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 12 entries in each of the rate and state variable arrays.
% There are a total of 34 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('k1 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,2) = strpad('k2 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,3) = strpad('k3 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,4) = strpad('k4 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,5) = strpad('k5 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,6) = strpad('k6 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,7) = strpad('k7 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,8) = strpad('k8 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,9) = strpad('k9 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,10) = strpad('k10 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,11) = strpad('k11 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,12) = strpad('k12 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,13) = strpad('k13 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,14) = strpad('k14 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,15) = strpad('k15 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,16) = strpad('k16 in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,17) = strpad('k2u in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,18) = strpad('k7u in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,19) = strpad('k16u in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,20) = strpad('az in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,21) = strpad('bz in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,22) = strpad('cz in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,23) = strpad('aw in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,24) = strpad('bw in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,25) = strpad('cw in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,26) = strpad('ai in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,27) = strpad('bi in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,28) = strpad('ci in component rate_constants (first_order_rate_constant)');
    LEGEND_STATES(:,1) = strpad('cyclin_CDK_active in component cyclin_CDK_active (dimensionless)');
    LEGEND_ALGEBRAIC(:,1) = strpad('kplus_z in component rate_constants (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,2) = strpad('kplus_w in component rate_constants (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,3) = strpad('kplus_i in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,32) = strpad('kminus_z in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,33) = strpad('kminus_w in component rate_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,34) = strpad('kminus_i in component rate_constants (first_order_rate_constant)');
    LEGEND_STATES(:,2) = strpad('cyclin in component cyclin (dimensionless)');
    LEGEND_STATES(:,3) = strpad('cyclin_CDK_inactive in component cyclin_CDK_inactive (dimensionless)');
    LEGEND_ALGEBRAIC(:,4) = strpad('CDK in component CDK (dimensionless)');
