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 =14;
end
% There are a total of 4 entries in each of the rate and state variable arrays.
% There are a total of 45 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_ALGEBRAIC(:,1) = strpad('t_modulo in component environment (msec)');
    LEGEND_CONSTANTS(:,1) = strpad('Acap in component general_parameters (cm2)');
    LEGEND_CONSTANTS(:,2) = strpad('V_myo in component general_parameters (uL)');
    LEGEND_CONSTANTS(:,3) = strpad('C_m in component general_parameters (uF_per_cm2)');
    LEGEND_CONSTANTS(:,4) = strpad('F in component general_parameters (C_per_mmole)');
    LEGEND_CONSTANTS(:,5) = strpad('T in component general_parameters (kelvin)');
    LEGEND_CONSTANTS(:,6) = strpad('R in component general_parameters (J_per_K_per_mol)');
    LEGEND_CONSTANTS(:,7) = strpad('CaM_tot in component general_parameters (uM)');
    LEGEND_CONSTANTS(:,8) = strpad('Km_CaM in component general_parameters (uM)');
    LEGEND_CONSTANTS(:,9) = strpad('Ca_o in component general_parameters (uM)');
    LEGEND_CONSTANTS(:,10) = strpad('Na_o in component general_parameters (uM)');
    LEGEND_CONSTANTS(:,11) = strpad('Ca_NSR in component general_parameters (uM)');
    LEGEND_CONSTANTS(:,12) = strpad('J_leak in component general_parameters (uM_per_msec)');
    LEGEND_ALGEBRAIC(:,2) = strpad('V in component action_potential (mV)');
    LEGEND_CONSTANTS(:,13) = strpad('t1 in component action_potential (msec)');
    LEGEND_CONSTANTS(:,14) = strpad('t2 in component action_potential (msec)');
    LEGEND_CONSTANTS(:,15) = strpad('p in component action_potential (dimensionless)');
    LEGEND_CONSTANTS(:,16) = strpad('A in component action_potential (mV)');
    LEGEND_CONSTANTS(:,17) = strpad('rest in component action_potential (mV)');
    LEGEND_ALGEBRAIC(:,4) = strpad('Ca_input in component calcium_input (uM_per_msec)');
    LEGEND_ALGEBRAIC(:,3) = strpad('tcalcium in component calcium_input (msec)');
    LEGEND_CONSTANTS(:,18) = strpad('Ca_tau1 in component calcium_input (msec)');
    LEGEND_CONSTANTS(:,19) = strpad('Ca_tau2 in component calcium_input (msec)');
    LEGEND_CONSTANTS(:,20) = strpad('Ca_pow in component calcium_input (dimensionless)');
    LEGEND_CONSTANTS(:,21) = strpad('Ca_amp in component calcium_input (uM_per_msec)');
    LEGEND_ALGEBRAIC(:,5) = strpad('INaCa in component NCX_current (uA_per_uF)');
    LEGEND_CONSTANTS(:,22) = strpad('Na_i in component NCX_current (uM)');
    LEGEND_CONSTANTS(:,23) = strpad('KmNa in component NCX_current (uM)');
    LEGEND_CONSTANTS(:,24) = strpad('KmCa in component NCX_current (uM)');
    LEGEND_CONSTANTS(:,25) = strpad('ksat in component NCX_current (dimensionless)');
    LEGEND_CONSTANTS(:,26) = strpad('eta in component NCX_current (dimensionless)');
    LEGEND_CONSTANTS(:,42) = strpad('kNaCa in component NCX_current (uA_per_uF)');
