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 1 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('time in component environment (minute)');
    LEGEND_CONSTANTS(:,1) = strpad('ANM in component aldosterone (dimensionless)');
    LEGEND_CONSTANTS(:,2) = strpad('CKE in component aldosterone (monovalent_mEq_per_litre)');
    LEGEND_CONSTANTS(:,16) = strpad('ANMAL in component angiotensin_control_of_aldosterone_secretion (dimensionless)');
    LEGEND_CONSTANTS(:,3) = strpad('ANMALD in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,17) = strpad('OSMAL in component osmotic_control_of_aldosterone_secretion (dimensionless)');
    LEGEND_CONSTANTS(:,21) = strpad('AMR1 in component aldosterone_secretion (dimensionless)');
    LEGEND_CONSTANTS(:,4) = strpad('AMKMUL in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,5) = strpad('ALDINF in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,6) = strpad('ALDKNS in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,18) = strpad('AMRBSC in component aldosterone_secretion (dimensionless)');
    LEGEND_CONSTANTS(:,19) = strpad('AMRT in component aldosterone_secretion (dimensionless)');
    LEGEND_CONSTANTS(:,20) = strpad('AMR in component aldosterone_secretion (dimensionless)');
    LEGEND_STATES(:,1) = strpad('AMC in component aldosterone_concentration (dimensionless)');
    LEGEND_CONSTANTS(:,7) = strpad('AMT in component parameter_values (minute)');
    LEGEND_ALGEBRAIC(:,2) = strpad('AM in component general_aldosterone_multiplier (dimensionless)');
    LEGEND_CONSTANTS(:,8) = strpad('AM1UL in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('AM1LL in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,10) = strpad('AMCSNS in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,11) = strpad('ALDMM in component parameter_values (dimensionless)');
    LEGEND_ALGEBRAIC(:,1) = strpad('AM1 in component general_aldosterone_multiplier (dimensionless)');
    LEGEND_ALGEBRAIC(:,5) = strpad('AMK in component aldosterone_effect_on_cell_membrane_K_transport (dimensionless)');
    LEGEND_CONSTANTS(:,12) = strpad('AMKM in component parameter_values (dimensionless)');
    LEGEND_ALGEBRAIC(:,3) = strpad('AMKT in component aldosterone_effect_on_cell_membrane_K_transport (dimensionless)');
    LEGEND_ALGEBRAIC(:,6) = strpad('AMNA in component aldosterone_effect_on_cell_membrane_Na_transport (dimensionless)');
    LEGEND_CONSTANTS(:,13) = strpad('AMNAM in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,14) = strpad('AMNAUL in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,15) = strpad('AMNALL in component parameter_values (dimensionless)');
    LEGEND_ALGEBRAIC(:,4) = strpad('AMNAT in component aldosterone_effect_on_cell_membrane_Na_transport (dimensionless)');
    LEGEND_RATES(:,1) = strpad('d/dt AMC in component aldosterone_concentration (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) = 0.987545;
    CONSTANTS(:,2) = 4.44092;
    CONSTANTS(:,3) = 2.5;
    CONSTANTS(:,4) = 12;
    CONSTANTS(:,5) = 0;
    CONSTANTS(:,6) = 0;
    STATES(:,1) = 1.0;
    CONSTANTS(:,7) = 60;
    CONSTANTS(:,8) = 5;
    CONSTANTS(:,9) = 0;
    CONSTANTS(:,10) = 0.65;
    CONSTANTS(:,11) = 2.5;
    CONSTANTS(:,12) = 0.5;
    CONSTANTS(:,13) = 0.8;
    CONSTANTS(:,14) = 15;
    CONSTANTS(:,15) = 0.04;
    CONSTANTS(:,16) =  (CONSTANTS(:,1) - 1.00000).*CONSTANTS(:,3)+1.00000;
    CONSTANTS(:,17) = (CONSTANTS(:,2) - 3.30000)./1.00000;
    CONSTANTS(:,18) =  CONSTANTS(:,16).*0.909000.*CONSTANTS(:,17);
    CONSTANTS(:,19) =  (CONSTANTS(:,18) - 1.00000).*CONSTANTS(:,4)+1.00000;
    CONSTANTS(:,20) = piecewise({CONSTANTS(:,19)<0.00000, 0.00000 }, CONSTANTS(:,19));
    CONSTANTS(:,21) = piecewise({CONSTANTS(:,6)>0.00000, CONSTANTS(:,6) }, CONSTANTS(:,20)+CONSTANTS(:,5));
    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(:,21) - STATES(:,1))./CONSTANTS(:,7);
   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(:,8) - (CONSTANTS(:,8) - 1.00000)./( ((CONSTANTS(:,9) - 1.00000)./(CONSTANTS(:,9) - CONSTANTS(:,8))).*(STATES(:,1) - 1.00000).*CONSTANTS(:,10)+1.00000);
    ALGEBRAIC(:,2) =  (ALGEBRAIC(:,1) - 1.00000).*CONSTANTS(:,11)+1.00000;
    ALGEBRAIC(:,3) =  (ALGEBRAIC(:,2) - 1.00000).*CONSTANTS(:,12)+1.00000;
    ALGEBRAIC(:,4) =  (ALGEBRAIC(:,2) - 1.00000).*CONSTANTS(:,13)+1.00000;
    ALGEBRAIC(:,5) = piecewise({ALGEBRAIC(:,3)<0.200000, 0.200000 }, ALGEBRAIC(:,3));
    ALGEBRAIC(:,6) = piecewise({ALGEBRAIC(:,4)<CONSTANTS(:,15), CONSTANTS(:,15) , ALGEBRAIC(:,4)>CONSTANTS(:,14), CONSTANTS(:,14) }, ALGEBRAIC(:,4));
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