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 =8;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 35 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('Y in component Y (dimensionless)');
    LEGEND_CONSTANTS(:,1) = strpad('k1 in component Y (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,7) = strpad('k2 in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,2) = strpad('k3 in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,1) = strpad('C in component C (dimensionless)');
    LEGEND_STATES(:,2) = strpad('M in component M (dimensionless)');
    LEGEND_ALGEBRAIC(:,8) = strpad('kwee in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,6) = strpad('kcdc25 in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_STATES(:,3) = strpad('preMPF in component preMPF (dimensionless)');
    LEGEND_STATES(:,4) = strpad('Cdc25P in component Cdc25P (dimensionless)');
    LEGEND_CONSTANTS(:,3) = strpad('k25 in component Cdc25P (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,4) = strpad('Km25 in component Cdc25P (dimensionless)');
    LEGEND_CONSTANTS(:,5) = strpad('k25r in component Cdc25P (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,34) = strpad('k25ro in component Cdc25P (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,6) = strpad('Km25r in component Cdc25P (dimensionless)');
    LEGEND_CONSTANTS(:,33) = strpad('p in component p (dimensionless)');
    LEGEND_ALGEBRAIC(:,3) = strpad('Cdc25 in component Cdc25 (dimensionless)');
    LEGEND_STATES(:,5) = strpad('Wee1 in component Wee1 (dimensionless)');
    LEGEND_CONSTANTS(:,7) = strpad('kw in component Wee1 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,8) = strpad('Kmw in component Wee1 (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('kwr in component Wee1 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,35) = strpad('kwro in component Wee1 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,10) = strpad('Kmwr in component Wee1 (dimensionless)');
    LEGEND_ALGEBRAIC(:,4) = strpad('Wee1P in component Wee1P (dimensionless)');
    LEGEND_STATES(:,6) = strpad('IEP in component IEP (dimensionless)');
    LEGEND_CONSTANTS(:,11) = strpad('kie in component IEP (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,12) = strpad('Kmie in component IEP (dimensionless)');
    LEGEND_CONSTANTS(:,13) = strpad('kier in component IEP (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,14) = strpad('Kmier in component IEP (dimensionless)');
    LEGEND_ALGEBRAIC(:,2) = strpad('IE in component IE (dimensionless)');
    LEGEND_STATES(:,7) = strpad('APC_ in component APC_ (dimensionless)');
    LEGEND_CONSTANTS(:,15) = strpad('kap in component APC_ (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,16) = strpad('Kmap in component APC_ (dimensionless)');
    LEGEND_CONSTANTS(:,17) = strpad('kapr in component APC_ (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,18) = strpad('Kmapr in component APC_ (dimensionless)');
    LEGEND_ALGEBRAIC(:,5) = strpad('APC in component APC (dimensionless)');
    LEGEND_CONSTANTS(:,19) = strpad('Cdc2tot in component C (dimensionless)');
    LEGEND_CONSTANTS(:,20) = strpad('Cdc25tot in component Cdc25 (dimensionless)');
    LEGEND_CONSTANTS(:,21) = strpad('Wee1tot in component Wee1P (dimensionless)');
    LEGEND_CONSTANTS(:,22) = strpad('IEtot in component IE (dimensionless)');
    LEGEND_CONSTANTS(:,23) = strpad('APCtot in component APC (dimensionless)');
    LEGEND_CONSTANTS(:,24) = strpad('R in component p (dimensionless)');
    LEGEND_CONSTANTS(:,25) = strpad('s in component p (dimensionless)');
    LEGEND_CONSTANTS(:,26) = strpad('q in component p (dimensionless)');
    LEGEND_CONSTANTS(:,27) = strpad('V2 in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,28) = strpad('V2_ in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,29) = strpad('V25 in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,30) = strpad('V25_ in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,31) = strpad('Vwee in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,32) = strpad('Vwee_ in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_RATES(:,1) = strpad('d/dt Y in component Y (dimensionless)');
