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 10 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('kf2 in component GEF (per_s)');
    LEGEND_CONSTANTS(:,2) = strpad('kb2 in component GEF (per_s)');
    LEGEND_CONSTANTS(:,3) = strpad('kf5 in component GEF (per_um_s)');
    LEGEND_CONSTANTS(:,4) = strpad('kb5 in component GEF (per_s)');
    LEGEND_CONSTANTS(:,5) = strpad('kf7 in component GEF (per_s)');
    LEGEND_CONSTANTS(:,6) = strpad('kb7 in component GEF (per_s)');
    LEGEND_CONSTANTS(:,7) = strpad('kf8 in component GEF (per_um_s)');
    LEGEND_CONSTANTS(:,8) = strpad('kb8 in component GEF (per_s)');
    LEGEND_CONSTANTS(:,9) = strpad('km1 in component GEF (um)');
    LEGEND_CONSTANTS(:,10) = strpad('Vmax1 in component GEF (per_s)');
    LEGEND_CONSTANTS(:,11) = strpad('km6 in component GEF (um)');
    LEGEND_CONSTANTS(:,12) = strpad('Vmax6 in component GEF (per_s)');
    LEGEND_STATES(:,1) = strpad('GEF_inact in component GEF (um)');
    LEGEND_STATES(:,2) = strpad('GEF in component GEF (um)');
    LEGEND_CONSTANTS(:,13) = strpad('PKA in component undefinedVariables (um)');
    LEGEND_STATES(:,3) = strpad('Ca4CAM in component GEF (um)');
    LEGEND_CONSTANTS(:,14) = strpad('PKC in component undefinedVariables (um)');
    LEGEND_STATES(:,4) = strpad('Gby in component GEF (um)');
    LEGEND_STATES(:,5) = strpad('CaM_GEF in component GEF (um)');
    LEGEND_STATES(:,6) = strpad('Gby_GEF in component GEF (um)');
    LEGEND_CONSTANTS(:,15) = strpad('kf12 in component GTPRAS (per_s)');
    LEGEND_CONSTANTS(:,16) = strpad('kb12 in component GTPRAS (per_s)');
    LEGEND_CONSTANTS(:,17) = strpad('km9 in component GTPRAS (um)');
    LEGEND_CONSTANTS(:,18) = strpad('Vmax9 in component GTPRAS (per_s)');
    LEGEND_CONSTANTS(:,19) = strpad('km10 in component GTPRAS (um)');
    LEGEND_CONSTANTS(:,20) = strpad('Vmax10 in component GTPRAS (per_s)');
    LEGEND_CONSTANTS(:,21) = strpad('km11 in component GTPRAS (um)');
    LEGEND_CONSTANTS(:,22) = strpad('Vmax11 in component GTPRAS (per_s)');
    LEGEND_CONSTANTS(:,23) = strpad('km13 in component GTPRAS (um)');
    LEGEND_CONSTANTS(:,24) = strpad('Vmax13 in component GTPRAS (per_s)');
    LEGEND_STATES(:,7) = strpad('GTP_RAS in component GTPRAS (um)');
    LEGEND_STATES(:,8) = strpad('GDP_RAS in component GTPRAS (um)');
    LEGEND_STATES(:,9) = strpad('GAP in component GAP (um)');
    LEGEND_CONSTANTS(:,25) = strpad('kf4 in component GAP (per_s)');
    LEGEND_CONSTANTS(:,26) = strpad('kb4 in component GAP (per_s)');
    LEGEND_CONSTANTS(:,27) = strpad('km3 in component GAP (um)');
    LEGEND_CONSTANTS(:,28) = strpad('Vmax3 in component GAP (per_s)');
    LEGEND_STATES(:,10) = strpad('GAPstar in component GAP (um)');
    LEGEND_CONSTANTS(:,29) = strpad('Ca4CAM in component undefinedVariables (um)');
    LEGEND_CONSTANTS(:,30) = strpad('Gby in component undefinedVariables (um)');
    LEGEND_RATES(:,1) = strpad('d/dt GEF_inact in component GEF (um)');
    LEGEND_RATES(:,2) = strpad('d/dt GEF in component GEF (um)');
    LEGEND_RATES(:,4) = strpad('d/dt Gby in component GEF (um)');
    LEGEND_RATES(:,5) = strpad('d/dt CaM_GEF in component GEF (um)');
    LEGEND_RATES(:,3) = strpad('d/dt Ca4CAM in component GEF (um)');
    LEGEND_RATES(:,6) = strpad('d/dt Gby_GEF in component GEF (um)');
    LEGEND_RATES(:,7) = strpad('d/dt GTP_RAS in component GTPRAS (um)');