    LEGEND_STATES(:,4) = strpad('APC in component APC (dimensionless)');
    LEGEND_STATES(:,5) = strpad('wee1 in component wee1 (dimensionless)');
    LEGEND_STATES(:,6) = strpad('Cdc25_2P in component Cdc25_2P (dimensionless)');
    LEGEND_STATES(:,7) = strpad('CKI in component CKI (dimensionless)');
    LEGEND_STATES(:,8) = strpad('cyclin_CDK_CKI in component cyclin_CDK_CKI (dimensionless)');
    LEGEND_STATES(:,9) = strpad('cyclin_CDK_CKI_P in component cyclin_CDK_CKI_P (dimensionless)');
    LEGEND_STATES(:,10) = strpad('Cdc25 in component Cdc25 (dimensionless)');
    LEGEND_STATES(:,11) = strpad('Cdc25_P in component Cdc25_P (dimensionless)');
    LEGEND_STATES(:,12) = strpad('wee1_P in component wee1_P (dimensionless)');
    LEGEND_CONSTANTS(:,29) = strpad('tau in component APC (minute)');
    LEGEND_ALGEBRAIC(:,5) = strpad('h_x in component APC (dimensionless)');
    LEGEND_CONSTANTS(:,30) = strpad('a in component APC (dimensionless)');
    LEGEND_CONSTANTS(:,31) = strpad('CDK_T in component CDK (dimensionless)');
    LEGEND_ALGEBRAIC(:,6) = strpad('cyclin_T in component cyclin_T (dimensionless)');
    LEGEND_RATES(:,2) = strpad('d/dt cyclin in component cyclin (dimensionless)');
    LEGEND_RATES(:,3) = strpad('d/dt cyclin_CDK_inactive in component cyclin_CDK_inactive (dimensionless)');
    LEGEND_RATES(:,1) = strpad('d/dt cyclin_CDK_active in component cyclin_CDK_active (dimensionless)');
    LEGEND_RATES(:,10) = strpad('d/dt Cdc25 in component Cdc25 (dimensionless)');
    LEGEND_RATES(:,11) = strpad('d/dt Cdc25_P in component Cdc25_P (dimensionless)');
    LEGEND_RATES(:,6) = strpad('d/dt Cdc25_2P in component Cdc25_2P (dimensionless)');
    LEGEND_RATES(:,5) = strpad('d/dt wee1 in component wee1 (dimensionless)');
    LEGEND_RATES(:,12) = strpad('d/dt wee1_P in component wee1_P (dimensionless)');
    LEGEND_RATES(:,4) = strpad('d/dt APC in component APC (dimensionless)');
    LEGEND_RATES(:,7) = strpad('d/dt CKI in component CKI (dimensionless)');
    LEGEND_RATES(:,8) = strpad('d/dt cyclin_CDK_CKI in component cyclin_CDK_CKI (dimensionless)');
    LEGEND_RATES(:,9) = strpad('d/dt cyclin_CDK_CKI_P in component cyclin_CDK_CKI_P (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) = 300;
    CONSTANTS(:,2) = 5;
    CONSTANTS(:,3) = 30;
    CONSTANTS(:,4) = 30;
    CONSTANTS(:,5) = 0.1;
    CONSTANTS(:,6) = 1;
    CONSTANTS(:,7) = 10;
    CONSTANTS(:,8) = 100;
    CONSTANTS(:,9) = 1;
    CONSTANTS(:,10) = 10;
    CONSTANTS(:,11) = 1;
    CONSTANTS(:,12) = 0;
    CONSTANTS(:,13) = 1;
    CONSTANTS(:,14) = 1;
    CONSTANTS(:,15) = 1;
    CONSTANTS(:,16) = 2;
    CONSTANTS(:,17) = 50;
    CONSTANTS(:,18) = 0;
    CONSTANTS(:,19) = 25;
    CONSTANTS(:,20) = 10;
    CONSTANTS(:,21) = 0.1;
    CONSTANTS(:,22) = 1;
    CONSTANTS(:,23) = 10;
    CONSTANTS(:,24) = 0.1;
    CONSTANTS(:,25) = 1;
    CONSTANTS(:,26) = 10;
    CONSTANTS(:,27) = 0.1;
    CONSTANTS(:,28) = 1;
    STATES(:,1) = 0.1;
    STATES(:,2) = 0;
    STATES(:,3) = 0.1;
    STATES(:,4) = 0;
    STATES(:,5) = 0;
    STATES(:,6) = 0;
    STATES(:,7) = 0;
    STATES(:,8) = 0;
    STATES(:,9) = 0;
    STATES(:,10) = 0;
    STATES(:,11) = 0;
    STATES(:,12) = 0;
