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 11 entries in each of the rate and state variable arrays.
% There are a total of 18 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 (second)');
    LEGEND_CONSTANTS(:,1) = strpad('k11 in component kinetic_constants (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,2) = strpad('k11_ in component kinetic_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,3) = strpad('k71 in component kinetic_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,4) = strpad('k72 in component kinetic_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,5) = strpad('k12 in component kinetic_constants (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,6) = strpad('k12_ in component kinetic_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,7) = strpad('k51 in component kinetic_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,8) = strpad('k52 in component kinetic_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,9) = strpad('k41 in component kinetic_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,10) = strpad('k31 in component kinetic_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,11) = strpad('k32 in component kinetic_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,12) = strpad('k42 in component kinetic_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,13) = strpad('k22 in component kinetic_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,14) = strpad('k22_ in component kinetic_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,15) = strpad('k21 in component kinetic_constants (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,16) = strpad('k21_ in component kinetic_constants (first_order_rate_constant)');
    LEGEND_STATES(:,1) = strpad('PB in component PB (micromolar)');
    LEGEND_CONSTANTS(:,17) = strpad('kreset1 in component kreset1 (first_order_rate_constant)');
    LEGEND_STATES(:,2) = strpad('A1 in component A1 (micromolar)');
    LEGEND_STATES(:,3) = strpad('A2 in component A2 (micromolar)');
    LEGEND_STATES(:,4) = strpad('PC1 in component PC1 (micromolar)');
    LEGEND_STATES(:,5) = strpad('PF1 in component PF1 (micromolar)');
    LEGEND_STATES(:,6) = strpad('PG1 in component PG1 (micromolar)');
    LEGEND_STATES(:,7) = strpad('PC2 in component PC2 (micromolar)');
    LEGEND_STATES(:,8) = strpad('PF2 in component PF2 (micromolar)');
    LEGEND_STATES(:,9) = strpad('PD1 in component PD1 (micromolar)');
    LEGEND_STATES(:,10) = strpad('PE1 in component PE1 (micromolar)');
    LEGEND_STATES(:,11) = strpad('PD2 in component PD2 (micromolar)');
    LEGEND_CONSTANTS(:,18) = strpad('PE2 in component PE2 (micromolar)');
    LEGEND_RATES(:,1) = strpad('d/dt PB in component PB (micromolar)');
    LEGEND_RATES(:,2) = strpad('d/dt A1 in component A1 (micromolar)');
    LEGEND_RATES(:,3) = strpad('d/dt A2 in component A2 (micromolar)');
    LEGEND_RATES(:,4) = strpad('d/dt PC1 in component PC1 (micromolar)');
    LEGEND_RATES(:,9) = strpad('d/dt PD1 in component PD1 (micromolar)');
    LEGEND_RATES(:,10) = strpad('d/dt PE1 in component PE1 (micromolar)');
    LEGEND_RATES(:,5) = strpad('d/dt PF1 in component PF1 (micromolar)');
    LEGEND_RATES(:,6) = strpad('d/dt PG1 in component PG1 (micromolar)');
    LEGEND_RATES(:,7) = strpad('d/dt PC2 in component PC2 (micromolar)');
    LEGEND_RATES(:,11) = strpad('d/dt PD2 in component PD2 (micromolar)');
    LEGEND_RATES(:,8) = strpad('d/dt PF2 in component PF2 (micromolar)');
    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) = 110.0;
    CONSTANTS(:,2) = 25.0;
    CONSTANTS(:,3) = 0.1;
    CONSTANTS(:,4) = 60.0;
    CONSTANTS(:,5) = 110.0;
    CONSTANTS(:,6) = 0.2;
    CONSTANTS(:,7) = 7.0;
    CONSTANTS(:,8) = 0.0;
    CONSTANTS(:,9) = 60.0;
    CONSTANTS(:,10) = 500.0;
    CONSTANTS(:,11) = 50.0;
    CONSTANTS(:,12) = 70.0;
    CONSTANTS(:,13) = 100.0;
    CONSTANTS(:,14) = 17.0;
    CONSTANTS(:,15) = 100.0;
    CONSTANTS(:,16) = 0.2;
    STATES(:,1) = 0.1;
    CONSTANTS(:,17) = 35.0;
    STATES(:,2) = 0.1;
    STATES(:,3) = 0.1;
    STATES(:,4) = 0.1;
    STATES(:,5) = 0.1;
    STATES(:,6) = 0.1;
    STATES(:,7) = 0.1;
    STATES(:,8) = 0.1;
    STATES(:,9) = 0.1;
    STATES(:,10) = 0.1;
    STATES(:,11) = 0.1;
    CONSTANTS(:,18) = 0.1;
    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(:,2).*STATES(:,4)+ CONSTANTS(:,3).*STATES(:,5)+ CONSTANTS(:,17).*STATES(:,6)+ CONSTANTS(:,6).*STATES(:,7)+ CONSTANTS(:,4).*STATES(:,8)) - ( CONSTANTS(:,1).*STATES(:,2).*STATES(:,1)+ CONSTANTS(:,5).*STATES(:,3).*STATES(:,1));
    RATES(:,2) =  CONSTANTS(:,2).*STATES(:,4) -  CONSTANTS(:,1).*STATES(:,2).*STATES(:,1);
    RATES(:,3) =  CONSTANTS(:,6).*STATES(:,7) -  CONSTANTS(:,5).*STATES(:,3).*STATES(:,1);
    RATES(:,4) = ( CONSTANTS(:,1).*STATES(:,2).*STATES(:,1) -  (CONSTANTS(:,2)+CONSTANTS(:,15)).*STATES(:,4))+ CONSTANTS(:,16).*STATES(:,9);
    RATES(:,9) =  CONSTANTS(:,15).*STATES(:,4) -  (CONSTANTS(:,16)+CONSTANTS(:,10)).*STATES(:,9);
    RATES(:,10) =  CONSTANTS(:,10).*STATES(:,9) -  CONSTANTS(:,9).*STATES(:,10);
    RATES(:,5) =  CONSTANTS(:,9).*STATES(:,10) -  (CONSTANTS(:,7)+CONSTANTS(:,3)).*STATES(:,5);
    RATES(:,6) =  CONSTANTS(:,7).*STATES(:,5) -  CONSTANTS(:,17).*STATES(:,6);
    RATES(:,7) = ( CONSTANTS(:,5).*STATES(:,3).*STATES(:,1) -  (CONSTANTS(:,6)+CONSTANTS(:,13)).*STATES(:,7))+ CONSTANTS(:,14).*STATES(:,11);
    RATES(:,11) =  CONSTANTS(:,13).*STATES(:,7) -  (CONSTANTS(:,14)+CONSTANTS(:,11)).*STATES(:,11);
    RATES(:,8) =  CONSTANTS(:,12).*CONSTANTS(:,18) -  (CONSTANTS(:,8)+CONSTANTS(:,4)).*STATES(:,8);
   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