    LEGEND_RATES(:,2) = strpad('d/dt M in component M (dimensionless)');
    LEGEND_RATES(:,3) = strpad('d/dt preMPF in component preMPF (dimensionless)');
    LEGEND_RATES(:,4) = strpad('d/dt Cdc25P in component Cdc25P (dimensionless)');
    LEGEND_RATES(:,5) = strpad('d/dt Wee1 in component Wee1 (dimensionless)');
    LEGEND_RATES(:,6) = strpad('d/dt IEP in component IEP (dimensionless)');
    LEGEND_RATES(:,7) = strpad('d/dt APC_ in component APC_ (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) = 0.01577552;
    CONSTANTS(:,1) = 0.024;
    CONSTANTS(:,2) = 1.15;
    STATES(:,2) = 0.0142077;
    STATES(:,3) = 0.02541723;
    STATES(:,4) = 0.4844362;
    CONSTANTS(:,3) = 18;
    CONSTANTS(:,4) = 0.1;
    CONSTANTS(:,5) = 0.8;
    CONSTANTS(:,6) = 1;
    STATES(:,5) = 0.5155638;
    CONSTANTS(:,7) = 18;
    CONSTANTS(:,8) = 0.1;
    CONSTANTS(:,9) = 0.8;
    CONSTANTS(:,10) = 1;
    STATES(:,6) = 0.002287817;
    CONSTANTS(:,11) = 4.5;
    CONSTANTS(:,12) = 0.01;
    CONSTANTS(:,13) = 0.34;
    CONSTANTS(:,14) = 0.01;
    STATES(:,7) = 0.5051103;
    CONSTANTS(:,15) = 0.3;
    CONSTANTS(:,16) = 0.01;
    CONSTANTS(:,17) = 0.3;
    CONSTANTS(:,18) = 1;
    CONSTANTS(:,19) = 1;
    CONSTANTS(:,20) = 1;
    CONSTANTS(:,21) = 1;
    CONSTANTS(:,22) = 1;
    CONSTANTS(:,23) = 1;
    CONSTANTS(:,24) = 1;
    CONSTANTS(:,25) = 0.021;
    CONSTANTS(:,26) = 1;
    CONSTANTS(:,27) = 0.01;
    CONSTANTS(:,28) = 0.6;
    CONSTANTS(:,29) = 0.04;
    CONSTANTS(:,30) = 0.4;
    CONSTANTS(:,31) = 0.025;
    CONSTANTS(:,32) = 2.5;
    CONSTANTS(:,33) =  CONSTANTS(:,25).*CONSTANTS(:,24)+CONSTANTS(:,26);
    CONSTANTS(:,34) = CONSTANTS(:,5)./CONSTANTS(:,33);
    CONSTANTS(:,35) = CONSTANTS(:,9)./CONSTANTS(:,33);
    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
    ALGEBRAIC(:,2) = CONSTANTS(:,22) - STATES(:,6);
    RATES(:,6) = ( CONSTANTS(:,11).*STATES(:,2).*ALGEBRAIC(:,2))./(CONSTANTS(:,12)+ALGEBRAIC(:,2)) - ( CONSTANTS(:,13).*STATES(:,6))./(CONSTANTS(:,14)+STATES(:,6));
    ALGEBRAIC(:,3) = CONSTANTS(:,20) - STATES(:,4);
    RATES(:,4) = ( CONSTANTS(:,3).*STATES(:,2).*ALGEBRAIC(:,3))./(CONSTANTS(:,4)+ALGEBRAIC(:,3)) - ( CONSTANTS(:,5).*STATES(:,4))./(CONSTANTS(:,6)+STATES(:,4));
    ALGEBRAIC(:,4) = CONSTANTS(:,21) - STATES(:,5);
    RATES(:,5) = (  - CONSTANTS(:,7).*STATES(:,2).*STATES(:,5))./(CONSTANTS(:,8)+STATES(:,5))+( CONSTANTS(:,9).*ALGEBRAIC(:,4))./(CONSTANTS(:,10)+ALGEBRAIC(:,4));
    ALGEBRAIC(:,5) = CONSTANTS(:,23) - STATES(:,7);
    RATES(:,7) = ( CONSTANTS(:,15).*STATES(:,6).*ALGEBRAIC(:,5))./(CONSTANTS(:,16)+ALGEBRAIC(:,5)) - ( CONSTANTS(:,17).*STATES(:,7))./(CONSTANTS(:,18)+STATES(:,7));
    ALGEBRAIC(:,7) =  CONSTANTS(:,27).*ALGEBRAIC(:,5)+ CONSTANTS(:,28).*STATES(:,7);
    ALGEBRAIC(:,1) = CONSTANTS(:,19) - (STATES(:,2)+STATES(:,3));
    RATES(:,1) = CONSTANTS(:,1) - ( ALGEBRAIC(:,7).*STATES(:,1)+ CONSTANTS(:,2).*STATES(:,1).*ALGEBRAIC(:,1));
    ALGEBRAIC(:,8) =  CONSTANTS(:,31).*ALGEBRAIC(:,4)+ CONSTANTS(:,32).*STATES(:,5);
    ALGEBRAIC(:,6) =  CONSTANTS(:,29).*ALGEBRAIC(:,3)+ CONSTANTS(:,30).*STATES(:,4);
    RATES(:,2) = ( ALGEBRAIC(:,6).*STATES(:,3)+ CONSTANTS(:,2).*STATES(:,1).*ALGEBRAIC(:,1)) - ( ALGEBRAIC(:,7).*STATES(:,2)+ ALGEBRAIC(:,8).*STATES(:,2));
    RATES(:,3) =  ALGEBRAIC(:,8).*STATES(:,2) - ( ALGEBRAIC(:,7).*STATES(:,3)+ ALGEBRAIC(:,6).*STATES(:,3));
   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(:,2) = CONSTANTS(:,22) - STATES(:,6);
    ALGEBRAIC(:,3) = CONSTANTS(:,20) - STATES(:,4);
    ALGEBRAIC(:,4) = CONSTANTS(:,21) - STATES(:,5);
    ALGEBRAIC(:,5) = CONSTANTS(:,23) - STATES(:,7);
    ALGEBRAIC(:,7) =  CONSTANTS(:,27).*ALGEBRAIC(:,5)+ CONSTANTS(:,28).*STATES(:,7);
    ALGEBRAIC(:,1) = CONSTANTS(:,19) - (STATES(:,2)+STATES(:,3));
    ALGEBRAIC(:,8) =  CONSTANTS(:,31).*ALGEBRAIC(:,4)+ CONSTANTS(:,32).*STATES(:,5);
    ALGEBRAIC(:,6) =  CONSTANTS(:,29).*ALGEBRAIC(:,3)+ CONSTANTS(:,30).*STATES(:,4);
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