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 =9;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 37 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 (second)');
    LEGEND_CONSTANTS(:,1) = strpad('R_T in component Parameters (dimensionless)');
    LEGEND_CONSTANTS(:,2) = strpad('K_1 in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,3) = strpad('K_2 in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,4) = strpad('k_r in component Parameters (per_second)');
    LEGEND_CONSTANTS(:,5) = strpad('k_p in component Parameters (per_second)');
    LEGEND_CONSTANTS(:,6) = strpad('k_e in component Parameters (per_second)');
    LEGEND_CONSTANTS(:,7) = strpad('xi in component Parameters (dimensionless)');
    LEGEND_CONSTANTS(:,8) = strpad('G_T in component Parameters (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('k_deg in component Parameters (per_second)');
    LEGEND_CONSTANTS(:,10) = strpad('k_a in component Parameters (per_second)');
    LEGEND_CONSTANTS(:,11) = strpad('k_d in component Parameters (per_second)');
    LEGEND_CONSTANTS(:,12) = strpad('PIP_2_T in component Parameters (dimensionless)');
    LEGEND_CONSTANTS(:,13) = strpad('r_r in component Parameters (per_second)');
    LEGEND_CONSTANTS(:,14) = strpad('delta in component Parameters (dimensionless)');
    LEGEND_CONSTANTS(:,15) = strpad('K_c in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,16) = strpad('alpha in component Parameters (per_second)');
    LEGEND_CONSTANTS(:,17) = strpad('N_a in component Parameters (per_micromole)');
    LEGEND_CONSTANTS(:,18) = strpad('v in component Parameters (litre)');
    LEGEND_CONSTANTS(:,19) = strpad('epsilon_r in component Parameters (dimensionless)');
    LEGEND_CONSTANTS(:,20) = strpad('d_1 in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,21) = strpad('d_2 in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,22) = strpad('d_3 in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,23) = strpad('d_5 in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,24) = strpad('a_2 in component Parameters (per_micromolar_per_second)');
    LEGEND_CONSTANTS(:,25) = strpad('B_e in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,26) = strpad('K_e in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,27) = strpad('B_ER in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,28) = strpad('K_ER in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,29) = strpad('B_x in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,30) = strpad('K_x in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,31) = strpad('k_3 in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,32) = strpad('eta_1 in component Parameters (per_second)');
    LEGEND_CONSTANTS(:,33) = strpad('eta_2 in component Parameters (per_second)');
    LEGEND_CONSTANTS(:,34) = strpad('eta_3 in component Parameters (flux)');
    LEGEND_CONSTANTS(:,35) = strpad('C_T in component Parameters (micromolar)');
    LEGEND_CONSTANTS(:,36) = strpad('L in component ligand (micromolar)');
    LEGEND_STATES(:,1) = strpad('RS in component RS (dimensionless)');
    LEGEND_STATES(:,2) = strpad('RS_p in component RS_p (dimensionless)');
    LEGEND_STATES(:,3) = strpad('G in component G_GTP (dimensionless)');
    LEGEND_ALGEBRAIC(:,1) = strpad('rho_r in component rho_r (dimensionless)');