    CONSTANTS(:,29) = 25;
    CONSTANTS(:,30) = 4;
    CONSTANTS(:,31) = 200;
    CONSTANTS(:,32) = CONSTANTS(:,20);
    CONSTANTS(:,33) = CONSTANTS(:,23);
    CONSTANTS(:,34) = CONSTANTS(:,26);
    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(:,5).*STATES(:,3)+ STATES(:,6).*STATES(:,3).*1.00000) -  CONSTANTS(:,6).*STATES(:,1)) -  STATES(:,5).*STATES(:,1).*1.00000) -  (CONSTANTS(:,7)+ CONSTANTS(:,18).*STATES(:,4)).*STATES(:,1)) -  CONSTANTS(:,14).*STATES(:,1).*STATES(:,7))+ CONSTANTS(:,15).*STATES(:,8)+ (CONSTANTS(:,16)+ CONSTANTS(:,19).*STATES(:,4)).*STATES(:,9);
    RATES(:,7) = ((CONSTANTS(:,12) -  CONSTANTS(:,13).*STATES(:,7)) -  CONSTANTS(:,12).*STATES(:,1).*STATES(:,7))+ CONSTANTS(:,15).*STATES(:,8);
    ALGEBRAIC(:,4) = ((((CONSTANTS(:,31) - STATES(:,1)) - STATES(:,3)) - STATES(:,8)) - STATES(:,9))./CONSTANTS(:,31);
    RATES(:,2) = ((CONSTANTS(:,1)+ CONSTANTS(:,4).*STATES(:,3)) -  CONSTANTS(:,3).*STATES(:,2).*ALGEBRAIC(:,4)) -  (CONSTANTS(:,2)+ CONSTANTS(:,17).*STATES(:,4)).*STATES(:,2);
    RATES(:,3) = ((( CONSTANTS(:,3).*STATES(:,2).*ALGEBRAIC(:,4)+ CONSTANTS(:,6).*STATES(:,1)+ STATES(:,5).*STATES(:,1).*1.00000) -  CONSTANTS(:,4).*STATES(:,3)) -  CONSTANTS(:,5).*STATES(:,3)) -  STATES(:,6).*STATES(:,3).*1.00000;
    ALGEBRAIC(:,1) = CONSTANTS(:,21)+ CONSTANTS(:,22).*STATES(:,1);
    RATES(:,10) = ((CONSTANTS(:,8)+ CONSTANTS(:,32).*STATES(:,11)) -  ALGEBRAIC(:,1).*STATES(:,10)) -  CONSTANTS(:,9).*STATES(:,10);
    RATES(:,11) = ( ALGEBRAIC(:,1).*(STATES(:,10) - STATES(:,11))+ CONSTANTS(:,32).*(STATES(:,6) - STATES(:,11))) -  CONSTANTS(:,9).*STATES(:,11);
    RATES(:,6) = ( ALGEBRAIC(:,1).*STATES(:,11) -  CONSTANTS(:,32).*STATES(:,6)) -  CONSTANTS(:,9).*STATES(:,6);
    ALGEBRAIC(:,2) = CONSTANTS(:,24)+ CONSTANTS(:,25).*STATES(:,1);
    RATES(:,5) = ((CONSTANTS(:,10)+ CONSTANTS(:,33).*STATES(:,12)) -  ALGEBRAIC(:,2).*STATES(:,5)) -  CONSTANTS(:,11).*STATES(:,5);
    RATES(:,12) = ( ALGEBRAIC(:,2).*STATES(:,5) -  CONSTANTS(:,33).*STATES(:,12)) -  CONSTANTS(:,11).*STATES(:,12);
    ALGEBRAIC(:,5) = power(STATES(:,1), 2.00000)./(power(CONSTANTS(:,30), 2.00000)+power(STATES(:,1), 2.00000));
    RATES(:,4) = (ALGEBRAIC(:,5) - STATES(:,4))./CONSTANTS(:,29);
    ALGEBRAIC(:,3) = CONSTANTS(:,27)+ CONSTANTS(:,28).*STATES(:,1);
    RATES(:,8) = (( CONSTANTS(:,14).*STATES(:,1).*STATES(:,7) -  CONSTANTS(:,15).*STATES(:,8))+ CONSTANTS(:,34).*STATES(:,9)) -  ALGEBRAIC(:,3).*STATES(:,8);
    RATES(:,9) = ( ALGEBRAIC(:,3).*STATES(:,8) -  CONSTANTS(:,34).*STATES(:,9)) -  (CONSTANTS(:,16)+ CONSTANTS(:,19).*STATES(:,4)).*STATES(:,9);
   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(:,31) - STATES(:,1)) - STATES(:,3)) - STATES(:,8)) - STATES(:,9))./CONSTANTS(:,31);
    ALGEBRAIC(:,1) = CONSTANTS(:,21)+ CONSTANTS(:,22).*STATES(:,1);
    ALGEBRAIC(:,2) = CONSTANTS(:,24)+ CONSTANTS(:,25).*STATES(:,1);
    ALGEBRAIC(:,5) = power(STATES(:,1), 2.00000)./(power(CONSTANTS(:,30), 2.00000)+power(STATES(:,1), 2.00000));
    ALGEBRAIC(:,3) = CONSTANTS(:,27)+ CONSTANTS(:,28).*STATES(:,1);
    ALGEBRAIC(:,6) = STATES(:,2)+STATES(:,1)+STATES(:,3);
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