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 6 entries in each of the rate and state variable arrays.
% There are a total of 9 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_STATES(:,1) = strpad('x_1 in component x_1 (picomolar)');
    LEGEND_CONSTANTS(:,1) = strpad('k_t in component model_parameters (per_minute)');
    LEGEND_CONSTANTS(:,2) = strpad('B_max in component model_parameters (picomolar)');
    LEGEND_CONSTANTS(:,3) = strpad('k_on in component model_parameters (per_picomolar_per_minute)');
    LEGEND_STATES(:,2) = strpad('x_2 in component x_2 (picomolar)');
    LEGEND_CONSTANTS(:,4) = strpad('k_off in component model_parameters (per_minute)');
    LEGEND_STATES(:,3) = strpad('x_3 in component x_3 (picomolar)');
    LEGEND_CONSTANTS(:,5) = strpad('k_ex in component model_parameters (per_minute)');
    LEGEND_STATES(:,4) = strpad('x_4 in component x_4 (picomolar)');
    LEGEND_CONSTANTS(:,6) = strpad('k_mob in component model_parameters (per_minute)');
    LEGEND_CONSTANTS(:,7) = strpad('k_e in component model_parameters (per_minute)');
    LEGEND_CONSTANTS(:,8) = strpad('k_di in component model_parameters (per_minute)');
    LEGEND_CONSTANTS(:,9) = strpad('k_de in component model_parameters (per_minute)');
    LEGEND_STATES(:,5) = strpad('x_5 in component x_5 (picomolar)');
    LEGEND_STATES(:,6) = strpad('x_6 in component x_6 (picomolar)');
    LEGEND_RATES(:,1) = strpad('d/dt x_1 in component x_1 (picomolar)');
    LEGEND_RATES(:,2) = strpad('d/dt x_2 in component x_2 (picomolar)');
    LEGEND_RATES(:,3) = strpad('d/dt x_3 in component x_3 (picomolar)');
    LEGEND_RATES(:,4) = strpad('d/dt x_4 in component x_4 (picomolar)');
    LEGEND_RATES(:,5) = strpad('d/dt x_5 in component x_5 (picomolar)');
    LEGEND_RATES(:,6) = strpad('d/dt x_6 in component x_6 (picomolar)');
    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) = 516;
    CONSTANTS(:,1) = 0.03294;
    CONSTANTS(:,2) = 129;
    CONSTANTS(:,3) = 0.10496e-3;
    STATES(:,2) = 2010.19;
    CONSTANTS(:,4) = 0.01721;
    STATES(:,3) = 0;
    CONSTANTS(:,5) = 0.00994;
    STATES(:,4) = 0;
    CONSTANTS(:,6) = 0.4178;
    CONSTANTS(:,7) = 0.07483;
    CONSTANTS(:,8) = 0.003179;
    CONSTANTS(:,9) = 0.0164;
    STATES(:,5) = 0;
    STATES(:,6) = 0;
    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).*CONSTANTS(:,2)+ CONSTANTS(:,6).*STATES(:,3)) -  CONSTANTS(:,1).*STATES(:,1)) -  CONSTANTS(:,3).*STATES(:,1).*STATES(:,2))+ CONSTANTS(:,4).*STATES(:,3)+ CONSTANTS(:,5).*STATES(:,4);
    RATES(:,2) =   - CONSTANTS(:,3).*STATES(:,1).*STATES(:,2)+ CONSTANTS(:,4).*STATES(:,3)+ CONSTANTS(:,5).*STATES(:,4);
    RATES(:,3) = ( CONSTANTS(:,3).*STATES(:,1).*STATES(:,2) -  CONSTANTS(:,4).*STATES(:,3)) -  CONSTANTS(:,7).*STATES(:,3);
    RATES(:,4) = (( CONSTANTS(:,7).*STATES(:,3) -  CONSTANTS(:,5).*STATES(:,4)) -  CONSTANTS(:,8).*STATES(:,4)) -  CONSTANTS(:,9).*STATES(:,4);
    RATES(:,5) =  CONSTANTS(:,8).*STATES(:,4);
    RATES(:,6) =  CONSTANTS(:,9).*STATES(:,4);
   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