    LEGEND_STATES(:,4) = strpad('IP_3 in component IP_3 (micromolar)');
    LEGEND_STATES(:,5) = strpad('PIP_2 in component PIP_2 (dimensionless)');
    LEGEND_ALGEBRAIC(:,2) = strpad('r_h in component r_h (per_second)');
    LEGEND_STATES(:,6) = strpad('C in component C (micromolar)');
    LEGEND_ALGEBRAIC(:,9) = strpad('C_ER in component C_ER (micromolar)');
    LEGEND_ALGEBRAIC(:,5) = strpad('beta in component beta (dimensionless)');
    LEGEND_STATES(:,7) = strpad('h in component h (dimensionless)');
    LEGEND_ALGEBRAIC(:,3) = strpad('m_infinit in component m_infinit (dimensionless)');
    LEGEND_ALGEBRAIC(:,8) = strpad('h_infinit in component h_infinit (dimensionless)');
    LEGEND_ALGEBRAIC(:,6) = strpad('tau_h in component tau_h (second)');
    LEGEND_ALGEBRAIC(:,4) = strpad('zeta in component zeta (micromolar)');
    LEGEND_ALGEBRAIC(:,7) = strpad('gamma in component gamma (dimensionless)');
    LEGEND_CONSTANTS(:,37) = strpad('RS_E in component RS_E (dimensionless)');
    LEGEND_RATES(:,1) = strpad('d/dt RS in component RS (dimensionless)');
    LEGEND_RATES(:,2) = strpad('d/dt RS_p in component RS_p (dimensionless)');
    LEGEND_RATES(:,3) = strpad('d/dt G in component G_GTP (dimensionless)');
    LEGEND_RATES(:,4) = strpad('d/dt IP_3 in component IP_3 (micromolar)');
    LEGEND_RATES(:,5) = strpad('d/dt PIP_2 in component PIP_2 (dimensionless)');
    LEGEND_RATES(:,6) = strpad('d/dt C in component C (micromolar)');
    LEGEND_RATES(:,7) = strpad('d/dt h in component h (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) = 2e4;
    CONSTANTS(:,2) = 5;
    CONSTANTS(:,3) = 100;
    CONSTANTS(:,4) = 1.75e-4;
    CONSTANTS(:,5) = 0.03;
    CONSTANTS(:,6) = 6e-3;
    CONSTANTS(:,7) = 0.85;
    CONSTANTS(:,8) = 1e5;
    CONSTANTS(:,9) = 1.25;
    CONSTANTS(:,10) = 0.017;
    CONSTANTS(:,11) = 0.15;
    CONSTANTS(:,12) = 5e7;
    CONSTANTS(:,13) = 10;
    CONSTANTS(:,14) = 1.238e-3;
    CONSTANTS(:,15) = 0.4;
    CONSTANTS(:,16) = 2.781e-5;
    CONSTANTS(:,17) = 6.02252e17;
    CONSTANTS(:,18) = 5e-13;
    CONSTANTS(:,19) = 0.185;
    CONSTANTS(:,20) = 0.13;
    CONSTANTS(:,21) = 1.05;
    CONSTANTS(:,22) = 0.943;
    CONSTANTS(:,23) = 0.0823;
    CONSTANTS(:,24) = 0.2;
    CONSTANTS(:,25) = 150;
    CONSTANTS(:,26) = 10;
    CONSTANTS(:,27) = 120000;
    CONSTANTS(:,28) = 1200;
    CONSTANTS(:,29) = 50;
    CONSTANTS(:,30) = 0.2;
    CONSTANTS(:,31) = 0.4;
    CONSTANTS(:,32) = 575;
    CONSTANTS(:,33) = 5.2;
    CONSTANTS(:,34) = 45;
    CONSTANTS(:,35) = 67;
    CONSTANTS(:,36) = 1000;
    STATES(:,1) = 1.7e4;
    STATES(:,2) = 0;
    STATES(:,3) = 0;
    STATES(:,4) = 0.01;
    STATES(:,5) = 49997000;
    STATES(:,6) = 0.0961;
    STATES(:,7) = 0.6155;
    CONSTANTS(:,37) =  (( CONSTANTS(:,4).*(1.00000+( (CONSTANTS(:,5)./CONSTANTS(:,6)).*(CONSTANTS(:,3)+CONSTANTS(:,36)))./(CONSTANTS(:,2)+CONSTANTS(:,36))))./(CONSTANTS(:,4)+( CONSTANTS(:,5).*CONSTANTS(:,36))./(CONSTANTS(:,2)+CONSTANTS(:,36))+( (( CONSTANTS(:,4).*CONSTANTS(:,5))./CONSTANTS(:,6)).*(CONSTANTS(:,3)+CONSTANTS(:,36)))./(CONSTANTS(:,2)+CONSTANTS(:,36)))).*CONSTANTS(:,7).*CONSTANTS(:,1)+ (1.00000 - CONSTANTS(:,7)).*CONSTANTS(:,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(:,4).*CONSTANTS(:,1) -  (CONSTANTS(:,4)+( CONSTANTS(:,5).*CONSTANTS(:,36))./(CONSTANTS(:,2)+CONSTANTS(:,36))).*STATES(:,1)) -  CONSTANTS(:,4).*STATES(:,2);
