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 11 entries in each of the rate and state variable arrays.
% There are a total of 30 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('t in component environment (s)');
    LEGEND_CONSTANTS(:,1) = strpad('kf5 in component RAF (per_um_s)');
    LEGEND_CONSTANTS(:,2) = strpad('kb5 in component RAF (per_s)');
    LEGEND_CONSTANTS(:,3) = strpad('km1 in component RAF (um)');
    LEGEND_CONSTANTS(:,4) = strpad('km2 in component RAF (um)');
    LEGEND_CONSTANTS(:,5) = strpad('km3 in component RAF (um)');
    LEGEND_CONSTANTS(:,6) = strpad('km4 in component RAF (um)');
    LEGEND_CONSTANTS(:,7) = strpad('Vmax1 in component RAF (per_s)');
    LEGEND_CONSTANTS(:,8) = strpad('Vmax2 in component RAF (per_s)');
    LEGEND_CONSTANTS(:,9) = strpad('Vmax3 in component RAF (per_s)');
    LEGEND_CONSTANTS(:,10) = strpad('Vmax4 in component RAF (per_s)');
    LEGEND_CONSTANTS(:,11) = strpad('PKC in component undefinedvariables (um)');
    LEGEND_CONSTANTS(:,12) = strpad('PP2A in component RAF (um)');
    LEGEND_STATES(:,1) = strpad('MAPK_star in component MAPK (um)');
    LEGEND_STATES(:,2) = strpad('Raf in component RAF (um)');
    LEGEND_STATES(:,3) = strpad('Raf_star in component RAF (um)');
    LEGEND_STATES(:,4) = strpad('Raf_star_star in component RAF (um)');
    LEGEND_STATES(:,5) = strpad('GTPRas in component RAF (um)');
    LEGEND_STATES(:,6) = strpad('GTPRasRaf_star in component RAF (um)');
    LEGEND_CONSTANTS(:,13) = strpad('km6 in component MAPKK (um)');
    LEGEND_CONSTANTS(:,14) = strpad('km7 in component MAPKK (um)');
    LEGEND_CONSTANTS(:,15) = strpad('km8 in component MAPKK (um)');
    LEGEND_CONSTANTS(:,16) = strpad('km9 in component MAPKK (um)');
    LEGEND_CONSTANTS(:,17) = strpad('Vmax6 in component MAPKK (per_s)');
    LEGEND_CONSTANTS(:,18) = strpad('Vmax7 in component MAPKK (per_s)');
    LEGEND_CONSTANTS(:,19) = strpad('Vmax8 in component MAPKK (per_s)');
    LEGEND_CONSTANTS(:,20) = strpad('Vmax9 in component MAPKK (per_s)');
    LEGEND_CONSTANTS(:,21) = strpad('PP2A in component MAPKK (um)');
    LEGEND_STATES(:,7) = strpad('MAPKK in component MAPKK (um)');
    LEGEND_STATES(:,8) = strpad('MAPKK_star in component MAPKK (um)');
    LEGEND_STATES(:,9) = strpad('MAPKK_star_star in component MAPKK (um)');
    LEGEND_CONSTANTS(:,22) = strpad('km10 in component MAPK (um)');
    LEGEND_CONSTANTS(:,23) = strpad('km11 in component MAPK (um)');
    LEGEND_CONSTANTS(:,24) = strpad('km12 in component MAPK (um)');
    LEGEND_CONSTANTS(:,25) = strpad('km13 in component MAPK (um)');
    LEGEND_CONSTANTS(:,26) = strpad('Vmax10 in component MAPK (per_s)');
    LEGEND_CONSTANTS(:,27) = strpad('Vmax11 in component MAPK (per_s)');
    LEGEND_CONSTANTS(:,28) = strpad('Vmax12 in component MAPK (per_s)');
    LEGEND_CONSTANTS(:,29) = strpad('Vmax13 in component MAPK (per_s)');
    LEGEND_STATES(:,10) = strpad('MAPK in component MAPK (um)');
    LEGEND_STATES(:,11) = strpad('MAPK_tyr in component MAPK (um)');
    LEGEND_CONSTANTS(:,30) = strpad('MKP1 in component MAPK (um)');
    LEGEND_RATES(:,6) = strpad('d/dt GTPRasRaf_star in component RAF (um)');
    LEGEND_RATES(:,5) = strpad('d/dt GTPRas in component RAF (um)');
    LEGEND_RATES(:,2) = strpad('d/dt Raf in component RAF (um)');
    LEGEND_RATES(:,3) = strpad('d/dt Raf_star in component RAF (um)');
    LEGEND_RATES(:,4) = strpad('d/dt Raf_star_star in component RAF (um)');
    LEGEND_RATES(:,7) = strpad('d/dt MAPKK in component MAPKK (um)');
    LEGEND_RATES(:,8) = strpad('d/dt MAPKK_star in component MAPKK (um)');
    LEGEND_RATES(:,9) = strpad('d/dt MAPKK_star_star in component MAPKK (um)');
    LEGEND_RATES(:,10) = strpad('d/dt MAPK in component MAPK (um)');
