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 6 entries in each of the rate and state variable arrays.
% There are a total of 21 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 AE1 (second)');
    LEGEND_CONSTANTS(:,1) = strpad('RT in component param (kJ_per_mol)');
    LEGEND_CONSTANTS(:,2) = strpad('K_Cl_o in component param (per_mol)');
    LEGEND_CONSTANTS(:,3) = strpad('K_Cl_i in component param (per_mol)');
    LEGEND_CONSTANTS(:,4) = strpad('K_HCO3_i in component param (per_mol)');
    LEGEND_CONSTANTS(:,5) = strpad('K_HCO3_o in component param (per_mol)');
    LEGEND_CONSTANTS(:,6) = strpad('K_E_o in component param (per_mol)');
    LEGEND_CONSTANTS(:,7) = strpad('K_ECl_o in component param (per_mol)');
    LEGEND_CONSTANTS(:,8) = strpad('K_ECl_i in component param (per_mol)');
    LEGEND_CONSTANTS(:,9) = strpad('K_E_i in component param (per_mol)');
    LEGEND_CONSTANTS(:,10) = strpad('K_EHCO3_i in component param (per_mol)');
    LEGEND_CONSTANTS(:,11) = strpad('K_EHCO3_o in component param (per_mol)');
    LEGEND_CONSTANTS(:,12) = strpad('K_Re1 in component param (mM_per_s)');
    LEGEND_CONSTANTS(:,13) = strpad('K_Re2 in component param (mM_per_s)');
    LEGEND_CONSTANTS(:,14) = strpad('K_Re3 in component param (mM_per_s)');
    LEGEND_CONSTANTS(:,15) = strpad('K_Re4 in component param (mM_per_s)');
    LEGEND_CONSTANTS(:,16) = strpad('K_Re5 in component param (mM_per_s)');
    LEGEND_CONSTANTS(:,17) = strpad('K_Re6 in component param (mM_per_s)');
    LEGEND_CONSTANTS(:,18) = strpad('q_Cl_o in component AE1 (mole)');
    LEGEND_CONSTANTS(:,19) = strpad('q_Cl_i in component AE1 (mole)');
    LEGEND_CONSTANTS(:,20) = strpad('q_HCO3_i in component AE1 (mole)');
    LEGEND_CONSTANTS(:,21) = strpad('q_HCO3_o in component AE1 (mole)');
    LEGEND_STATES(:,1) = strpad('q_E_o in component AE1 (mole)');
    LEGEND_STATES(:,2) = strpad('q_ECl_o in component AE1 (mole)');
    LEGEND_STATES(:,3) = strpad('q_ECl_i in component AE1 (mole)');
    LEGEND_STATES(:,4) = strpad('q_E_i in component AE1 (mole)');
    LEGEND_STATES(:,5) = strpad('q_EHCO3_i in component AE1 (mole)');
    LEGEND_STATES(:,6) = strpad('q_EHCO3_o in component AE1 (mole)');
    LEGEND_ALGEBRAIC(:,1) = strpad('v_Re1 in component AE1 (mM_per_s)');
    LEGEND_ALGEBRAIC(:,2) = strpad('v_Re2 in component AE1 (mM_per_s)');
    LEGEND_ALGEBRAIC(:,3) = strpad('v_Re3 in component AE1 (mM_per_s)');
    LEGEND_ALGEBRAIC(:,4) = strpad('v_Re4 in component AE1 (mM_per_s)');
    LEGEND_ALGEBRAIC(:,5) = strpad('v_Re5 in component AE1 (mM_per_s)');
    LEGEND_ALGEBRAIC(:,6) = strpad('v_Re6 in component AE1 (mM_per_s)');
    LEGEND_RATES(:,1) = strpad('d/dt q_E_o in component AE1 (mole)');
    LEGEND_RATES(:,2) = strpad('d/dt q_ECl_o in component AE1 (mole)');
    LEGEND_RATES(:,3) = strpad('d/dt q_ECl_i in component AE1 (mole)');
    LEGEND_RATES(:,4) = strpad('d/dt q_E_i in component AE1 (mole)');
