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 6 entries in each of the rate and state variable arrays.
% There are a total of 11 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('t in component main (second)');
    LEGEND_CONSTANTS(:,1) = strpad('RT in component main (J_per_mol)');
    LEGEND_STATES(:,1) = strpad('q_1 in component main (mole)');
    LEGEND_STATES(:,2) = strpad('q_2 in component main (mole)');
    LEGEND_STATES(:,3) = strpad('q_3 in component main (mole)');
    LEGEND_STATES(:,4) = strpad('q_4 in component main (mole)');
    LEGEND_STATES(:,5) = strpad('q_e0 in component main (mole)');
    LEGEND_STATES(:,6) = strpad('q_e1 in component main (mole)');
    LEGEND_ALGEBRAIC(:,15) = strpad('v_1 in component main (mol_per_s)');
    LEGEND_ALGEBRAIC(:,16) = strpad('v_2 in component main (mol_per_s)');
    LEGEND_ALGEBRAIC(:,1) = strpad('u_1 in component main (J_per_mol)');
    LEGEND_ALGEBRAIC(:,3) = strpad('u_2 in component main (J_per_mol)');
    LEGEND_ALGEBRAIC(:,5) = strpad('u_3 in component main (J_per_mol)');
    LEGEND_ALGEBRAIC(:,7) = strpad('u_4 in component main (J_per_mol)');
    LEGEND_ALGEBRAIC(:,9) = strpad('u_e0 in component main (J_per_mol)');
    LEGEND_ALGEBRAIC(:,12) = strpad('u_e1 in component main (J_per_mol)');
    LEGEND_ALGEBRAIC(:,10) = strpad('u_f_1 in component main (J_per_mol)');
    LEGEND_ALGEBRAIC(:,13) = strpad('u_r_1 in component main (J_per_mol)');
    LEGEND_ALGEBRAIC(:,14) = strpad('u_f_2 in component main (J_per_mol)');
    LEGEND_ALGEBRAIC(:,11) = strpad('u_r_2 in component main (J_per_mol)');
    LEGEND_CONSTANTS(:,2) = strpad('K_q_1 in component main (per_mol)');
    LEGEND_CONSTANTS(:,3) = strpad('K_q_2 in component main (per_mol)');
    LEGEND_CONSTANTS(:,4) = strpad('K_q_3 in component main (per_mol)');
    LEGEND_CONSTANTS(:,5) = strpad('K_q_4 in component main (per_mol)');
    LEGEND_CONSTANTS(:,6) = strpad('K_q_e0 in component main (per_mol)');
    LEGEND_CONSTANTS(:,7) = strpad('K_q_e1 in component main (per_mol)');
    LEGEND_CONSTANTS(:,8) = strpad('kappa_1 in component main (mol_per_s)');
    LEGEND_CONSTANTS(:,9) = strpad('kappa_2 in component main (mol_per_s)');
    LEGEND_ALGEBRAIC(:,2) = strpad('q_e_tot in component main (mole)');
    LEGEND_ALGEBRAIC(:,4) = strpad('A_f in component main (per_mol3_per_s)');
    LEGEND_ALGEBRAIC(:,6) = strpad('A_r in component main (per_mol3_per_s)');
    LEGEND_CONSTANTS(:,10) = strpad('B_f in component main (per_mol3)');
    LEGEND_CONSTANTS(:,11) = strpad('B_r in component main (per_mol3)');
    LEGEND_ALGEBRAIC(:,8) = strpad('v_SS in component main (mol_per_s)');
    LEGEND_RATES(:,1) = strpad('d/dt q_1 in component main (mole)');
    LEGEND_RATES(:,2) = strpad('d/dt q_2 in component main (mole)');
    LEGEND_RATES(:,3) = strpad('d/dt q_3 in component main (mole)');
    LEGEND_RATES(:,4) = strpad('d/dt q_4 in component main (mole)');
    LEGEND_RATES(:,5) = strpad('d/dt q_e0 in component main (mole)');
    LEGEND_RATES(:,6) = strpad('d/dt q_e1 in component main (mole)');
    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) = 2578.73058;
    STATES(:,1) = 3;
    STATES(:,2) = 1;
    STATES(:,3) = 0;
    STATES(:,4) = 0;
    STATES(:,5) = 1;
    STATES(:,6) = 1;
    CONSTANTS(:,2) = 2;
    CONSTANTS(:,3) = 2;
    CONSTANTS(:,4) = 2;
