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 =16;
end
% There are a total of 9 entries in each of the rate and state variable arrays.
% There are a total of 16 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('A in component A (molecules)');
    LEGEND_ALGEBRAIC(:,1) = strpad('RXN1 in component RXN1 (flux)');
    LEGEND_ALGEBRAIC(:,2) = strpad('RXN2 in component RXN2 (flux)');
    LEGEND_ALGEBRAIC(:,5) = strpad('RXN5 in component RXN5 (flux)');
    LEGEND_ALGEBRAIC(:,11) = strpad('RXN11 in component RXN11 (flux)');
    LEGEND_ALGEBRAIC(:,6) = strpad('RXN6 in component RXN6 (flux)');
    LEGEND_ALGEBRAIC(:,10) = strpad('RXN10 in component RXN10 (flux)');
    LEGEND_ALGEBRAIC(:,12) = strpad('RXN12 in component RXN12 (flux)');
    LEGEND_STATES(:,2) = strpad('C in component C (molecules)');
    LEGEND_ALGEBRAIC(:,3) = strpad('RXN3 in component RXN3 (flux)');
    LEGEND_STATES(:,3) = strpad('DA in component DA (molecules)');
    LEGEND_ALGEBRAIC(:,7) = strpad('RXN7 in component RXN7 (flux)');
    LEGEND_STATES(:,4) = strpad('DAp in component DAp (molecules)');
    LEGEND_ALGEBRAIC(:,8) = strpad('RXN8 in component RXN8 (flux)');
    LEGEND_STATES(:,5) = strpad('DR in component DR (molecules)');
    LEGEND_ALGEBRAIC(:,13) = strpad('RXN13 in component RXN13 (flux)');
    LEGEND_STATES(:,6) = strpad('DRP in component DRP (molecules)');
    LEGEND_ALGEBRAIC(:,14) = strpad('RXN14 in component RXN14 (flux)');
    LEGEND_STATES(:,7) = strpad('MA in component MA (molecules)');
    LEGEND_ALGEBRAIC(:,9) = strpad('RXN9 in component RXN9 (flux)');
    LEGEND_STATES(:,8) = strpad('MR in component MR (molecules)');
    LEGEND_ALGEBRAIC(:,15) = strpad('RXN15 in component RXN15 (flux)');
    LEGEND_ALGEBRAIC(:,16) = strpad('RXN16 in component RXN16 (flux)');
    LEGEND_STATES(:,9) = strpad('R in component R (molecules)');
    LEGEND_ALGEBRAIC(:,4) = strpad('RXN4 in component RXN4 (flux)');
    LEGEND_CONSTANTS(:,1) = strpad('Gamma_1 in component RXN1 (second_order_rate)');
    LEGEND_CONSTANTS(:,2) = strpad('Delta_1 in component RXN2 (first_order_rate)');
    LEGEND_CONSTANTS(:,3) = strpad('Delta_2 in component RXN3 (first_order_rate)');
    LEGEND_CONSTANTS(:,4) = strpad('Delta_3 in component RXN4 (first_order_rate)');
    LEGEND_CONSTANTS(:,5) = strpad('Gamma_2 in component RXN5 (second_order_rate)');
    LEGEND_CONSTANTS(:,6) = strpad('Thetha_1 in component RXN6 (first_order_rate)');
    LEGEND_CONSTANTS(:,7) = strpad('Alpha_1 in component RXN7 (first_order_rate)');
