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 8 entries in each of the rate and state variable arrays.
% There are a total of 12 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('km2 in component PIPtoDAG (um)');
    LEGEND_CONSTANTS(:,2) = strpad('km6 in component PIPtoDAG (um)');
    LEGEND_CONSTANTS(:,3) = strpad('Vmax2 in component PIPtoDAG (per_s)');
    LEGEND_CONSTANTS(:,4) = strpad('Vmax6 in component PIPtoDAG (per_s)');
    LEGEND_STATES(:,1) = strpad('PIP2 in component PIPtoDAG (um)');
    LEGEND_STATES(:,2) = strpad('DAG in component PIPtoDAG (um)');
    LEGEND_STATES(:,3) = strpad('IP3 in component PIPtoDAG (um)');
    LEGEND_STATES(:,4) = strpad('CaPLCg in component PLC (um)');
    LEGEND_STATES(:,5) = strpad('CaPLCg_star in component PLC (um)');
    LEGEND_CONSTANTS(:,5) = strpad('kf1 in component PLC (per_um_s)');
    LEGEND_CONSTANTS(:,6) = strpad('kb1 in component PLC (per_s)');
    LEGEND_CONSTANTS(:,7) = strpad('kf3 in component PLC (per_s)');
    LEGEND_CONSTANTS(:,8) = strpad('kf5 in component PLC (per_um_s)');
    LEGEND_CONSTANTS(:,9) = strpad('kb5 in component PLC (per_s)');
    LEGEND_CONSTANTS(:,10) = strpad('km4 in component PLC (um)');
    LEGEND_CONSTANTS(:,11) = strpad('Vmax4 in component PLC (per_s)');
    LEGEND_STATES(:,6) = strpad('PLCg in component PLC (um)');
    LEGEND_STATES(:,7) = strpad('PLCg_star in component PLC (um)');
    LEGEND_CONSTANTS(:,12) = strpad('EGF_EGFR in component UndefinedVariables (um)');
    LEGEND_STATES(:,8) = strpad('Ca in component PLC (um)');
    LEGEND_RATES(:,1) = strpad('d/dt PIP2 in component PIPtoDAG (um)');
    LEGEND_RATES(:,2) = strpad('d/dt DAG in component PIPtoDAG (um)');
    LEGEND_RATES(:,3) = strpad('d/dt IP3 in component PIPtoDAG (um)');
    LEGEND_RATES(:,6) = strpad('d/dt PLCg in component PLC (um)');
    LEGEND_RATES(:,4) = strpad('d/dt CaPLCg in component PLC (um)');
    LEGEND_RATES(:,5) = strpad('d/dt CaPLCg_star in component PLC (um)');
    LEGEND_RATES(:,7) = strpad('d/dt PLCg_star in component PLC (um)');
    LEGEND_RATES(:,8) = strpad('d/dt Ca in component PLC (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) = 97;
    CONSTANTS(:,2) = 19.79166667;
    CONSTANTS(:,3) = 14;
    CONSTANTS(:,4) = 57;
    STATES(:,1) = 10;
    STATES(:,2) = 0;
    STATES(:,3) = 0;
    STATES(:,4) = 0;
    STATES(:,5) = 0;
    CONSTANTS(:,5) = 0.0003;
    CONSTANTS(:,6) = 10;
    CONSTANTS(:,7) = 0.05;
    CONSTANTS(:,8) = 0.00002;
    CONSTANTS(:,9) = 10;
    CONSTANTS(:,10) = 0.33333333333;
    CONSTANTS(:,11) = 0.2;
    STATES(:,6) = 0.82;
    STATES(:,7) = 0;
    CONSTANTS(:,12) = 0.1;
    STATES(:,8) = 0.1;
    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) = (  - STATES(:,4).*CONSTANTS(:,3).*STATES(:,1))./(CONSTANTS(:,1)+STATES(:,1)) - ( STATES(:,5).*CONSTANTS(:,4).*STATES(:,1))./(CONSTANTS(:,2)+STATES(:,1));
    RATES(:,2) = ( STATES(:,4).*CONSTANTS(:,3).*STATES(:,1))./(CONSTANTS(:,1)+STATES(:,1))+( STATES(:,5).*CONSTANTS(:,4).*STATES(:,1))./(CONSTANTS(:,2)+STATES(:,1));
    RATES(:,3) = ( STATES(:,4).*CONSTANTS(:,3).*STATES(:,1))./(CONSTANTS(:,1)+STATES(:,1))+( STATES(:,5).*CONSTANTS(:,4).*STATES(:,1))./(CONSTANTS(:,2)+STATES(:,1));
    RATES(:,6) =   - STATES(:,8).*STATES(:,6).*CONSTANTS(:,5)+ STATES(:,4).*CONSTANTS(:,6);
    RATES(:,4) = ( - (  - STATES(:,8).*STATES(:,6).*CONSTANTS(:,5)+ STATES(:,4).*CONSTANTS(:,6))+ CONSTANTS(:,7).*STATES(:,5)) - ( CONSTANTS(:,11).*CONSTANTS(:,12).*STATES(:,4))./(CONSTANTS(:,10)+STATES(:,4));
    RATES(:,5) = ( - ( CONSTANTS(:,7).*STATES(:,5) - ( CONSTANTS(:,11).*CONSTANTS(:,12).*STATES(:,4))./(CONSTANTS(:,10)+STATES(:,4)))+ STATES(:,8).*STATES(:,7).*CONSTANTS(:,8)) -  CONSTANTS(:,9).*STATES(:,5);
    RATES(:,7) =   - STATES(:,8).*STATES(:,7).*CONSTANTS(:,8)+ CONSTANTS(:,9).*STATES(:,5);
    RATES(:,8) = (  - STATES(:,8).*STATES(:,6).*CONSTANTS(:,5)+ STATES(:,4).*CONSTANTS(:,6)+ CONSTANTS(:,9).*STATES(:,5)) -  STATES(:,8).*STATES(:,7).*CONSTANTS(:,8);
   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