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 3 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 (hour)');
    LEGEND_CONSTANTS(:,16) = strpad('F_b in component gastrointestinal_compartment (dimensionless)');
    LEGEND_STATES(:,1) = strpad('A_dopa_b in component gastrointestinal_compartment (umole)');
    LEGEND_CONSTANTS(:,1) = strpad('ka_b in component gastrointestinal_compartment (per_hour)');
    LEGEND_CONSTANTS(:,10) = strpad('F_G in component gastrointestinal_compartment (dimensionless)');
    LEGEND_CONSTANTS(:,14) = strpad('F_H in component gastrointestinal_compartment (dimensionless)');
    LEGEND_CONSTANTS(:,12) = strpad('CL_H in component gastrointestinal_compartment (liter_per_hour)');
    LEGEND_CONSTANTS(:,2) = strpad('Q in component gastrointestinal_compartment (liter_per_hour)');
    LEGEND_CONSTANTS(:,3) = strpad('f_H in component gastrointestinal_compartment (dimensionless)');
    LEGEND_CONSTANTS(:,4) = strpad('CL_dopa_0 in component L_dopa_clearance (liter_per_hour)');
    LEGEND_STATES(:,2) = strpad('C_dopa_b in component body_compartment_L_dopa (uM)');
    LEGEND_CONSTANTS(:,5) = strpad('V_dopa in component body_compartment_L_dopa (liter)');
    LEGEND_CONSTANTS(:,18) = strpad('CL_dopa in component L_dopa_clearance (liter_per_hour)');
    LEGEND_STATES(:,3) = strpad('C_OMD_b in component body_compartment_3_OMD (uM)');
    LEGEND_CONSTANTS(:,6) = strpad('CL_OMD_b in component body_compartment_3_OMD (liter_per_hour)');
    LEGEND_CONSTANTS(:,7) = strpad('V_OMD_b in component body_compartment_3_OMD (liter)');
    LEGEND_CONSTANTS(:,15) = strpad('CL_COMT in component L_dopa_clearance (liter_per_hour)');
    LEGEND_CONSTANTS(:,13) = strpad('CL_AADC in component L_dopa_clearance (liter_per_hour)');
    LEGEND_CONSTANTS(:,11) = strpad('CL_AADC0 in component L_dopa_clearance (liter_per_hour)');
    LEGEND_CONSTANTS(:,8) = strpad('C1_M in component L_dopa_clearance (uM)');
    LEGEND_CONSTANTS(:,17) = strpad('CL_REST in component L_dopa_clearance (liter_per_hour)');
    LEGEND_CONSTANTS(:,9) = strpad('ki in component L_dopa_clearance (uM)');
    LEGEND_RATES(:,1) = strpad('d/dt A_dopa_b in component gastrointestinal_compartment (umole)');
    LEGEND_RATES(:,2) = strpad('d/dt C_dopa_b in component body_compartment_L_dopa (uM)');
    LEGEND_RATES(:,3) = strpad('d/dt C_OMD_b in component body_compartment_3_OMD (uM)');
    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) = 101;
    CONSTANTS(:,1) = 2.11;
    CONSTANTS(:,2) = 0.828;
    CONSTANTS(:,3) = 0.13;
    CONSTANTS(:,4) = 0.823;
    STATES(:,2) = 0;
    CONSTANTS(:,5) = 0.496;
    STATES(:,3) = 0;
    CONSTANTS(:,6) = 0.012;
    CONSTANTS(:,7) = 0.196;
    CONSTANTS(:,8) = 0;
    CONSTANTS(:,9) = 0.00246;
    CONSTANTS(:,10) = 0.244000;
    CONSTANTS(:,11) =  CONSTANTS(:,4).*0.690000;
    CONSTANTS(:,12) =  CONSTANTS(:,3).*CONSTANTS(:,4);
    CONSTANTS(:,13) = CONSTANTS(:,11)./(1.00000+CONSTANTS(:,8)./CONSTANTS(:,9));
    CONSTANTS(:,14) = 1.00000 - CONSTANTS(:,12)./CONSTANTS(:,2);
    CONSTANTS(:,15) =  CONSTANTS(:,4).*0.100000;
    CONSTANTS(:,16) =  CONSTANTS(:,14).*CONSTANTS(:,10);
    CONSTANTS(:,17) =  CONSTANTS(:,4).*0.210000;
    CONSTANTS(:,18) = CONSTANTS(:,13)+CONSTANTS(:,15)+CONSTANTS(:,17);
    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(:,1).*STATES(:,1);
    RATES(:,2) =  (1.00000./CONSTANTS(:,5)).*( CONSTANTS(:,1).*STATES(:,1).*CONSTANTS(:,16) -  CONSTANTS(:,18).*STATES(:,2));
    RATES(:,3) =  (1.00000./CONSTANTS(:,7)).*( CONSTANTS(:,15).*STATES(:,2) -  CONSTANTS(:,6).*STATES(:,3));
   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