    LEGEND_STATES(:,1) = strpad('Ca_cyt in component differential_equations (uM)');
    LEGEND_CONSTANTS(:,27) = strpad('SERCA_TOT in component serca_parameters (uM)');
    LEGEND_CONSTANTS(:,28) = strpad('CaMKII_reg in component serca_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,29) = strpad('PKA_reg in component serca_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,30) = strpad('PSR in component serca_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,31) = strpad('Kmf_PLBKO in component serca_parameters (uM)');
    LEGEND_CONSTANTS(:,32) = strpad('Kmf_PLB in component serca_parameters (uM)');
    LEGEND_CONSTANTS(:,33) = strpad('Kmr_PLBKO in component serca_parameters (uM)');
    LEGEND_CONSTANTS(:,34) = strpad('Kmr_PLB in component serca_parameters (uM)');
    LEGEND_CONSTANTS(:,35) = strpad('PLB_tot in component serca_parameters (uM)');
    LEGEND_CONSTANTS(:,36) = strpad('kplb_pos in component serca_parameters (per_msec)');
    LEGEND_CONSTANTS(:,37) = strpad('kplb_neg in component serca_parameters (per_msec)');
    LEGEND_ALGEBRAIC(:,6) = strpad('EC_50_fwd in component serca_parameters (uM)');
    LEGEND_ALGEBRAIC(:,7) = strpad('EC_50_rev in component serca_parameters (uM)');
    LEGEND_STATES(:,2) = strpad('PLB_dephosph in component differential_equations (uM)');
    LEGEND_CONSTANTS(:,45) = strpad('k_cyt_serca in component transition_parameters (per_uM2_per_msec)');
    LEGEND_ALGEBRAIC(:,8) = strpad('k_serca_cyt in component transition_parameters (per_msec)');
    LEGEND_CONSTANTS(:,43) = strpad('k_serca_sr in component transition_parameters (per_msec)');
    LEGEND_ALGEBRAIC(:,9) = strpad('k_sr_serca in component transition_parameters (per_uM2_per_msec)');
    LEGEND_CONSTANTS(:,44) = strpad('br_cyt_serca in component transition_parameters (per_uM2_per_msec)');
    LEGEND_CONSTANTS(:,38) = strpad('br_serca_sr in component transition_parameters (per_msec)');
    LEGEND_ALGEBRAIC(:,13) = strpad('J_up in component calcium_fluxes (uM_per_msec)');
    LEGEND_ALGEBRAIC(:,10) = strpad('J_cyt_serca in component calcium_fluxes (uM_per_msec)');
    LEGEND_ALGEBRAIC(:,11) = strpad('J_serca_sr in component calcium_fluxes (uM_per_msec)');
    LEGEND_STATES(:,3) = strpad('Ca_serca in component differential_equations (uM)');
    LEGEND_CONSTANTS(:,39) = strpad('LTRPN_tot in component calcium_buffering (uM)');
    LEGEND_CONSTANTS(:,40) = strpad('kltrpn_pos in component calcium_buffering (per_uM_per_msec)');
    LEGEND_CONSTANTS(:,41) = strpad('kltrpn_neg in component calcium_buffering (per_msec)');
    LEGEND_ALGEBRAIC(:,14) = strpad('J_LTRPN in component calcium_buffering (uM_per_msec)');
    LEGEND_ALGEBRAIC(:,12) = strpad('B_i in component calcium_buffering (dimensionless)');
    LEGEND_STATES(:,4) = strpad('LTRPN in component differential_equations (uM)');