    LEGEND_RATES(:,5) = strpad('d/dt q_EHCO3_i in component AE1 (mole)');
    LEGEND_RATES(:,6) = strpad('d/dt q_EHCO3_o in component AE1 (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) = 2.5;
    CONSTANTS(:,2) = 1.34784535e+00;
    CONSTANTS(:,3) = 1.34809503e+00;
    CONSTANTS(:,4) = 8.37243345e-01;
    CONSTANTS(:,5) = 8.37398440e-01;
    CONSTANTS(:,6) = 3.42812779e+00;
    CONSTANTS(:,7) = 2.30943735e+02;
    CONSTANTS(:,8) = 2.50575623e+01;
    CONSTANTS(:,9) = 3.71610024e-01;
    CONSTANTS(:,10) = 6.15805309e+01;
    CONSTANTS(:,11) = 5.68610961e+02;
    CONSTANTS(:,12) = 2.16462852e+01;
    CONSTANTS(:,13) = 2.43394395e+00;
    CONSTANTS(:,14) = 1.99577523e+02;
    CONSTANTS(:,15) = 3.21470643e+02;
    CONSTANTS(:,16) = 2.19265742e+00;
    CONSTANTS(:,17) = 3.48281500e+01;
    CONSTANTS(:,18) = 114;
    CONSTANTS(:,19) = 29;
    CONSTANTS(:,20) = 0.0;
    CONSTANTS(:,21) = 26;
    STATES(:,1) = 0.01738;
    STATES(:,2) = 0.0396;
    STATES(:,3) = 0.274;
    STATES(:,4) = 0.473;
    STATES(:,5) = 0.0621;
    STATES(:,6) = 0.00228;
    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(:,12).*( CONSTANTS(:,2).*CONSTANTS(:,18).*CONSTANTS(:,6).*STATES(:,1) -  CONSTANTS(:,7).*STATES(:,2));
    ALGEBRAIC(:,2) =  CONSTANTS(:,13).*( CONSTANTS(:,7).*STATES(:,2) -  CONSTANTS(:,8).*STATES(:,3));
    RATES(:,2) = ALGEBRAIC(:,1) - ALGEBRAIC(:,2);
    ALGEBRAIC(:,3) =  CONSTANTS(:,14).*( CONSTANTS(:,8).*STATES(:,3) -  CONSTANTS(:,3).*CONSTANTS(:,19).*CONSTANTS(:,9).*STATES(:,4));
    RATES(:,3) = ALGEBRAIC(:,2) - ALGEBRAIC(:,3);
    ALGEBRAIC(:,4) =  CONSTANTS(:,15).*( CONSTANTS(:,4).*CONSTANTS(:,20).*CONSTANTS(:,9).*STATES(:,4) -  CONSTANTS(:,10).*STATES(:,5));
    RATES(:,4) = ALGEBRAIC(:,3) - ALGEBRAIC(:,4);
    ALGEBRAIC(:,5) =  CONSTANTS(:,16).*( CONSTANTS(:,10).*STATES(:,5) -  CONSTANTS(:,11).*STATES(:,6));
    RATES(:,5) = ALGEBRAIC(:,4) - ALGEBRAIC(:,5);
    ALGEBRAIC(:,6) =  CONSTANTS(:,17).*( CONSTANTS(:,11).*STATES(:,6) -  CONSTANTS(:,5).*CONSTANTS(:,21).*CONSTANTS(:,6).*STATES(:,1));
    RATES(:,1) = ALGEBRAIC(:,6) - ALGEBRAIC(:,1);
    RATES(:,6) = ALGEBRAIC(:,5) - ALGEBRAIC(:,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) =  CONSTANTS(:,12).*( CONSTANTS(:,2).*CONSTANTS(:,18).*CONSTANTS(:,6).*STATES(:,1) -  CONSTANTS(:,7).*STATES(:,2));
    ALGEBRAIC(:,2) =  CONSTANTS(:,13).*( CONSTANTS(:,7).*STATES(:,2) -  CONSTANTS(:,8).*STATES(:,3));
    ALGEBRAIC(:,3) =  CONSTANTS(:,14).*( CONSTANTS(:,8).*STATES(:,3) -  CONSTANTS(:,3).*CONSTANTS(:,19).*CONSTANTS(:,9).*STATES(:,4));
    ALGEBRAIC(:,4) =  CONSTANTS(:,15).*( CONSTANTS(:,4).*CONSTANTS(:,20).*CONSTANTS(:,9).*STATES(:,4) -  CONSTANTS(:,10).*STATES(:,5));
    ALGEBRAIC(:,5) =  CONSTANTS(:,16).*( CONSTANTS(:,10).*STATES(:,5) -  CONSTANTS(:,11).*STATES(:,6));
    ALGEBRAIC(:,6) =  CONSTANTS(:,17).*( CONSTANTS(:,11).*STATES(:,6) -  CONSTANTS(:,5).*CONSTANTS(:,21).*CONSTANTS(:,6).*STATES(:,1));
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