    CONSTANTS(:,5) = 2;
    CONSTANTS(:,6) = 2;
    CONSTANTS(:,7) = 2;
    CONSTANTS(:,8) = 0.20;
    CONSTANTS(:,9) = 0.1;
    CONSTANTS(:,10) =  (( (CONSTANTS(:,6)./CONSTANTS(:,7)).*CONSTANTS(:,8))./(CONSTANTS(:,8)+CONSTANTS(:,9))).*CONSTANTS(:,2).*power(CONSTANTS(:,3), 2.00000);
    CONSTANTS(:,11) =  (( (CONSTANTS(:,6)./CONSTANTS(:,7)).*CONSTANTS(:,8))./(CONSTANTS(:,8)+CONSTANTS(:,9))).*CONSTANTS(:,4).*power(CONSTANTS(:,5), 2.00000);
    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) =  CONSTANTS(:,1).*log( CONSTANTS(:,2).*STATES(:,1));
    ALGEBRAIC(:,3) =  CONSTANTS(:,1).*log( CONSTANTS(:,3).*STATES(:,2));
    ALGEBRAIC(:,9) =  CONSTANTS(:,1).*log( CONSTANTS(:,6).*STATES(:,5));
    ALGEBRAIC(:,10) = ALGEBRAIC(:,1)+ 2.00000.*ALGEBRAIC(:,3)+ALGEBRAIC(:,9);
    ALGEBRAIC(:,12) =  CONSTANTS(:,1).*log( CONSTANTS(:,7).*STATES(:,6));
    ALGEBRAIC(:,13) = ALGEBRAIC(:,12);
    ALGEBRAIC(:,15) =  CONSTANTS(:,8).*(exp(ALGEBRAIC(:,10)./CONSTANTS(:,1)) - exp(ALGEBRAIC(:,13)./CONSTANTS(:,1)));
    RATES(:,1) =  - ALGEBRAIC(:,15);
    RATES(:,2) =   - 2.00000.*ALGEBRAIC(:,15);
    ALGEBRAIC(:,14) = ALGEBRAIC(:,12);
    ALGEBRAIC(:,5) =  CONSTANTS(:,1).*log( CONSTANTS(:,4).*STATES(:,3));
    ALGEBRAIC(:,7) =  CONSTANTS(:,1).*log( CONSTANTS(:,5).*STATES(:,4));
    ALGEBRAIC(:,11) = ALGEBRAIC(:,5)+ 2.00000.*ALGEBRAIC(:,7)+ALGEBRAIC(:,9);
    ALGEBRAIC(:,16) =  CONSTANTS(:,9).*(exp(ALGEBRAIC(:,14)./CONSTANTS(:,1)) - exp(ALGEBRAIC(:,11)./CONSTANTS(:,1)));
    RATES(:,3) = ALGEBRAIC(:,16);
    RATES(:,4) =  2.00000.*ALGEBRAIC(:,16);
    RATES(:,5) = ALGEBRAIC(:,16) - ALGEBRAIC(:,15);
    RATES(:,6) = ALGEBRAIC(:,15) - 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) =  CONSTANTS(:,1).*log( CONSTANTS(:,2).*STATES(:,1));
    ALGEBRAIC(:,3) =  CONSTANTS(:,1).*log( CONSTANTS(:,3).*STATES(:,2));
    ALGEBRAIC(:,9) =  CONSTANTS(:,1).*log( CONSTANTS(:,6).*STATES(:,5));
    ALGEBRAIC(:,10) = ALGEBRAIC(:,1)+ 2.00000.*ALGEBRAIC(:,3)+ALGEBRAIC(:,9);
    ALGEBRAIC(:,12) =  CONSTANTS(:,1).*log( CONSTANTS(:,7).*STATES(:,6));
    ALGEBRAIC(:,13) = ALGEBRAIC(:,12);
    ALGEBRAIC(:,15) =  CONSTANTS(:,8).*(exp(ALGEBRAIC(:,10)./CONSTANTS(:,1)) - exp(ALGEBRAIC(:,13)./CONSTANTS(:,1)));
    ALGEBRAIC(:,14) = ALGEBRAIC(:,12);
    ALGEBRAIC(:,5) =  CONSTANTS(:,1).*log( CONSTANTS(:,4).*STATES(:,3));
    ALGEBRAIC(:,7) =  CONSTANTS(:,1).*log( CONSTANTS(:,5).*STATES(:,4));
    ALGEBRAIC(:,11) = ALGEBRAIC(:,5)+ 2.00000.*ALGEBRAIC(:,7)+ALGEBRAIC(:,9);
    ALGEBRAIC(:,16) =  CONSTANTS(:,9).*(exp(ALGEBRAIC(:,14)./CONSTANTS(:,1)) - exp(ALGEBRAIC(:,11)./CONSTANTS(:,1)));
    ALGEBRAIC(:,2) = STATES(:,5)+STATES(:,6);
    ALGEBRAIC(:,4) =  (( ALGEBRAIC(:,2).*CONSTANTS(:,6).*CONSTANTS(:,8).*CONSTANTS(:,9))./(CONSTANTS(:,8)+CONSTANTS(:,9))).*CONSTANTS(:,2).*power(CONSTANTS(:,3), 2.00000);
    ALGEBRAIC(:,6) =  (( ALGEBRAIC(:,2).*CONSTANTS(:,6).*CONSTANTS(:,8).*CONSTANTS(:,9))./(CONSTANTS(:,8)+CONSTANTS(:,9))).*CONSTANTS(:,4).*power(CONSTANTS(:,5), 2.00000);
    ALGEBRAIC(:,8) = ( ALGEBRAIC(:,4).*STATES(:,1).*power(STATES(:,2), 2.00000) -  ALGEBRAIC(:,6).*STATES(:,3).*power(STATES(:,4), 2.00000))./(1.00000+ CONSTANTS(:,10).*STATES(:,1).*power(STATES(:,2), 2.00000)+ CONSTANTS(:,11).*STATES(:,3).*power(STATES(:,4), 2.00000));
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