    LEGEND_RATES(:,8) = strpad('d/dt GDP_RAS in component GTPRAS (um)');
    LEGEND_RATES(:,9) = strpad('d/dt GAP in component GAP (um)');
    LEGEND_RATES(:,10) = strpad('d/dt GAPstar in component GAP (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) = 1;
    CONSTANTS(:,2) = 0;
    CONSTANTS(:,3) = 0.0001;
    CONSTANTS(:,4) = 1;
    CONSTANTS(:,5) = 1;
    CONSTANTS(:,6) = 0;
    CONSTANTS(:,7) = 0.00001;
    CONSTANTS(:,8) = 1;
    CONSTANTS(:,9) = 7.5;
    CONSTANTS(:,10) = 9;
    CONSTANTS(:,11) = 3.33333333333;
    CONSTANTS(:,12) = 4;
    STATES(:,1) = 0.1;
    STATES(:,2) = 0;
    CONSTANTS(:,13) = 1;
    STATES(:,3) = 1;
    CONSTANTS(:,14) = 1;
    STATES(:,4) = 1;
    STATES(:,5) = 0;
    STATES(:,6) = 0;
    CONSTANTS(:,15) = 0.0001;
    CONSTANTS(:,16) = 0;
    CONSTANTS(:,17) = 0.50505;
    CONSTANTS(:,18) = 0.02;
    CONSTANTS(:,19) = 0.50505;
    CONSTANTS(:,20) = 0.02;
    CONSTANTS(:,21) = 0.50505;
    CONSTANTS(:,22) = 0.02;
    CONSTANTS(:,23) = 1.0104;
    CONSTANTS(:,24) = 10;
    STATES(:,7) = 0;
    STATES(:,8) = 0.2;
    STATES(:,9) = 0.002;
    CONSTANTS(:,25) = 0.1;
    CONSTANTS(:,26) = 0;
    CONSTANTS(:,27) = 3.33333333333;
    CONSTANTS(:,28) = 4;
    STATES(:,10) = 0;
    CONSTANTS(:,29) = 1;
    CONSTANTS(:,30) = 1;
    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(:,13).*CONSTANTS(:,10).*STATES(:,2))./(CONSTANTS(:,9)+STATES(:,2))+( CONSTANTS(:,14).*CONSTANTS(:,12).*STATES(:,2))./(CONSTANTS(:,11)+STATES(:,2))) -  CONSTANTS(:,1).*STATES(:,1)) -  CONSTANTS(:,5).*STATES(:,1);
    RATES(:,2) = ((( - (((( CONSTANTS(:,13).*CONSTANTS(:,10).*STATES(:,2))./(CONSTANTS(:,9)+STATES(:,2))+( CONSTANTS(:,14).*CONSTANTS(:,12).*STATES(:,2))./(CONSTANTS(:,11)+STATES(:,2))) -  CONSTANTS(:,1).*STATES(:,1)) -  CONSTANTS(:,5).*STATES(:,1)) -  CONSTANTS(:,3).*STATES(:,3).*STATES(:,2))+ CONSTANTS(:,4).*STATES(:,5)) -  CONSTANTS(:,7).*STATES(:,2).*STATES(:,4))+ CONSTANTS(:,8).*STATES(:,6);
    RATES(:,4) =   - CONSTANTS(:,7).*STATES(:,2).*STATES(:,4)+ CONSTANTS(:,8).*STATES(:,6);
    RATES(:,5) =   - CONSTANTS(:,4).*STATES(:,5)+ CONSTANTS(:,3).*STATES(:,2).*STATES(:,3);
    RATES(:,3) =  - (  - CONSTANTS(:,4).*STATES(:,5)+ CONSTANTS(:,3).*STATES(:,2).*STATES(:,3));
    RATES(:,6) =  - (  - CONSTANTS(:,7).*STATES(:,2).*STATES(:,4)+ CONSTANTS(:,8).*STATES(:,6));
    RATES(:,7) = ((  - STATES(:,9).*CONSTANTS(:,24).*STATES(:,7))./(CONSTANTS(:,23)+STATES(:,7)) -  CONSTANTS(:,15).*STATES(:,7))+( STATES(:,1).*CONSTANTS(:,20).*STATES(:,8))./(CONSTANTS(:,19)+STATES(:,8))+( STATES(:,6).*CONSTANTS(:,22).*STATES(:,8))./(CONSTANTS(:,21)+STATES(:,8))+( STATES(:,5).*CONSTANTS(:,18).*STATES(:,8))./(CONSTANTS(:,17)+STATES(:,8));
    RATES(:,8) =  - (((  - STATES(:,9).*CONSTANTS(:,24).*STATES(:,7))./(CONSTANTS(:,23)+STATES(:,7)) -  CONSTANTS(:,15).*STATES(:,7))+( STATES(:,1).*CONSTANTS(:,20).*STATES(:,8))./(CONSTANTS(:,19)+STATES(:,8))+( STATES(:,6).*CONSTANTS(:,22).*STATES(:,8))./(CONSTANTS(:,21)+STATES(:,8))+( STATES(:,5).*CONSTANTS(:,18).*STATES(:,8))./(CONSTANTS(:,17)+STATES(:,8)));
    RATES(:,9) = (  - CONSTANTS(:,14).*CONSTANTS(:,28).*STATES(:,9))./(CONSTANTS(:,27)+STATES(:,9))+ CONSTANTS(:,25).*STATES(:,10);
    RATES(:,10) = ( CONSTANTS(:,14).*CONSTANTS(:,28).*STATES(:,9))./(CONSTANTS(:,27)+STATES(:,9)) -  CONSTANTS(:,25).*STATES(:,10);
   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