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 =13;
end
% There are a total of 2 entries in each of the rate and state variable arrays.
% There are a total of 41 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 (minute)');
    LEGEND_CONSTANTS(:,1) = strpad('PA in component autonomics (mmHg)');
    LEGEND_CONSTANTS(:,2) = strpad('PO2ART in component autonomics (mmHg)');
    LEGEND_CONSTANTS(:,3) = strpad('PLA in component autonomics (mmHg)');
    LEGEND_CONSTANTS(:,4) = strpad('PRA in component autonomics (mmHg)');
    LEGEND_CONSTANTS(:,5) = strpad('PPA in component autonomics (mmHg)');
    LEGEND_CONSTANTS(:,32) = strpad('PA1 in component pressure_driving_autonomic_receptors (mmHg)');
    LEGEND_CONSTANTS(:,6) = strpad('CRRFLX in component parameter_values (mmHg)');
    LEGEND_CONSTANTS(:,7) = strpad('EXE in component parameter_values (mmHg)');
    LEGEND_CONSTANTS(:,33) = strpad('AUC in component chemoreceptors_effect_of_PA (dimensionless)');
    LEGEND_CONSTANTS(:,8) = strpad('AUC1 in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,38) = strpad('AUC3 in component chemoreceptors_effect_of_art_PO2 (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('O2CHMO in component parameter_values (per_mmHg)');
    LEGEND_CONSTANTS(:,35) = strpad('AUC2 in component chemoreceptors_effect_of_art_PO2 (dimensionless)');
    LEGEND_ALGEBRAIC(:,1) = strpad('AU6C in component arterial_baroreceptor_reflex (dimensionless)');
    LEGEND_CONSTANTS(:,10) = strpad('AUX in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,11) = strpad('AUK in component parameter_values (per_minute)');
    LEGEND_CONSTANTS(:,12) = strpad('BAROTC in component parameter_values (minute)');
    LEGEND_CONSTANTS(:,34) = strpad('AUB in component arterial_baroreceptor_reflex (dimensionless)');
    LEGEND_CONSTANTS(:,36) = strpad('A1B in component arterial_baroreceptor_reflex (dimensionless)');
    LEGEND_CONSTANTS(:,37) = strpad('AU6A in component arterial_baroreceptor_reflex (dimensionless)');
    LEGEND_CONSTANTS(:,13) = strpad('AU4 in component arterial_baroreceptor_reflex (dimensionless)');
    LEGEND_STATES(:,1) = strpad('AU6 in component arterial_baroreceptor_reflex (dimensionless)');
    LEGEND_CONSTANTS(:,39) = strpad('AUN in component CNS_ischemic_reflex (dimensionless)');
    LEGEND_CONSTANTS(:,14) = strpad('AUN1 in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,40) = strpad('AULP in component autonomic_response_to_vasculature_pressure (dimensionless)');
    LEGEND_CONSTANTS(:,15) = strpad('AULPM in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,41) = strpad('AUEX in component autonomic_response_to_exercise (dimensionless)');
    LEGEND_CONSTANTS(:,16) = strpad('EXC in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,17) = strpad('EXCXP in component parameter_values (dimensionless)');
    LEGEND_ALGEBRAIC(:,5) = strpad('AUTTL in component total_autonomic_stimulation (dimensionless)');
    LEGEND_ALGEBRAIC(:,3) = strpad('AUTTL1 in component total_autonomic_stimulation (dimensionless)');
    LEGEND_CONSTANTS(:,18) = strpad('EXCML in component parameter_values (dimensionless)');
    LEGEND_ALGEBRAIC(:,4) = strpad('AU in component actual_autonomic_stimulation (dimensionless)');
