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 =0;
end
% There are a total of 9 entries in each of the rate and state variable arrays.
% There are a total of 40 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 (hour)');
    LEGEND_STATES(:,1) = strpad('pRB in component pRB (CONC)');
    LEGEND_CONSTANTS(:,1) = strpad('k1 in component model_parameters (dimensionless)');
    LEGEND_STATES(:,2) = strpad('E2F1 in component E2F1 (CONC)');
    LEGEND_CONSTANTS(:,2) = strpad('km1 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,3) = strpad('j11 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,4) = strpad('j61 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,5) = strpad('k16 in component model_parameters (dimensionless)');
    LEGEND_STATES(:,3) = strpad('CycDa in component CycDa (CONC)');
    LEGEND_CONSTANTS(:,6) = strpad('k61 in component model_parameters (dimensionless)');
    LEGEND_STATES(:,4) = strpad('pRBp in component pRBp (CONC)');
    LEGEND_CONSTANTS(:,7) = strpad('phi_pRB in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,8) = strpad('kp in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('k2 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,10) = strpad('a in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,11) = strpad('km2 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,12) = strpad('j12 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,13) = strpad('j62 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,14) = strpad('phi_E2F1 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,15) = strpad('k34 in component model_parameters (dimensionless)');
    LEGEND_STATES(:,5) = strpad('CycDi in component CycDi (CONC)');
    LEGEND_CONSTANTS(:,16) = strpad('km4 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,17) = strpad('k43 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,18) = strpad('phi_CycDa in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,19) = strpad('k3 in component model_parameters (dimensionless)');
    LEGEND_STATES(:,6) = strpad('AP1 in component AP1 (CONC)');
    LEGEND_CONSTANTS(:,20) = strpad('k23 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,21) = strpad('j13 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,22) = strpad('j63 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,23) = strpad('phi_CycDi in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,24) = strpad('Fm in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,25) = strpad('k25 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,26) = strpad('j15 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,27) = strpad('j65 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,28) = strpad('phi_AP1 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,29) = strpad('k67 in component model_parameters (dimensionless)');
    LEGEND_STATES(:,7) = strpad('CycEa in component CycEa (CONC)');
    LEGEND_CONSTANTS(:,30) = strpad('k76 in component model_parameters (dimensionless)');
    LEGEND_STATES(:,8) = strpad('pRBpp in component pRBpp (CONC)');
    LEGEND_CONSTANTS(:,31) = strpad('phi_pRBp in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,32) = strpad('phi_pRBpp in component model_parameters (dimensionless)');
    LEGEND_STATES(:,9) = strpad('CycEi in component CycEi (CONC)');
    LEGEND_CONSTANTS(:,33) = strpad('k28 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,34) = strpad('j18 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,35) = strpad('j68 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,36) = strpad('k98 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,37) = strpad('k89 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,38) = strpad('km9 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,39) = strpad('phi_CycEi in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,40) = strpad('phi_CycEa in component model_parameters (dimensionless)');
    LEGEND_RATES(:,1) = strpad('d/dt pRB in component pRB (CONC)');
    LEGEND_RATES(:,2) = strpad('d/dt E2F1 in component E2F1 (CONC)');
