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 =11;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 14 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_STATES(:,1) = strpad('q_GTP in component environment (fmol)');
    LEGEND_STATES(:,2) = strpad('q_E5c in component environment (fmol)');
    LEGEND_STATES(:,3) = strpad('q_cGMP in component environment (fmol)');
    LEGEND_STATES(:,4) = strpad('q_PDE in component environment (fmol)');
    LEGEND_STATES(:,5) = strpad('q_GTP_E5c in component environment (fmol)');
    LEGEND_STATES(:,6) = strpad('q_cGMP_PDE in component environment (fmol)');
    LEGEND_STATES(:,7) = strpad('q_GMP in component environment (fmol)');
    LEGEND_ALGEBRAIC(:,8) = strpad('v_R_1a_cGMP in component cGMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,9) = strpad('v_R_1b_cGMP in component cGMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,10) = strpad('v_R_2a_cGMP in component cGMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,11) = strpad('v_R_2b_cGMP in component cGMP (fmol_per_sec)');
    LEGEND_CONSTANTS(:,1) = strpad('kappa_R_1a_cGMP in component cGMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,2) = strpad('kappa_R_1b_cGMP in component cGMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,3) = strpad('kappa_R_2a_cGMP in component cGMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,4) = strpad('kappa_R_2b_cGMP in component cGMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,5) = strpad('K_GTP in component cGMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,6) = strpad('K_E5c in component cGMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,7) = strpad('K_cGMP in component cGMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,8) = strpad('K_PDE in component cGMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,9) = strpad('K_GTP_E5c in component cGMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,10) = strpad('K_cGMP_PDE in component cGMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,11) = strpad('K_GMP in component cGMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,12) = strpad('R in component constants (J_per_K_per_mol)');
    LEGEND_CONSTANTS(:,13) = strpad('T in component constants (kelvin)');
    LEGEND_ALGEBRAIC(:,1) = strpad('mu_GTP in component cGMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,2) = strpad('mu_E5c in component cGMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,3) = strpad('mu_cGMP in component cGMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,4) = strpad('mu_PDE in component cGMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,5) = strpad('mu_GTP_E5c in component cGMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,6) = strpad('mu_cGMP_PDE in component cGMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,7) = strpad('mu_GMP in component cGMP (J_per_mol)');
    LEGEND_CONSTANTS(:,14) = strpad('F in component constants (C_per_mol)');
    LEGEND_RATES(:,1) = strpad('d/dt q_GTP in component environment (fmol)');
    LEGEND_RATES(:,2) = strpad('d/dt q_E5c in component environment (fmol)');
    LEGEND_RATES(:,3) = strpad('d/dt q_cGMP in component environment (fmol)');
    LEGEND_RATES(:,4) = strpad('d/dt q_PDE in component environment (fmol)');
    LEGEND_RATES(:,5) = strpad('d/dt q_GTP_E5c in component environment (fmol)');
    LEGEND_RATES(:,6) = strpad('d/dt q_cGMP_PDE in component environment (fmol)');
    LEGEND_RATES(:,7) = strpad('d/dt q_GMP in component environment (fmol)');
    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) = 1e-18;
    STATES(:,2) = 1e-18;
    STATES(:,3) = 1e-18;
    STATES(:,4) = 1e-18;
    STATES(:,5) = 1e-18;
    STATES(:,6) = 1e-18;
    STATES(:,7) = 1e-18;
    CONSTANTS(:,1) = 1772.99;
    CONSTANTS(:,2) = 0.0302117;
    CONSTANTS(:,3) = 73652.7;
    CONSTANTS(:,4) = 0.0143623;
    CONSTANTS(:,5) = 1600.8;
    CONSTANTS(:,6) = 0.0255983;
    CONSTANTS(:,7) = 0.0939434;
    CONSTANTS(:,8) = 10.5002;
    CONSTANTS(:,9) = 152.027;
    CONSTANTS(:,10) = 7.31926;
    CONSTANTS(:,11) = 0.000481761;
    CONSTANTS(:,12) = 8.31;
    CONSTANTS(:,13) = 310;
    CONSTANTS(:,14) = 96485;
    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(:,13).*log( CONSTANTS(:,5).*STATES(:,1));
    ALGEBRAIC(:,2) =  CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,6).*STATES(:,2));
    ALGEBRAIC(:,5) =  CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,9).*STATES(:,5));
    ALGEBRAIC(:,8) =  CONSTANTS(:,1).*(exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,2))./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp(ALGEBRAIC(:,5)./( CONSTANTS(:,12).*CONSTANTS(:,13))));
    RATES(:,1) =  - ALGEBRAIC(:,8);
    ALGEBRAIC(:,3) =  CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,7).*STATES(:,3));
    ALGEBRAIC(:,9) =  CONSTANTS(:,2).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,2))./( CONSTANTS(:,12).*CONSTANTS(:,13))));
    RATES(:,2) =  - ALGEBRAIC(:,8)+ALGEBRAIC(:,9);
    RATES(:,5) = ALGEBRAIC(:,8) - ALGEBRAIC(:,9);
    ALGEBRAIC(:,4) =  CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,8).*STATES(:,4));
    ALGEBRAIC(:,6) =  CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,10).*STATES(:,6));
    ALGEBRAIC(:,10) =  CONSTANTS(:,3).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,4))./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,12).*CONSTANTS(:,13))));
    ALGEBRAIC(:,7) =  CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,11).*STATES(:,7));
    ALGEBRAIC(:,11) =  CONSTANTS(:,4).*(exp((ALGEBRAIC(:,6)+ALGEBRAIC(:,3))./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,4))./( CONSTANTS(:,12).*CONSTANTS(:,13))));
    RATES(:,3) = (ALGEBRAIC(:,9) - ALGEBRAIC(:,10)) - ALGEBRAIC(:,11);
    RATES(:,4) =  - ALGEBRAIC(:,10)+ALGEBRAIC(:,11);
    RATES(:,6) = ALGEBRAIC(:,10) - ALGEBRAIC(:,11);
    RATES(:,7) = ALGEBRAIC(:,11);
   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(:,13).*log( CONSTANTS(:,5).*STATES(:,1));
    ALGEBRAIC(:,2) =  CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,6).*STATES(:,2));
    ALGEBRAIC(:,5) =  CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,9).*STATES(:,5));
    ALGEBRAIC(:,8) =  CONSTANTS(:,1).*(exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,2))./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp(ALGEBRAIC(:,5)./( CONSTANTS(:,12).*CONSTANTS(:,13))));
    ALGEBRAIC(:,3) =  CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,7).*STATES(:,3));
    ALGEBRAIC(:,9) =  CONSTANTS(:,2).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,2))./( CONSTANTS(:,12).*CONSTANTS(:,13))));
    ALGEBRAIC(:,4) =  CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,8).*STATES(:,4));
    ALGEBRAIC(:,6) =  CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,10).*STATES(:,6));
    ALGEBRAIC(:,10) =  CONSTANTS(:,3).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,4))./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,12).*CONSTANTS(:,13))));
    ALGEBRAIC(:,7) =  CONSTANTS(:,12).*CONSTANTS(:,13).*log( CONSTANTS(:,11).*STATES(:,7));
    ALGEBRAIC(:,11) =  CONSTANTS(:,4).*(exp((ALGEBRAIC(:,6)+ALGEBRAIC(:,3))./( CONSTANTS(:,12).*CONSTANTS(:,13))) - exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,4))./( CONSTANTS(:,12).*CONSTANTS(:,13))));
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