    LEGEND_CONSTANTS(:,19) = strpad('AUDMP in component parameter_values (minute)');
    LEGEND_CONSTANTS(:,20) = strpad('AUMAX in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,21) = strpad('AUMIN in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,22) = strpad('AUSLP in component parameter_values (dimensionless)');
    LEGEND_ALGEBRAIC(:,8) = strpad('DAU in component actual_autonomic_stimulation (per_minute)');
    LEGEND_STATES(:,2) = strpad('AU1 in component actual_autonomic_stimulation (dimensionless)');
    LEGEND_ALGEBRAIC(:,2) = strpad('AUT in component actual_autonomic_stimulation (dimensionless)');
    LEGEND_ALGEBRAIC(:,6) = strpad('VVR in component autonomic_drive_on_target_organs_and_tissues (litre)');
    LEGEND_ALGEBRAIC(:,9) = strpad('AUH in component autonomic_drive_on_target_organs_and_tissues (dimensionless)');
    LEGEND_ALGEBRAIC(:,10) = strpad('AUR in component autonomic_drive_on_target_organs_and_tissues (dimensionless)');
    LEGEND_ALGEBRAIC(:,11) = strpad('AOM in component autonomic_drive_on_target_organs_and_tissues (dimensionless)');
    LEGEND_ALGEBRAIC(:,12) = strpad('AUM in component autonomic_drive_on_target_organs_and_tissues (dimensionless)');
    LEGEND_ALGEBRAIC(:,13) = strpad('AVE in component autonomic_drive_on_target_organs_and_tissues (dimensionless)');
    LEGEND_CONSTANTS(:,23) = strpad('VV9 in component parameter_values (litre)');
    LEGEND_CONSTANTS(:,24) = strpad('AUL in component parameter_values (litre)');
    LEGEND_CONSTANTS(:,25) = strpad('AUV in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,26) = strpad('AUS in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,27) = strpad('O2A in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,28) = strpad('AUM1 in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,29) = strpad('AUM2 in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,30) = strpad('AUY in component parameter_values (dimensionless)');
    LEGEND_ALGEBRAIC(:,7) = strpad('AUO in component autonomic_drive_on_target_organs_and_tissues (dimensionless)');
    LEGEND_CONSTANTS(:,31) = strpad('MDMP in component parameter_values (dimensionless)');
    LEGEND_RATES(:,1) = strpad('d/dt AU6 in component arterial_baroreceptor_reflex (dimensionless)');
    LEGEND_RATES(:,2) = strpad('d/dt AU1 in component actual_autonomic_stimulation (dimensionless)');
    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) = 103.525;
    CONSTANTS(:,2) = 97.0439;
    CONSTANTS(:,3) = 2;
    CONSTANTS(:,4) = 0.00852183;
    CONSTANTS(:,5) = 15.6376;
    CONSTANTS(:,6) = 0;
    CONSTANTS(:,7) = 0;
    CONSTANTS(:,8) = 0.3;
    CONSTANTS(:,9) = 0.01;
    CONSTANTS(:,10) = 1;
    CONSTANTS(:,11) = 0.004;
    CONSTANTS(:,12) = 0.16;
    CONSTANTS(:,13) = -0.060024;
    STATES(:,1) = 1.00132;
    CONSTANTS(:,14) = 0.5;
    CONSTANTS(:,15) = 0;
    CONSTANTS(:,16) = 1;
    CONSTANTS(:,17) = 1.0;
    CONSTANTS(:,18) = 0.01;
    CONSTANTS(:,19) = 0.3;
    CONSTANTS(:,20) = 5.0;
    CONSTANTS(:,21) = 0.4;
    CONSTANTS(:,22) = 1.5;
    STATES(:,2) = 1.00007;
    CONSTANTS(:,23) = 2.51;
    CONSTANTS(:,24) = 1.5;
    CONSTANTS(:,25) = 0.55;
    CONSTANTS(:,26) = 1;
    CONSTANTS(:,27) = 0.1;
    CONSTANTS(:,28) = 3;
    CONSTANTS(:,29) = 1;
    CONSTANTS(:,30) = 0;
