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 6 entries in each of the rate and state variable arrays.
% There are a total of 28 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('H_1 in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,2) = strpad('H_2 in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,3) = strpad('H_3 in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,4) = strpad('H_4 in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,5) = strpad('K_1 in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,6) = strpad('K_2 in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,7) = strpad('K_3 in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,8) = strpad('K_4 in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('V_M1 in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,10) = strpad('V_M3 in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,11) = strpad('U_M1 in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,12) = strpad('U_M3 in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,13) = strpad('V_2 in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,14) = strpad('V_4 in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,15) = strpad('U_2 in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,16) = strpad('U_4 in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,17) = strpad('K_c1 in component parameters (micromolar)');
    LEGEND_CONSTANTS(:,18) = strpad('K_c2 in component parameters (micromolar)');
    LEGEND_CONSTANTS(:,19) = strpad('K_d1 in component parameters (micromolar)');
    LEGEND_CONSTANTS(:,20) = strpad('K_d2 in component parameters (micromolar)');
    LEGEND_CONSTANTS(:,21) = strpad('v_d1 in component parameters (flux)');
    LEGEND_CONSTANTS(:,22) = strpad('v_d2 in component parameters (flux)');
    LEGEND_CONSTANTS(:,23) = strpad('v_i1 in component parameters (flux)');
    LEGEND_CONSTANTS(:,24) = strpad('v_i2 in component parameters (flux)');
    LEGEND_CONSTANTS(:,25) = strpad('k_d1 in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,26) = strpad('k_d2 in component parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,27) = strpad('K_im1 in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,28) = strpad('K_im2 in component parameters (dimensionless)');
    LEGEND_STATES(:,1) = strpad('C_1 in component C_1 (micromolar)');
    LEGEND_STATES(:,2) = strpad('M_2 in component M_2 (dimensionless)');
    LEGEND_STATES(:,3) = strpad('X_1 in component X_1 (dimensionless)');
    LEGEND_STATES(:,4) = strpad('M_1 in component M_1 (dimensionless)');
    LEGEND_ALGEBRAIC(:,1) = strpad('V_1 in component V_1 (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,2) = strpad('V_3 in component V_3 (first_order_rate_constant)');
    LEGEND_STATES(:,5) = strpad('C_2 in component C_2 (micromolar)');
    LEGEND_STATES(:,6) = strpad('X_2 in component X_2 (dimensionless)');
    LEGEND_ALGEBRAIC(:,3) = strpad('U_1 in component U_1 (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,4) = strpad('U_3 in component U_3 (first_order_rate_constant)');
    LEGEND_RATES(:,1) = strpad('d/dt C_1 in component C_1 (micromolar)');
    LEGEND_RATES(:,4) = strpad('d/dt M_1 in component M_1 (dimensionless)');
    LEGEND_RATES(:,3) = strpad('d/dt X_1 in component X_1 (dimensionless)');
    LEGEND_RATES(:,5) = strpad('d/dt C_2 in component C_2 (micromolar)');
    LEGEND_RATES(:,2) = strpad('d/dt M_2 in component M_2 (dimensionless)');
    LEGEND_RATES(:,6) = strpad('d/dt X_2 in component X_2 (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) = 0.01;
    CONSTANTS(:,2) = 0.01;
    CONSTANTS(:,3) = 0.01;
    CONSTANTS(:,4) = 0.01;
    CONSTANTS(:,5) = 0.01;
    CONSTANTS(:,6) = 0.01;
    CONSTANTS(:,7) = 0.01;
    CONSTANTS(:,8) = 0.01;
    CONSTANTS(:,9) = 0.3;
    CONSTANTS(:,10) = 0.1;
    CONSTANTS(:,11) = 0.3;
    CONSTANTS(:,12) = 0.1;
    CONSTANTS(:,13) = 0.15;
    CONSTANTS(:,14) = 0.05;
    CONSTANTS(:,15) = 0.15;
    CONSTANTS(:,16) = 0.05;
    CONSTANTS(:,17) = 0.5;
    CONSTANTS(:,18) = 0.5;
    CONSTANTS(:,19) = 0.02;
    CONSTANTS(:,20) = 0.02;
    CONSTANTS(:,21) = 0.025;
    CONSTANTS(:,22) = 0.025;
    CONSTANTS(:,23) = 0.05;
    CONSTANTS(:,24) = 0.05;
    CONSTANTS(:,25) = 0.001;
    CONSTANTS(:,26) = 0.001;
    CONSTANTS(:,27) = 0.03;
    CONSTANTS(:,28) = 0.03;
    STATES(:,1) = 2;
    STATES(:,2) = 0;
    STATES(:,3) = 0;
    STATES(:,4) = 1;
    STATES(:,5) = 0;
    STATES(:,6) = 0;
    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(:,23).*CONSTANTS(:,27))./(CONSTANTS(:,27)+STATES(:,2)) - ( CONSTANTS(:,21).*STATES(:,3).*STATES(:,1))./(CONSTANTS(:,19)+STATES(:,1))) -  CONSTANTS(:,25).*STATES(:,1);
    RATES(:,5) = (( CONSTANTS(:,24).*CONSTANTS(:,28))./(CONSTANTS(:,28)+STATES(:,4)) - ( CONSTANTS(:,22).*STATES(:,6).*STATES(:,5))./(CONSTANTS(:,20)+STATES(:,5))) -  CONSTANTS(:,26).*STATES(:,5);
    ALGEBRAIC(:,1) =  (STATES(:,1)./(CONSTANTS(:,17)+STATES(:,1))).*CONSTANTS(:,9);
    RATES(:,4) = ( ALGEBRAIC(:,1).*(1.00000 - STATES(:,4)))./(CONSTANTS(:,5)+(1.00000 - STATES(:,4))) - ( CONSTANTS(:,13).*STATES(:,4))./(CONSTANTS(:,6)+STATES(:,4));
    ALGEBRAIC(:,2) =  STATES(:,4).*CONSTANTS(:,10);
    RATES(:,3) = ( ALGEBRAIC(:,2).*(1.00000 - STATES(:,3)))./(CONSTANTS(:,7)+(1.00000 - STATES(:,3))) - ( CONSTANTS(:,14).*STATES(:,3))./(CONSTANTS(:,8)+STATES(:,3));
    ALGEBRAIC(:,3) =  (STATES(:,5)./(CONSTANTS(:,18)+STATES(:,5))).*CONSTANTS(:,11);
    RATES(:,2) = ( ALGEBRAIC(:,3).*(1.00000 - STATES(:,2)))./(CONSTANTS(:,1)+(1.00000 - STATES(:,2))) - ( CONSTANTS(:,15).*STATES(:,2))./(CONSTANTS(:,2)+STATES(:,2));
    ALGEBRAIC(:,4) =  STATES(:,2).*CONSTANTS(:,12);
    RATES(:,6) = ( ALGEBRAIC(:,4).*(1.00000 - STATES(:,6)))./(CONSTANTS(:,3)+(1.00000 - STATES(:,6))) - ( CONSTANTS(:,16).*STATES(:,6))./(CONSTANTS(:,4)+STATES(:,6));
   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(:,1)./(CONSTANTS(:,17)+STATES(:,1))).*CONSTANTS(:,9);
    ALGEBRAIC(:,2) =  STATES(:,4).*CONSTANTS(:,10);
    ALGEBRAIC(:,3) =  (STATES(:,5)./(CONSTANTS(:,18)+STATES(:,5))).*CONSTANTS(:,11);
    ALGEBRAIC(:,4) =  STATES(:,2).*CONSTANTS(:,12);
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