS(:,17).*STATES(:,12)+ CONSTANTS(:,6).*STATES(:,12)) - ( CONSTANTS(:,4).*STATES(:,7)+ CONSTANTS(:,16).*STATES(:,10).*STATES(:,7)+ CONSTANTS(:,5).*STATES(:,4).*STATES(:,7));
    ALGEBRAIC(:,2) = STATES(:,5) - CONSTANTS(:,19);
    ALGEBRAIC(:,6) = piecewise({ALGEBRAIC(:,2)<0.00000, 0.00000 }, 1.00000);
    RATES(:,10) =  CONSTANTS(:,18).*ALGEBRAIC(:,6);
    RATES(:,6) = ( CONSTANTS(:,5).*STATES(:,4).*STATES(:,1)+ CONSTANTS(:,4).*STATES(:,11)+ CONSTANTS(:,3).*STATES(:,8)) - ( CONSTANTS(:,6).*STATES(:,6)+ CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,6)+ CONSTANTS(:,1).*STATES(:,2).*STATES(:,6));
    RATES(:,8) = ( CONSTANTS(:,5).*STATES(:,4).*STATES(:,3)+ CONSTANTS(:,4).*STATES(:,12)+ CONSTANTS(:,1).*STATES(:,2).*STATES(:,6)) - ( CONSTANTS(:,6).*STATES(:,8)+ CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,8)+ CONSTANTS(:,3).*STATES(:,8));
    RATES(:,11) = ( CONSTANTS(:,5).*STATES(:,4).*STATES(:,5)+ CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,6)) - ( CONSTANTS(:,6).*STATES(:,11)+ CONSTANTS(:,4).*STATES(:,11)+ CONSTANTS(:,16).*STATES(:,10).*STATES(:,11)+ CONSTANTS(:,17).*STATES(:,11));
    RATES(:,12) = ( CONSTANTS(:,5).*STATES(:,4).*STATES(:,7)+ CONSTANTS(:,2).*ALGEBRAIC(:,5).*STATES(:,8)) - ( CONSTANTS(:,6).*STATES(:,12)+ CONSTANTS(:,4).*STATES(:,12)+ CONSTANTS(:,16).*CONSTANTS(:,20).*STATES(:,12)+ CONSTANTS(:,17).*STATES(:,12));
   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) = STATES(:,5)+STATES(:,7)+STATES(:,11)+STATES(:,12);
    ALGEBRAIC(:,5) = (CONSTANTS(:,21)+power(ALGEBRAIC(:,1), CONSTANTS(:,22)))./(power(CONSTANTS(:,23), CONSTANTS(:,22))+power(ALGEBRAIC(:,1), CONSTANTS(:,22)));
    ALGEBRAIC(:,2) = STATES(:,5) - CONSTANTS(:,19);
    ALGEBRAIC(:,6) = piecewise({ALGEBRAIC(:,2)<0.00000, 0.00000 }, 1.00000);
    ALGEBRAIC(:,3) = STATES(:,8)+STATES(:,6)+STATES(:,12)+STATES(:,11)+STATES(:,7)+STATES(:,5)+STATES(:,1)+STATES(:,3);
    ALGEBRAIC(:,4) = (STATES(:,4)+STATES(:,8)+STATES(:,6)+STATES(:,12)+STATES(:,11)+STATES(:,13))./3.00000;
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