    CONSTANTS(:,31) = 0;
    CONSTANTS(:,32) = piecewise({CONSTANTS(:,6)>1.00000e-07, CONSTANTS(:,6) }, CONSTANTS(:,1) - CONSTANTS(:,7));
    CONSTANTS(:,33) = piecewise({CONSTANTS(:,32)<80.0000&CONSTANTS(:,32)>=40.0000,  0.00500000.*(80.0000 - CONSTANTS(:,32)).*CONSTANTS(:,8) , CONSTANTS(:,32)<40.0000,  0.200000.*CONSTANTS(:,8) }, 0.00000);
    CONSTANTS(:,34) = piecewise({CONSTANTS(:,32)<160.000&CONSTANTS(:,32)>=80.0000,  0.0166670.*(160.000 - CONSTANTS(:,32)) , CONSTANTS(:,32)<80.0000, 1.33360 }, 0.00000);
    CONSTANTS(:,35) = piecewise({CONSTANTS(:,2)<80.0000&CONSTANTS(:,2)>=40.0000,  CONSTANTS(:,9).*(80.0000 - CONSTANTS(:,2)) , CONSTANTS(:,2)<40.0000,  CONSTANTS(:,9).*40.0000 }, 0.00000);
    CONSTANTS(:,36) =  (CONSTANTS(:,34) - 1.00000).*CONSTANTS(:,10)+1.00000;
    CONSTANTS(:,37) = CONSTANTS(:,36) - CONSTANTS(:,13);
    CONSTANTS(:,38) = CONSTANTS(:,33)+CONSTANTS(:,35);
    CONSTANTS(:,39) = piecewise({CONSTANTS(:,32)<40.0000,  0.0400000.*(40.0000 - CONSTANTS(:,32)).*CONSTANTS(:,14) }, 0.00000);
    CONSTANTS(:,40) =  (15.0000./(CONSTANTS(:,3)+CONSTANTS(:,4)+CONSTANTS(:,5)) - 1.00000).*CONSTANTS(:,15)+1.00000;
    CONSTANTS(:,41) = power(CONSTANTS(:,16), 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(:,37) - STATES(:,1))./CONSTANTS(:,12);
    ALGEBRAIC(:,1) = STATES(:,1);
    ALGEBRAIC(:,3) =  ( CONSTANTS(:,41).*CONSTANTS(:,40).*(CONSTANTS(:,38)+ALGEBRAIC(:,1)+CONSTANTS(:,39)) - 1.00000).*CONSTANTS(:,18)+1.00000;
    ALGEBRAIC(:,5) = piecewise({ALGEBRAIC(:,3)<0.00000, 0.00000 }, ALGEBRAIC(:,3));
    ALGEBRAIC(:,8) = (ALGEBRAIC(:,5) - STATES(:,2))./CONSTANTS(:,19);
    RATES(:,2) = ALGEBRAIC(:,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
    ALGEBRAIC(:,1) = STATES(:,1);
    ALGEBRAIC(:,3) =  ( CONSTANTS(:,41).*CONSTANTS(:,40).*(CONSTANTS(:,38)+ALGEBRAIC(:,1)+CONSTANTS(:,39)) - 1.00000).*CONSTANTS(:,18)+1.00000;
    ALGEBRAIC(:,5) = piecewise({ALGEBRAIC(:,3)<0.00000, 0.00000 }, ALGEBRAIC(:,3));
    ALGEBRAIC(:,8) = (ALGEBRAIC(:,5) - STATES(:,2))./CONSTANTS(:,19);
    ALGEBRAIC(:,2) = CONSTANTS(:,20) - (CONSTANTS(:,20) - 1.00000)./exp( CONSTANTS(:,22).*(STATES(:,2) - 1.00000));
    ALGEBRAIC(:,4) = piecewise({ALGEBRAIC(:,2)<CONSTANTS(:,21), CONSTANTS(:,21) }, ALGEBRAIC(:,2));
    ALGEBRAIC(:,6) = (CONSTANTS(:,23) -  ALGEBRAIC(:,4).*CONSTANTS(:,24))+CONSTANTS(:,24);
    ALGEBRAIC(:,7) = ALGEBRAIC(:,4) - 1.00000;
    ALGEBRAIC(:,9) =  ALGEBRAIC(:,7).*CONSTANTS(:,25)+1.00000;
    ALGEBRAIC(:,10) =  ALGEBRAIC(:,7).*CONSTANTS(:,26)+1.00000;
    ALGEBRAIC(:,11) =  ALGEBRAIC(:,7).*CONSTANTS(:,27)+1.00000;
    ALGEBRAIC(:,12) = power( ALGEBRAIC(:,7).*CONSTANTS(:,28)+1.00000, CONSTANTS(:,29));
    ALGEBRAIC(:,13) =  ALGEBRAIC(:,7).*CONSTANTS(:,30)+1.00000;
end

% Compute result of a piecewise function
function x = piecewise(cases, default)
    set = [0];
    for i = 1:2:length(cases)
        if (length(cases{i+1}) == 1)
            x(cases{i} & ~set,:) = cases{i+1};
        else
            x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set);
        end
        set = set | cases{i};
        if(set), break, end
    end
    if (length(default) == 1)
        x(~set,:) = default;
    else
        x(~set,:) = default(~set);
    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