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 5 entries in each of the rate and state variable arrays.
% There are a total of 21 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_STATES(:,1) = strpad('G_a in component G_a (micromolar)');
    LEGEND_CONSTANTS(:,1) = strpad('k1 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,2) = strpad('k2 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,3) = strpad('k3 in component model_parameters (dimensionless)');
    LEGEND_STATES(:,2) = strpad('PLC in component PLC (micromolar)');
    LEGEND_STATES(:,3) = strpad('Ca_cyt in component Ca_cyt (micromolar)');
    LEGEND_CONSTANTS(:,4) = strpad('K4 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,5) = strpad('k5 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,6) = strpad('K6 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,7) = strpad('k7 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,8) = strpad('k8 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('K9 in component model_parameters (dimensionless)');
    LEGEND_STATES(:,4) = strpad('Ca_ER in component Ca_ER (micromolar)');
    LEGEND_CONSTANTS(:,10) = strpad('k10 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,11) = strpad('K11 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,12) = strpad('k16 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,13) = strpad('K17 in component model_parameters (dimensionless)');
    LEGEND_STATES(:,5) = strpad('Ca_mit in component Ca_mit (micromolar)');
    LEGEND_CONSTANTS(:,14) = strpad('k18 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,15) = strpad('K19 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,16) = strpad('k20 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,17) = strpad('K21 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,18) = strpad('k12 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,19) = strpad('k13 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,20) = strpad('k14 in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,21) = strpad('K15 in component model_parameters (dimensionless)');
    LEGEND_RATES(:,1) = strpad('d/dt G_a in component G_a (micromolar)');
    LEGEND_RATES(:,2) = strpad('d/dt PLC in component PLC (micromolar)');
    LEGEND_RATES(:,4) = strpad('d/dt Ca_ER in component Ca_ER (micromolar)');
    LEGEND_RATES(:,5) = strpad('d/dt Ca_mit in component Ca_mit (micromolar)');
    LEGEND_RATES(:,3) = strpad('d/dt Ca_cyt in component Ca_cyt (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;
    CONSTANTS(:,1) = 0.01;
    CONSTANTS(:,2) = 1.42;
    CONSTANTS(:,3) = 0.64;
    STATES(:,2) = 0.01;
    STATES(:,3) = 0.01;
    CONSTANTS(:,4) = 0.19;
    CONSTANTS(:,5) = 4.88;
    CONSTANTS(:,6) = 1.18;
    CONSTANTS(:,7) = 2.08;
    CONSTANTS(:,8) = 32.24;
    CONSTANTS(:,9) = 29.09;
    STATES(:,4) = 10;
    CONSTANTS(:,10) = 0.7;
    CONSTANTS(:,11) = 3;
    CONSTANTS(:,12) = 7;
    CONSTANTS(:,13) = 0.05;
    STATES(:,5) = 0.001;
    CONSTANTS(:,14) = 79;
    CONSTANTS(:,15) = 3.5;
    CONSTANTS(:,16) = 0.81;
    CONSTANTS(:,17) = 4.5;
    CONSTANTS(:,18) = 2.8;
    CONSTANTS(:,19) = 13.4;
    CONSTANTS(:,20) = 153;
    CONSTANTS(:,21) = 0.16;
    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(:,1)+ CONSTANTS(:,2).*STATES(:,1)) - ( CONSTANTS(:,3).*STATES(:,1).*STATES(:,2))./(STATES(:,1)+CONSTANTS(:,4))) - ( CONSTANTS(:,5).*STATES(:,3).*STATES(:,1))./(STATES(:,1)+CONSTANTS(:,6));
    RATES(:,2) =  CONSTANTS(:,7).*STATES(:,1) - ( CONSTANTS(:,8).*STATES(:,2))./(STATES(:,2)+CONSTANTS(:,9));
    RATES(:,4) =   - (STATES(:,4) - STATES(:,3)).*(( CONSTANTS(:,10).*STATES(:,3).*power(STATES(:,2), 4.00000))./(power(STATES(:,2), 4.00000)+power(CONSTANTS(:,11), 4.00000)))+( CONSTANTS(:,12).*STATES(:,3))./(STATES(:,3)+CONSTANTS(:,13));
    RATES(:,5) = ( CONSTANTS(:,14).*power(STATES(:,3), 8.00000))./(power(CONSTANTS(:,15), 8.00000)+power(STATES(:,3), 8.00000)) -  (STATES(:,5) - STATES(:,3)).*(( CONSTANTS(:,16).*STATES(:,3))./(STATES(:,3)+CONSTANTS(:,17)));
    RATES(:,3) = (((( (STATES(:,4) - STATES(:,3)).*(( CONSTANTS(:,10).*STATES(:,3).*power(STATES(:,2), 4.00000))./(power(STATES(:,2), 4.00000)+power(CONSTANTS(:,11), 4.00000)))+ CONSTANTS(:,18).*STATES(:,2)+ CONSTANTS(:,19).*STATES(:,1)) - ( CONSTANTS(:,20).*STATES(:,3))./(CONSTANTS(:,21)+STATES(:,3))) - ( CONSTANTS(:,12).*STATES(:,3))./(CONSTANTS(:,13)+STATES(:,3))) - ( CONSTANTS(:,14).*power(STATES(:,3), 8.00000))./(power(CONSTANTS(:,15), 8.00000)+power(STATES(:,3), 8.00000)))+ (STATES(:,5) - STATES(:,3)).*(( CONSTANTS(:,16).*STATES(:,3))./(STATES(:,3)+CONSTANTS(:,17)));
   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