    LEGEND_RATES(:,11) = strpad('d/dt MAPK_tyr in component MAPK (um)');
    LEGEND_RATES(:,1) = strpad('d/dt MAPK_star in component MAPK (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 = [];
    CONSTANTS(:,1) = 0.00004;
    CONSTANTS(:,2) = 0.5;
    CONSTANTS(:,3) = 66.666666667;
    CONSTANTS(:,4) = 25.64166667;
    CONSTANTS(:,5) = 15.6565;
    CONSTANTS(:,6) = 15.6565;
    CONSTANTS(:,7) = 4;
    CONSTANTS(:,8) = 10;
    CONSTANTS(:,9) = 6;
    CONSTANTS(:,10) = 6;
    CONSTANTS(:,11) = 0.1;
    CONSTANTS(:,12) = 0.224;
    STATES(:,1) = 0;
    STATES(:,2) = 0.1;
    STATES(:,3) = 0;
    STATES(:,4) = 0;
    STATES(:,5) = 0.1;
    STATES(:,6) = 0;
    CONSTANTS(:,13) = 0.159091667;
    CONSTANTS(:,14) = 0.159091667;
    CONSTANTS(:,15) = 15.6565;
    CONSTANTS(:,16) = 15.6565;
    CONSTANTS(:,17) = 0.105;
    CONSTANTS(:,18) = 0.105;
    CONSTANTS(:,19) = 6;
    CONSTANTS(:,20) = 6;
    CONSTANTS(:,21) = 0.224;
    STATES(:,7) = 0.18;
    STATES(:,8) = 0;
    STATES(:,9) = 0;
    CONSTANTS(:,22) = 0.046296667;
    CONSTANTS(:,23) = 0.046296667;
    CONSTANTS(:,24) = 0.066666667;
    CONSTANTS(:,25) = 0.066666667;
    CONSTANTS(:,26) = 0.15;
    CONSTANTS(:,27) = 0.15;
    CONSTANTS(:,28) = 1;
    CONSTANTS(:,29) = 1;
    STATES(:,10) = 0.36;
    STATES(:,11) = 0;
    CONSTANTS(:,30) = 0.032;
    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(:,6) =  STATES(:,5).*STATES(:,3).*CONSTANTS(:,1) -  STATES(:,6).*CONSTANTS(:,2);
    RATES(:,5) =   - STATES(:,5).*STATES(:,3).*CONSTANTS(:,1)+ STATES(:,6).*CONSTANTS(:,2);
    RATES(:,2) = (  - CONSTANTS(:,11).*STATES(:,2).*CONSTANTS(:,7))./(CONSTANTS(:,3)+STATES(:,2))+( STATES(:,3).*CONSTANTS(:,12).*CONSTANTS(:,9))./(CONSTANTS(:,5)+STATES(:,3));
    RATES(:,3) = ((( CONSTANTS(:,11).*STATES(:,2).*CONSTANTS(:,7))./(CONSTANTS(:,3)+STATES(:,2)) - ( STATES(:,3).*CONSTANTS(:,12).*CONSTANTS(:,9))./(CONSTANTS(:,5)+STATES(:,3))) - ( STATES(:,3).*STATES(:,1).*CONSTANTS(:,8))./(CONSTANTS(:,4)+STATES(:,3)))+( STATES(:,4).*CONSTANTS(:,12).*CONSTANTS(:,10))./(CONSTANTS(:,6)+STATES(:,4));
    RATES(:,4) = ( STATES(:,3).*STATES(:,1).*CONSTANTS(:,8))./(CONSTANTS(:,4)+STATES(:,3)) - ( STATES(:,4).*CONSTANTS(:,12).*CONSTANTS(:,10))./(CONSTANTS(:,6)+STATES(:,4));
    RATES(:,7) = (  - STATES(:,7).*CONSTANTS(:,17).*STATES(:,6))./(CONSTANTS(:,13)+STATES(:,7))+( STATES(:,8).*CONSTANTS(:,19).*CONSTANTS(:,21))./(CONSTANTS(:,15)+STATES(:,8));
    RATES(:,8) = ((( STATES(:,7).*CONSTANTS(:,17).*STATES(:,6))./(CONSTANTS(:,13)+STATES(:,7)) - ( STATES(:,8).*CONSTANTS(:,19).*CONSTANTS(:,21))./(CONSTANTS(:,15)+STATES(:,8))) - ( STATES(:,8).*CONSTANTS(:,18).*STATES(:,6))./(CONSTANTS(:,14)+STATES(:,8)))+( STATES(:,9).*CONSTANTS(:,20).*CONSTANTS(:,21))./(CONSTANTS(:,16)+STATES(:,9));
    RATES(:,9) = ( STATES(:,8).*CONSTANTS(:,18).*STATES(:,6))./(CONSTANTS(:,14)+STATES(:,8)) - ( STATES(:,9).*CONSTANTS(:,20).*CONSTANTS(:,21))./(CONSTANTS(:,16)+STATES(:,9));
    RATES(:,10) = (  - STATES(:,10).*CONSTANTS(:,26).*STATES(:,9))./(CONSTANTS(:,22)+STATES(:,10))+( STATES(:,11).*CONSTANTS(:,28).*CONSTANTS(:,30))./(CONSTANTS(:,24)+STATES(:,11));
    RATES(:,11) = ((( STATES(:,10).*CONSTANTS(:,26).*STATES(:,9))./(CONSTANTS(:,22)+STATES(:,10)) - ( STATES(:,11).*CONSTANTS(:,28).*CONSTANTS(:,30))./(CONSTANTS(:,24)+STATES(:,11))) - ( STATES(:,11).*CONSTANTS(:,27).*STATES(:,9))./(CONSTANTS(:,23)+STATES(:,11)))+( STATES(:,1).*CONSTANTS(:,29).*CONSTANTS(:,30))./(CONSTANTS(:,25)+STATES(:,1));
    RATES(:,1) = ( STATES(:,11).*CONSTANTS(:,27).*STATES(:,9))./(CONSTANTS(:,23)+STATES(:,11)) - ( STATES(:,1).*CONSTANTS(:,29).*CONSTANTS(:,30))./(CONSTANTS(:,25)+STATES(:,1));
   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