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 =2;
end
% There are a total of 1 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 (msec)');
    LEGEND_CONSTANTS(:,1) = strpad('Ca_cyt in component general_parameters (uM)');
    LEGEND_CONSTANTS(:,2) = strpad('Ca_NSR in component general_parameters (uM)');
    LEGEND_CONSTANTS(:,3) = strpad('CaMKII_reg in component general_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,4) = strpad('SERCA_TOT in component serca_parameters (uM)');
    LEGEND_CONSTANTS(:,5) = strpad('PSR in component serca_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,6) = strpad('Kmf_PLBKO in component serca_parameters (uM)');
    LEGEND_CONSTANTS(:,7) = strpad('Kmf_PLB in component serca_parameters (uM)');
    LEGEND_CONSTANTS(:,8) = strpad('Kmr_PLBKO in component serca_parameters (uM)');
    LEGEND_CONSTANTS(:,9) = strpad('Kmr_PLB in component serca_parameters (uM)');
    LEGEND_CONSTANTS(:,13) = strpad('EC_50_fwd in component serca_parameters (uM)');
    LEGEND_CONSTANTS(:,11) = strpad('EC_50_rev in component serca_parameters (uM)');
    LEGEND_CONSTANTS(:,16) = strpad('k_cyt_serca in component transition_parameters (per_msec_per_uM2)');
    LEGEND_CONSTANTS(:,17) = strpad('k_serca_cyt in component transition_parameters (per_msec)');
    LEGEND_CONSTANTS(:,12) = strpad('k_serca_sr in component transition_parameters (per_msec)');
    LEGEND_CONSTANTS(:,14) = strpad('k_sr_serca in component transition_parameters (per_msec_per_uM2)');
    LEGEND_CONSTANTS(:,15) = strpad('br_cyt_serca in component transition_parameters (per_msec_per_uM2)');
    LEGEND_CONSTANTS(:,10) = strpad('br_serca_sr in component transition_parameters (per_msec)');
    LEGEND_ALGEBRAIC(:,1) = strpad('J_cyt_serca in component calcium_fluxes (uM_per_msec)');
    LEGEND_ALGEBRAIC(:,2) = strpad('J_serca_sr in component calcium_fluxes (uM_per_msec)');
    LEGEND_STATES(:,1) = strpad('Ca_serca in component calcium_bound_serca (uM)');
    LEGEND_RATES(:,1) = strpad('d/dt Ca_serca in component calcium_bound_serca (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) = 0.25;
    CONSTANTS(:,2) = 760;
    CONSTANTS(:,3) = 0;
    CONSTANTS(:,4) = 47;
    CONSTANTS(:,5) = 1;
    CONSTANTS(:,6) = 0.15;
    CONSTANTS(:,7) = 0.15;
    CONSTANTS(:,8) = 2500;
    CONSTANTS(:,9) = 1110;
    CONSTANTS(:,10) = 0.00625;
    STATES(:,1) = 12;
    CONSTANTS(:,11) = CONSTANTS(:,8) -  CONSTANTS(:,9).*CONSTANTS(:,5);
    CONSTANTS(:,12) =  CONSTANTS(:,10).*(1.00000+ 0.700000.*CONSTANTS(:,3));
    CONSTANTS(:,13) =  (CONSTANTS(:,6)+ CONSTANTS(:,7).*CONSTANTS(:,5)).*(1.00000+ 0.270000.*CONSTANTS(:,3));
    CONSTANTS(:,14) = CONSTANTS(:,10)./power(CONSTANTS(:,11), 2.00000);
    CONSTANTS(:,15) =  1000.00.*CONSTANTS(:,10);
    CONSTANTS(:,16) =  CONSTANTS(:,15).*(1.00000+ 0.700000.*CONSTANTS(:,3));
    CONSTANTS(:,17) =  power(CONSTANTS(:,13), 2.00000).*CONSTANTS(:,15);
    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(:,16).*power(CONSTANTS(:,1), 2.00000).*(CONSTANTS(:,4) - STATES(:,1)) -  CONSTANTS(:,17).*STATES(:,1);
    ALGEBRAIC(:,2) =  CONSTANTS(:,12).*STATES(:,1) -  CONSTANTS(:,14).*power(CONSTANTS(:,2), 2.00000).*(CONSTANTS(:,4) - STATES(:,1));
    RATES(:,1) = ALGEBRAIC(:,1) - ALGEBRAIC(:,2);
   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(:,16).*power(CONSTANTS(:,1), 2.00000).*(CONSTANTS(:,4) - STATES(:,1)) -  CONSTANTS(:,17).*STATES(:,1);
    ALGEBRAIC(:,2) =  CONSTANTS(:,12).*STATES(:,1) -  CONSTANTS(:,14).*power(CONSTANTS(:,2), 2.00000).*(CONSTANTS(:,4) - 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