    LEGEND_CONSTANTS(:,8) = strpad('Alpha_2 in component RXN8 (first_order_rate)');
    LEGEND_CONSTANTS(:,9) = strpad('Delta_4 in component RXN9 (first_order_rate)');
    LEGEND_CONSTANTS(:,10) = strpad('BetaA_1 in component RXN10 (first_order_rate)');
    LEGEND_CONSTANTS(:,11) = strpad('Gamma_3 in component RXN11 (second_order_rate)');
    LEGEND_CONSTANTS(:,12) = strpad('Theta_2 in component RXN12 (first_order_rate)');
    LEGEND_CONSTANTS(:,13) = strpad('Alpha_3 in component RXN13 (first_order_rate)');
    LEGEND_CONSTANTS(:,14) = strpad('Alpha_4 in component RXN14 (first_order_rate)');
    LEGEND_CONSTANTS(:,15) = strpad('Delta_5 in component RXN15 (first_order_rate)');
    LEGEND_CONSTANTS(:,16) = strpad('BetaR_1 in component RXN16 (first_order_rate)');
    LEGEND_RATES(:,1) = strpad('d/dt A in component A (molecules)');
    LEGEND_RATES(:,2) = strpad('d/dt C in component C (molecules)');
    LEGEND_RATES(:,3) = strpad('d/dt DA in component DA (molecules)');
    LEGEND_RATES(:,4) = strpad('d/dt DAp in component DAp (molecules)');
    LEGEND_RATES(:,5) = strpad('d/dt DR in component DR (molecules)');
    LEGEND_RATES(:,6) = strpad('d/dt DRP in component DRP (molecules)');
    LEGEND_RATES(:,7) = strpad('d/dt MA in component MA (molecules)');
    LEGEND_RATES(:,8) = strpad('d/dt MR in component MR (molecules)');
    LEGEND_RATES(:,9) = strpad('d/dt R in component R (molecules)');
    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) = 0.0;
    STATES(:,2) = 0.0;
    STATES(:,3) = 1;
    STATES(:,4) = 0.0;
    STATES(:,5) = 1;
    STATES(:,6) = 1;
    STATES(:,7) = 0.0;
    STATES(:,8) = 0.0;
    STATES(:,9) = 0.0;
    CONSTANTS(:,1) = 2;
    CONSTANTS(:,2) = 1;
    CONSTANTS(:,3) = 1;
    CONSTANTS(:,4) = 0.2;
    CONSTANTS(:,5) = 1;
    CONSTANTS(:,6) = 50;
    CONSTANTS(:,7) = 50;
    CONSTANTS(:,8) = 500;
    CONSTANTS(:,9) = 10;
    CONSTANTS(:,10) = 50;
    CONSTANTS(:,11) = 1;
    CONSTANTS(:,12) = 100;
    CONSTANTS(:,13) = 0.01;
    CONSTANTS(:,14) = 50;
    CONSTANTS(:,15) = 0.5;
    CONSTANTS(:,16) = 5;
    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(:,1) =  STATES(:,1).*STATES(:,9).*CONSTANTS(:,1);
    ALGEBRAIC(:,3) =  STATES(:,2).*CONSTANTS(:,3);
    RATES(:,2) =  (1.00000./1.00000).*(  - 1.00000.*ALGEBRAIC(:,3)+ALGEBRAIC(:,1));
    ALGEBRAIC(:,5) =  STATES(:,1).*STATES(:,3).*CONSTANTS(:,5);
    ALGEBRAIC(:,6) =  STATES(:,4).*CONSTANTS(:,6);
    ALGEBRAIC(:,7) =  STATES(:,3).*CONSTANTS(:,7);
    RATES(:,3) =  (1.00000./1.00000).*( -1.00000.*ALGEBRAIC(:,5)+ -1.00000.*ALGEBRAIC(:,7)+ALGEBRAIC(:,6)+ALGEBRAIC(:,7));