    LEGEND_RATES(:,3) = strpad('d/dt CycDa in component CycDa (CONC)');
    LEGEND_RATES(:,5) = strpad('d/dt CycDi in component CycDi (CONC)');
    LEGEND_RATES(:,6) = strpad('d/dt AP1 in component AP1 (CONC)');
    LEGEND_RATES(:,4) = strpad('d/dt pRBp in component pRBp (CONC)');
    LEGEND_RATES(:,8) = strpad('d/dt pRBpp in component pRBpp (CONC)');
    LEGEND_RATES(:,9) = strpad('d/dt CycEi in component CycEi (CONC)');
    LEGEND_RATES(:,7) = strpad('d/dt CycEa in component CycEa (CONC)');
    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) = 1;
    STATES(:,2) = 0;
    CONSTANTS(:,2) = 0.5;
    CONSTANTS(:,3) = 0.5;
    CONSTANTS(:,4) = 5;
    CONSTANTS(:,5) = 0.4;
    STATES(:,3) = 0;
    CONSTANTS(:,6) = 0.3;
    STATES(:,4) = 0;
    CONSTANTS(:,7) = 0.005;
    CONSTANTS(:,8) = 0.05;
    CONSTANTS(:,9) = 1.6;
    CONSTANTS(:,10) = 0.04;
    CONSTANTS(:,11) = 4;
    CONSTANTS(:,12) = 5;
    CONSTANTS(:,13) = 8;
    CONSTANTS(:,14) = 0.1;
    CONSTANTS(:,15) = 0.04;
    STATES(:,5) = 0;
    CONSTANTS(:,16) = 0.3;
    CONSTANTS(:,17) = 0.01;
    CONSTANTS(:,18) = 0.03;
    CONSTANTS(:,19) = 0.05;
    STATES(:,6) = 0;
    CONSTANTS(:,20) = 0.3;
    CONSTANTS(:,21) = 0.002;
    CONSTANTS(:,22) = 2;
    CONSTANTS(:,23) = 0.023;
    CONSTANTS(:,24) = 0;
    CONSTANTS(:,25) = 0.9;
    CONSTANTS(:,26) = 0.001;
    CONSTANTS(:,27) = 6;
    CONSTANTS(:,28) = 0.01;
    CONSTANTS(:,29) = 0.7;
    STATES(:,7) = 0;
    CONSTANTS(:,30) = 0.1;
    STATES(:,8) = 0;
    CONSTANTS(:,31) = 0.06;
    CONSTANTS(:,32) = 0.04;
    STATES(:,9) = 0;
    CONSTANTS(:,33) = 0.06;
    CONSTANTS(:,34) = 0.6;
    CONSTANTS(:,35) = 7;
    CONSTANTS(:,36) = 0.01;
    CONSTANTS(:,37) = 0.07;
    CONSTANTS(:,38) = 0.005;
    CONSTANTS(:,39) = 0.06;
    CONSTANTS(:,40) = 0.05;
    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(:,1).*(STATES(:,2)./(CONSTANTS(:,2)+STATES(:,2))).*(CONSTANTS(:,3)./( CONSTANTS(:,3).*STATES(:,1))).*(CONSTANTS(:,4)./( CONSTANTS(:,4).*STATES(:,4))) -  CONSTANTS(:,5).*STATES(:,1).*STATES(:,3))+ CONSTANTS(:,6).*STATES(:,4)) -  CONSTANTS(:,7).*STATES(:,1);
    RATES(:,2) = (CONSTANTS(:,8)+ CONSTANTS(:,9).*((power(CONSTANTS(:,10), 2.00000)+power(STATES(:,2), 2.00000))./(power(CONSTANTS(:,11), 2.00000)+power(STATES(:,2), 2.00000))).*(CONSTANTS(:,12)./(CONSTANTS(:,12)+STATES(:,4))).*(CONSTANTS(:,13)./(CONSTANTS(:,13)+STATES(:,4)))) -  CONSTANTS(:,14).*STATES(:,2);
    RATES(:,3) = (( CONSTANTS(:,15).*STATES(:,5).*STATES(:,3))./(CONSTANTS(:,16)+STATES(:,3)) -  CONSTANTS(:,15).*STATES(:,3)) -  CONSTANTS(:,18).*STATES(:,3);
    RATES(:,5) = (( CONSTANTS(:,19).*STATES(:,6)+ CONSTANTS(:,20).*STATES(:,2).*(CONSTANTS(:,21)./(CONSTANTS(:,21)+STATES(:,1))).*(CONSTANTS(:,22)./(CONSTANTS(:,22)+STATES(:,4)))+ CONSTANTS(:,17).*STATES(:,3)) -  CONSTANTS(:,15).*STATES(:,5).*(STATES(:,3)./(CONSTANTS(:,16)+STATES(:,3)))) -  CONSTANTS(:,23).*STATES(:,5);
    RATES(:,6) = (CONSTANTS(:,24)+ CONSTANTS(:,25).*STATES(:,2).*(CONSTANTS(:,26)./(CONSTANTS(:,26)+STATES(:,1))).*(CONSTANTS(:,27)./(CONSTANTS(:,27)+STATES(:,4)))) -  CONSTANTS(:,28).*STATES(:,6);
    RATES(:,4) = ((( CONSTANTS(:,5).*STATES(:,1).*STATES(:,3) -  CONSTANTS(:,6).*STATES(:,4)) -  CONSTANTS(:,29).*STATES(:,4).*STATES(:,7))+ CONSTANTS(:,30).*STATES(:,8)) -  CONSTANTS(:,31).*STATES(:,4);
    RATES(:,8) = ( CONSTANTS(:,29).*STATES(:,4).*STATES(:,7) -  CONSTANTS(:,30).*STATES(:,8)) -  CONSTANTS(:,32).*STATES(:,8);
    RATES(:,9) = (( CONSTANTS(:,33).*STATES(:,2).*(CONSTANTS(:,34)./(CONSTANTS(:,34)+STATES(:,1))).*(CONSTANTS(:,35)./(CONSTANTS(:,35)+STATES(:,4)))+ CONSTANTS(:,36).*STATES(:,7)) -  CONSTANTS(:,37).*STATES(:,9).*(STATES(:,7)./(CONSTANTS(:,38)+STATES(:,7)))) -  CONSTANTS(:,39).*STATES(:,9);
    RATES(:,7) = ( CONSTANTS(:,37).*STATES(:,9).*(STATES(:,7)./(CONSTANTS(:,38)+STATES(:,7))) -  CONSTANTS(:,36).*STATES(:,7)) -  CONSTANTS(:,40).*STATES(:,7);
   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
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