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 =8;
end
% There are a total of 4 entries in each of the rate and state variable arrays.
% There are a total of 17 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('Ca_cyt in component Ca_cyt (micromolar)');
    LEGEND_ALGEBRAIC(:,1) = strpad('J_ERch in component J_ERch (micromolar)');
    LEGEND_ALGEBRAIC(:,4) = strpad('J_ERpump in component J_ERpump (micromolar)');
    LEGEND_ALGEBRAIC(:,7) = strpad('J_in in component J_in (micromolar)');
    LEGEND_ALGEBRAIC(:,8) = strpad('J_out in component J_out (micromolar)');
    LEGEND_STATES(:,2) = strpad('Ca_ER in component Ca_ER (micromolar)');
    LEGEND_STATES(:,3) = strpad('PLC in component PLC (micromolar)');
    LEGEND_ALGEBRAIC(:,2) = strpad('J_PLCact in component J_PLCact (micromolar)');
    LEGEND_ALGEBRAIC(:,5) = strpad('J_PLCinact in component J_PLCinact (micromolar)');
    LEGEND_STATES(:,4) = strpad('G_alpha in component G_alpha (micromolar)');
    LEGEND_ALGEBRAIC(:,3) = strpad('J_actG_alpha in component J_actG_alpha (micromolar)');
    LEGEND_ALGEBRAIC(:,6) = strpad('J_inactG_alpha in component J_inactG_alpha (micromolar)');
    LEGEND_CONSTANTS(:,1) = strpad('k_10 in component J_ERch (dimensionless)');
    LEGEND_CONSTANTS(:,2) = strpad('K_11 in component J_ERch (dimensionless)');
    LEGEND_CONSTANTS(:,3) = strpad('K_17 in component J_ERpump (dimensionless)');
    LEGEND_CONSTANTS(:,4) = strpad('k_16 in component J_ERpump (dimensionless)');
    LEGEND_CONSTANTS(:,5) = strpad('K_12 in component J_in (dimensionless)');
    LEGEND_CONSTANTS(:,6) = strpad('k_13 in component J_in (dimensionless)');
    LEGEND_CONSTANTS(:,7) = strpad('k_14 in component J_out (dimensionless)');
    LEGEND_CONSTANTS(:,8) = strpad('K_15 in component J_out (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('k_7 in component J_PLCact (dimensionless)');
    LEGEND_CONSTANTS(:,10) = strpad('k_8 in component J_PLCinact (dimensionless)');
    LEGEND_CONSTANTS(:,11) = strpad('K_9 in component J_PLCinact (dimensionless)');
    LEGEND_CONSTANTS(:,12) = strpad('k_1 in component J_actG_alpha (dimensionless)');
    LEGEND_CONSTANTS(:,13) = strpad('k_2 in component J_actG_alpha (dimensionless)');
    LEGEND_CONSTANTS(:,14) = strpad('k_3 in component J_inactG_alpha (dimensionless)');
    LEGEND_CONSTANTS(:,15) = strpad('K_4 in component J_inactG_alpha (dimensionless)');
    LEGEND_CONSTANTS(:,16) = strpad('k_5 in component J_inactG_alpha (dimensionless)');
    LEGEND_CONSTANTS(:,17) = strpad('K_6 in component J_inactG_alpha (dimensionless)');
    LEGEND_RATES(:,1) = strpad('d/dt Ca_cyt in component Ca_cyt (micromolar)');