    ALGEBRAIC(:,8) =  STATES(:,4).*CONSTANTS(:,8);
    RATES(:,4) =  (1.00000./1.00000).*( -1.00000.*ALGEBRAIC(:,6)+ -1.00000.*ALGEBRAIC(:,8)+ALGEBRAIC(:,5)+ALGEBRAIC(:,8));
    ALGEBRAIC(:,10) =  STATES(:,7).*CONSTANTS(:,10);
    ALGEBRAIC(:,9) =  STATES(:,7).*CONSTANTS(:,9);
    RATES(:,7) =  (1.00000./1.00000).*( -1.00000.*ALGEBRAIC(:,9)+ -1.00000.*ALGEBRAIC(:,10)+ALGEBRAIC(:,7)+ALGEBRAIC(:,8)+ALGEBRAIC(:,10));
    ALGEBRAIC(:,2) =  STATES(:,1).*CONSTANTS(:,2);
    ALGEBRAIC(:,11) =  STATES(:,1).*STATES(:,5).*CONSTANTS(:,11);
    ALGEBRAIC(:,12) =  STATES(:,6).*CONSTANTS(:,12);
    RATES(:,1) =  (1.00000./1.00000).*(  - 1.00000.*ALGEBRAIC(:,1)+  - 1.00000.*ALGEBRAIC(:,2)+  - 1.00000.*ALGEBRAIC(:,5)+  - 1.00000.*ALGEBRAIC(:,11)+ALGEBRAIC(:,6)+ALGEBRAIC(:,10)+ALGEBRAIC(:,12));
    ALGEBRAIC(:,13) =  STATES(:,5).*CONSTANTS(:,13);
    RATES(:,5) =  (1.00000./1.00000).*( -1.00000.*ALGEBRAIC(:,11)+ -1.00000.*ALGEBRAIC(:,13)+ALGEBRAIC(:,12)+ALGEBRAIC(:,13));
    ALGEBRAIC(:,14) =  STATES(:,6).*CONSTANTS(:,14);
    RATES(:,6) =  (1.00000./1.00000).*( -1.00000.*ALGEBRAIC(:,12)+ -1.00000.*ALGEBRAIC(:,14)+ALGEBRAIC(:,11)+ALGEBRAIC(:,14));
    ALGEBRAIC(:,15) =  STATES(:,8).*CONSTANTS(:,15);
    ALGEBRAIC(:,16) =  STATES(:,8).*CONSTANTS(:,16);
    RATES(:,8) =  (1.00000./1.00000).*( -1.00000.*ALGEBRAIC(:,15)+ -1.00000.*ALGEBRAIC(:,16)+ALGEBRAIC(:,13)+ALGEBRAIC(:,14)+ALGEBRAIC(:,16));
    ALGEBRAIC(:,4) =  STATES(:,9).*CONSTANTS(:,4);
    RATES(:,9) =  (1.00000./1.00000).*( -1.00000.*ALGEBRAIC(:,1)+ -1.00000.*ALGEBRAIC(:,4)+ALGEBRAIC(:,3)+ALGEBRAIC(:,16));
   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).*STATES(:,9).*CONSTANTS(:,1);
    ALGEBRAIC(:,3) =  STATES(:,2).*CONSTANTS(:,3);
    ALGEBRAIC(:,5) =  STATES(:,1).*STATES(:,3).*CONSTANTS(:,5);
    ALGEBRAIC(:,6) =  STATES(:,4).*CONSTANTS(:,6);
    ALGEBRAIC(:,7) =  STATES(:,3).*CONSTANTS(:,7);
    ALGEBRAIC(:,8) =  STATES(:,4).*CONSTANTS(:,8);
    ALGEBRAIC(:,10) =  STATES(:,7).*CONSTANTS(:,10);
    ALGEBRAIC(:,9) =  STATES(:,7).*CONSTANTS(:,9);
    ALGEBRAIC(:,2) =  STATES(:,1).*CONSTANTS(:,2);
    ALGEBRAIC(:,11) =  STATES(:,1).*STATES(:,5).*CONSTANTS(:,11);
    ALGEBRAIC(:,12) =  STATES(:,6).*CONSTANTS(:,12);
    ALGEBRAIC(:,13) =  STATES(:,5).*CONSTANTS(:,13);
    ALGEBRAIC(:,14) =  STATES(:,6).*CONSTANTS(:,14);
    ALGEBRAIC(:,15) =  STATES(:,8).*CONSTANTS(:,15);
    ALGEBRAIC(:,16) =  STATES(:,8).*CONSTANTS(:,16);
    ALGEBRAIC(:,4) =  STATES(:,9).*CONSTANTS(:,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