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 15 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('kf8 in component PIPtoDAG (per_s)');
    LEGEND_CONSTANTS(:,2) = strpad('kf9 in component PIPtoDAG (per_s)');
    LEGEND_CONSTANTS(:,3) = strpad('km6 in component PIPtoDAG (um)');
    LEGEND_CONSTANTS(:,4) = strpad('Vmax6 in component PIPtoDAG (per_s)');
    LEGEND_CONSTANTS(:,5) = strpad('km7 in component PIPtoDAG (um)');
    LEGEND_CONSTANTS(:,6) = strpad('Vmax7 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('CaPLC in component PLC (um)');
    LEGEND_STATES(:,5) = strpad('CaGqPLC in component PLC (um)');
    LEGEND_STATES(:,6) = strpad('Inositol in component PIPtoDAG (um)');
    LEGEND_STATES(:,7) = strpad('PC in component PIPtoDAG (um)');
    LEGEND_CONSTANTS(:,7) = strpad('kf1 in component PLC (per_um_s)');
    LEGEND_CONSTANTS(:,8) = strpad('kb1 in component PLC (per_s)');
    LEGEND_CONSTANTS(:,9) = strpad('kf2 in component PLC (per_um_s)');
    LEGEND_CONSTANTS(:,10) = strpad('kb2 in component PLC (per_s)');
    LEGEND_CONSTANTS(:,11) = strpad('kf3 in component PLC (per_um_s)');
    LEGEND_CONSTANTS(:,12) = strpad('kb3 in component PLC (per_s)');
    LEGEND_CONSTANTS(:,13) = strpad('kf4 in component PLC (per_um_s)');
    LEGEND_CONSTANTS(:,14) = strpad('kb4 in component PLC (per_s)');
    LEGEND_CONSTANTS(:,15) = strpad('kf5 in component PLC (per_s)');
    LEGEND_STATES(:,8) = strpad('PLC in component PLC (um)');
    LEGEND_STATES(:,9) = strpad('Gq in component PLC (um)');
    LEGEND_STATES(:,10) = strpad('Ca in component PLC (um)');
    LEGEND_STATES(:,11) = strpad('GqPLC 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(:,7) = strpad('d/dt PC in component PIPtoDAG (um)');
    LEGEND_RATES(:,6) = strpad('d/dt Inositol in component PIPtoDAG (um)');
    LEGEND_RATES(:,8) = strpad('d/dt PLC in component PLC (um)');
    LEGEND_RATES(:,9) = strpad('d/dt Gq in component PLC (um)');
    LEGEND_RATES(:,10) = strpad('d/dt Ca in component PLC (um)');
    LEGEND_RATES(:,11) = strpad('d/dt GqPLC in component PLC (um)');
    LEGEND_RATES(:,4) = strpad('d/dt CaPLC in component PLC (um)');
    LEGEND_RATES(:,5) = strpad('d/dt CaGqPLC 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) = 0.15;
    CONSTANTS(:,2) = 2.5;
    CONSTANTS(:,3) = 5;
    CONSTANTS(:,4) = 48;
    CONSTANTS(:,5) = 19.84166667;
    CONSTANTS(:,6) = 10;
    STATES(:,1) = 10;
    STATES(:,2) = 0;
    STATES(:,3) = 0;
    STATES(:,4) = 0;
    STATES(:,5) = 0;
    STATES(:,6) = 0;
    STATES(:,7) = 0;
    CONSTANTS(:,7) = 0.000005;
    CONSTANTS(:,8) = 1;
    CONSTANTS(:,9) = 0.0000042;
    CONSTANTS(:,10) = 1;
    CONSTANTS(:,11) = 0.00005;
    CONSTANTS(:,12) = 1;
    CONSTANTS(:,13) = 0.0000042;
    CONSTANTS(:,14) = 1;
    CONSTANTS(:,15) = 0.0133;
    STATES(:,8) = 0.8;
    STATES(:,9) = 0.15;
    STATES(:,10) = 0.1;
    STATES(:,11) = 0;
    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(:,6).*STATES(:,1))./(CONSTANTS(:,5)+STATES(:,1)) - ( STATES(:,5).*CONSTANTS(:,4).*STATES(:,1))./(CONSTANTS(:,3)+STATES(:,1));
    RATES(:,2) = ( STATES(:,4).*CONSTANTS(:,6).*STATES(:,1))./(CONSTANTS(:,5)+STATES(:,1)) -  CONSTANTS(:,1).*STATES(:,2);
    RATES(:,3) = ( STATES(:,5).*CONSTANTS(:,4).*STATES(:,1))./(CONSTANTS(:,3)+STATES(:,1)) -  CONSTANTS(:,2).*STATES(:,3);
    RATES(:,7) =  CONSTANTS(:,1).*STATES(:,2);
    RATES(:,6) =  CONSTANTS(:,2).*STATES(:,3);
    RATES(:,8) = ((  - STATES(:,8).*STATES(:,10).*CONSTANTS(:,7)+ STATES(:,4).*CONSTANTS(:,8)) -  STATES(:,8).*STATES(:,9).*CONSTANTS(:,9))+ STATES(:,11).*CONSTANTS(:,10);
    RATES(:,9) = (  - STATES(:,8).*STATES(:,9).*CONSTANTS(:,9)+ STATES(:,11).*CONSTANTS(:,10)+ STATES(:,5).*CONSTANTS(:,14)) -  STATES(:,4).*STATES(:,9).*CONSTANTS(:,13);
    RATES(:,10) = ((  - STATES(:,8).*STATES(:,10).*CONSTANTS(:,7)+ STATES(:,4).*CONSTANTS(:,8)) -  STATES(:,10).*STATES(:,11).*CONSTANTS(:,11))+ STATES(:,5).*CONSTANTS(:,12);
    RATES(:,11) = (( STATES(:,8).*STATES(:,9).*CONSTANTS(:,9) -  STATES(:,11).*CONSTANTS(:,10)) -  STATES(:,10).*STATES(:,11).*CONSTANTS(:,11))+ STATES(:,5).*CONSTANTS(:,12);
    RATES(:,4) = (( STATES(:,8).*STATES(:,10).*CONSTANTS(:,7) -  STATES(:,4).*CONSTANTS(:,8))+ STATES(:,5).*CONSTANTS(:,15)+ STATES(:,5).*CONSTANTS(:,14)) -  STATES(:,4).*STATES(:,9).*CONSTANTS(:,13);
    RATES(:,5) = ((( STATES(:,11).*STATES(:,10).*CONSTANTS(:,11) -  STATES(:,5).*CONSTANTS(:,12))+ STATES(:,4).*STATES(:,9).*CONSTANTS(:,13)) -  STATES(:,5).*CONSTANTS(:,14)) -  STATES(:,5).*CONSTANTS(:,15);
   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