    RATES(:,2) =  CONSTANTS(:,36).*(( CONSTANTS(:,5).*STATES(:,1))./(CONSTANTS(:,2)+CONSTANTS(:,36)) - ( CONSTANTS(:,6).*STATES(:,2))./(CONSTANTS(:,3)+CONSTANTS(:,36)));
    ALGEBRAIC(:,1) = ( CONSTANTS(:,36).*STATES(:,1))./( CONSTANTS(:,7).*CONSTANTS(:,1).*(CONSTANTS(:,2)+CONSTANTS(:,36)));
    RATES(:,3) =  CONSTANTS(:,10).*(CONSTANTS(:,14)+ALGEBRAIC(:,1)).*(CONSTANTS(:,8) - STATES(:,3)) -  CONSTANTS(:,11).*STATES(:,3);
    ALGEBRAIC(:,2) =  (( CONSTANTS(:,16).*STATES(:,6))./(CONSTANTS(:,15)+STATES(:,6))).*STATES(:,3);
    RATES(:,4) = ( ALGEBRAIC(:,2).*STATES(:,5))./( CONSTANTS(:,17).*CONSTANTS(:,18)) -  CONSTANTS(:,9).*STATES(:,4);
    RATES(:,5) = (  - (ALGEBRAIC(:,2)+CONSTANTS(:,13)).*STATES(:,5) -  CONSTANTS(:,13).*CONSTANTS(:,17).*CONSTANTS(:,18).*STATES(:,4))+ CONSTANTS(:,13).*CONSTANTS(:,12);
    ALGEBRAIC(:,4) = ( CONSTANTS(:,21).*(STATES(:,4)+CONSTANTS(:,20)))./(STATES(:,4)+CONSTANTS(:,22));
    ALGEBRAIC(:,8) = ALGEBRAIC(:,4)./(ALGEBRAIC(:,4)+STATES(:,6));
    ALGEBRAIC(:,6) = power( CONSTANTS(:,24).*(ALGEBRAIC(:,4)+STATES(:,6)),  - 1.00000);
    RATES(:,7) = (ALGEBRAIC(:,8) - STATES(:,7))./ALGEBRAIC(:,6);
    ALGEBRAIC(:,7) = power(1.00000+CONSTANTS(:,25)./(CONSTANTS(:,26)+STATES(:,6))+CONSTANTS(:,29)./(CONSTANTS(:,30)+STATES(:,6)),  - 1.00000);
    ALGEBRAIC(:,9) =  (CONSTANTS(:,28)./( CONSTANTS(:,27).*CONSTANTS(:,19))).*(CONSTANTS(:,35) - STATES(:,6)./ALGEBRAIC(:,7));
    ALGEBRAIC(:,5) = power(1.00000+( CONSTANTS(:,26).*CONSTANTS(:,25))./power(CONSTANTS(:,26)+STATES(:,6), 2.00000)+( CONSTANTS(:,30).*CONSTANTS(:,29))./power(CONSTANTS(:,30)+STATES(:,6), 2.00000),  - 1.00000);
    ALGEBRAIC(:,3) = ( (STATES(:,4)./(CONSTANTS(:,20)+STATES(:,4))).*STATES(:,6))./(CONSTANTS(:,23)+STATES(:,6));
    RATES(:,6) =  ALGEBRAIC(:,5).*( CONSTANTS(:,19).*( CONSTANTS(:,32).*power(ALGEBRAIC(:,3), 3.00000).*power(STATES(:,7), 3.00000)+CONSTANTS(:,33)).*(ALGEBRAIC(:,9) - STATES(:,6)) - ( CONSTANTS(:,34).*power(STATES(:,6), 2.00000))./(power(CONSTANTS(:,31), 2.00000)+power(STATES(:,6), 2.00000)));
   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(:,36).*STATES(:,1))./( CONSTANTS(:,7).*CONSTANTS(:,1).*(CONSTANTS(:,2)+CONSTANTS(:,36)));
    ALGEBRAIC(:,2) =  (( CONSTANTS(:,16).*STATES(:,6))./(CONSTANTS(:,15)+STATES(:,6))).*STATES(:,3);
    ALGEBRAIC(:,4) = ( CONSTANTS(:,21).*(STATES(:,4)+CONSTANTS(:,20)))./(STATES(:,4)+CONSTANTS(:,22));
    ALGEBRAIC(:,8) = ALGEBRAIC(:,4)./(ALGEBRAIC(:,4)+STATES(:,6));
    ALGEBRAIC(:,6) = power( CONSTANTS(:,24).*(ALGEBRAIC(:,4)+STATES(:,6)),  - 1.00000);
    ALGEBRAIC(:,7) = power(1.00000+CONSTANTS(:,25)./(CONSTANTS(:,26)+STATES(:,6))+CONSTANTS(:,29)./(CONSTANTS(:,30)+STATES(:,6)),  - 1.00000);
    ALGEBRAIC(:,9) =  (CONSTANTS(:,28)./( CONSTANTS(:,27).*CONSTANTS(:,19))).*(CONSTANTS(:,35) - STATES(:,6)./ALGEBRAIC(:,7));
    ALGEBRAIC(:,5) = power(1.00000+( CONSTANTS(:,26).*CONSTANTS(:,25))./power(CONSTANTS(:,26)+STATES(:,6), 2.00000)+( CONSTANTS(:,30).*CONSTANTS(:,29))./power(CONSTANTS(:,30)+STATES(:,6), 2.00000),  - 1.00000);
    ALGEBRAIC(:,3) = ( (STATES(:,4)./(CONSTANTS(:,20)+STATES(:,4))).*STATES(:,6))./(CONSTANTS(:,23)+STATES(:,6));
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