    LEGEND_RATES(:,2) = strpad('d/dt Ca_ER in component Ca_ER (micromolar)');
    LEGEND_RATES(:,3) = strpad('d/dt PLC in component PLC (micromolar)');
    LEGEND_RATES(:,4) = strpad('d/dt G_alpha in component G_alpha (micromolar)');
    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) = 0.01;
    STATES(:,2) = 20;
    STATES(:,3) = 0.01;
    STATES(:,4) = 0.01;
    CONSTANTS(:,1) = 5;
    CONSTANTS(:,2) = 3;
    CONSTANTS(:,3) = 0.05;
    CONSTANTS(:,4) = 5.37;
    CONSTANTS(:,5) = 2.8;
    CONSTANTS(:,6) = 13.4;
    CONSTANTS(:,7) = 153;
    CONSTANTS(:,8) = 0.16;
    CONSTANTS(:,9) = 2.08;
    CONSTANTS(:,10) = 32.24;
    CONSTANTS(:,11) = 29.09;
    CONSTANTS(:,12) = 0.01;
    CONSTANTS(:,13) = 0.1;
    CONSTANTS(:,14) = 0.64;
    CONSTANTS(:,15) = 0.09;
    CONSTANTS(:,16) = 4.88;
    CONSTANTS(:,17) = 1.18;
    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
    ALGEBRAIC(:,1) =  CONSTANTS(:,1).*STATES(:,1).*STATES(:,3).*(STATES(:,2)./(CONSTANTS(:,2)+STATES(:,2)));
    ALGEBRAIC(:,4) =  CONSTANTS(:,4).*(STATES(:,1)./(CONSTANTS(:,3)+STATES(:,2)));
    RATES(:,2) =  (ALGEBRAIC(:,4) - ALGEBRAIC(:,1)).*1.00000;
    ALGEBRAIC(:,2) =  CONSTANTS(:,9).*STATES(:,4);
    ALGEBRAIC(:,5) =  CONSTANTS(:,10).*(STATES(:,3)./(CONSTANTS(:,11)+STATES(:,3)));
    RATES(:,3) =  (ALGEBRAIC(:,2) - ALGEBRAIC(:,5)).*1.00000;
    ALGEBRAIC(:,3) = CONSTANTS(:,12)+ CONSTANTS(:,13).*STATES(:,4);
    ALGEBRAIC(:,6) =  CONSTANTS(:,14).*STATES(:,3).*(STATES(:,4)./(CONSTANTS(:,15)+STATES(:,4)))+ CONSTANTS(:,16).*STATES(:,1).*(STATES(:,4)./(CONSTANTS(:,17)+STATES(:,4)));
    RATES(:,4) =  (ALGEBRAIC(:,3) - ALGEBRAIC(:,6)).*1.00000;
    ALGEBRAIC(:,7) =  CONSTANTS(:,5).*STATES(:,3)+ CONSTANTS(:,6).*STATES(:,4);
    ALGEBRAIC(:,8) =  CONSTANTS(:,7).*(STATES(:,1)./(CONSTANTS(:,8)+STATES(:,1)));
    RATES(:,1) =  (((ALGEBRAIC(:,1) - ALGEBRAIC(:,4))+ALGEBRAIC(:,7)) - ALGEBRAIC(:,8)).*1.00000;
   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(:,1).*STATES(:,1).*STATES(:,3).*(STATES(:,2)./(CONSTANTS(:,2)+STATES(:,2)));
    ALGEBRAIC(:,4) =  CONSTANTS(:,4).*(STATES(:,1)./(CONSTANTS(:,3)+STATES(:,2)));
    ALGEBRAIC(:,2) =  CONSTANTS(:,9).*STATES(:,4);
    ALGEBRAIC(:,5) =  CONSTANTS(:,10).*(STATES(:,3)./(CONSTANTS(:,11)+STATES(:,3)));
    ALGEBRAIC(:,3) = CONSTANTS(:,12)+ CONSTANTS(:,13).*STATES(:,4);
    ALGEBRAIC(:,6) =  CONSTANTS(:,14).*STATES(:,3).*(STATES(:,4)./(CONSTANTS(:,15)+STATES(:,4)))+ CONSTANTS(:,16).*STATES(:,1).*(STATES(:,4)./(CONSTANTS(:,17)+STATES(:,4)));
    ALGEBRAIC(:,7) =  CONSTANTS(:,5).*STATES(:,3)+ CONSTANTS(:,6).*STATES(:,4);
    ALGEBRAIC(:,8) =  CONSTANTS(:,7).*(STATES(:,1)./(CONSTANTS(:,8)+STATES(:,1)));
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