    LEGEND_RATES(:,1) = strpad('d/dt Ca_cyt in component differential_equations (uM)');
    LEGEND_RATES(:,4) = strpad('d/dt LTRPN in component differential_equations (uM)');
    LEGEND_RATES(:,2) = strpad('d/dt PLB_dephosph in component differential_equations (uM)');
    LEGEND_RATES(:,3) = strpad('d/dt Ca_serca in component differential_equations (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) = 1.534e-4;
    CONSTANTS(:,2) = 25.84e-6;
    CONSTANTS(:,3) = 1;
    CONSTANTS(:,4) = 96.5;
    CONSTANTS(:,5) = 298;
    CONSTANTS(:,6) = 8.314;
    CONSTANTS(:,7) = 24;
    CONSTANTS(:,8) = 2.38;
    CONSTANTS(:,9) = 1000;
    CONSTANTS(:,10) = 140000;
    CONSTANTS(:,11) = 760;
    CONSTANTS(:,12) = 0.0003;
    CONSTANTS(:,13) = 0.5;
    CONSTANTS(:,14) = 8;
    CONSTANTS(:,15) = 2;
    CONSTANTS(:,16) = 150;
    CONSTANTS(:,17) = -80;
    CONSTANTS(:,18) = 1.5;
    CONSTANTS(:,19) = 14;
    CONSTANTS(:,20) = 2;
    CONSTANTS(:,21) = 2.9;
    CONSTANTS(:,22) = 14000;
    CONSTANTS(:,23) = 87500;
    CONSTANTS(:,24) = 1380;
    CONSTANTS(:,25) = 0.1;
    CONSTANTS(:,26) = 0.35;
    STATES(:,1) = 0.1;
    CONSTANTS(:,27) = 47;
    CONSTANTS(:,28) = 0.1;
    CONSTANTS(:,29) = 0.1;
    CONSTANTS(:,30) = 1;
    CONSTANTS(:,31) = 0.15;
    CONSTANTS(:,32) = 0.15;
    CONSTANTS(:,33) = 2500;
    CONSTANTS(:,34) = 1110;
    CONSTANTS(:,35) = 1;
    CONSTANTS(:,36) = 1;
    CONSTANTS(:,37) = 6.8;
    STATES(:,2) = 0.1;
    CONSTANTS(:,38) = 0.00625;
    STATES(:,3) = 5;
    CONSTANTS(:,39) = 70;
    CONSTANTS(:,40) = 0.1;
    CONSTANTS(:,41) = 0.06;
    STATES(:,4) = 11;
    CONSTANTS(:,42) =  125.000.*2.50000;
    CONSTANTS(:,43) =  CONSTANTS(:,38).*(1.00000+ 0.700000.*CONSTANTS(:,28));
    CONSTANTS(:,44) =  1000.00.*CONSTANTS(:,38);
    CONSTANTS(:,45) =  CONSTANTS(:,44).*(1.00000+ 0.700000.*CONSTANTS(:,28));
    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(:,4) =  CONSTANTS(:,40).*STATES(:,1).*(CONSTANTS(:,39) - STATES(:,4)) -  CONSTANTS(:,41).*STATES(:,4);
    RATES(:,2) =  CONSTANTS(:,36).*(CONSTANTS(:,35) - STATES(:,2)) -  CONSTANTS(:,37).*power(CONSTANTS(:,28)+CONSTANTS(:,29), 2.00000).*STATES(:,2);
    ALGEBRAIC(:,6) =  (CONSTANTS(:,31)+( CONSTANTS(:,32).*CONSTANTS(:,30).*STATES(:,2))./1.00000).*(1.00000+ 0.270000.*CONSTANTS(:,28));
    ALGEBRAIC(:,8) =  power(ALGEBRAIC(:,6), 2.00000).*CONSTANTS(:,44);
    ALGEBRAIC(:,10) =  CONSTANTS(:,45).*power(STATES(:,1), 2.00000).*(CONSTANTS(:,27) - STATES(:,3)) -  ALGEBRAIC(:,8).*STATES(:,3);
    ALGEBRAIC(:,7) = CONSTANTS(:,33) - ( CONSTANTS(:,34).*CONSTANTS(:,30).*STATES(:,2))./1.00000;
    ALGEBRAIC(:,9) = CONSTANTS(:,38)./power(ALGEBRAIC(:,7), 2.00000);
    ALGEBRAIC(:,11) =  CONSTANTS(:,43).*STATES(:,3) -  ALGEBRAIC(:,9).*power(CONSTANTS(:,11), 2.00000).*(CONSTANTS(:,27) - STATES(:,3));
    RATES(:,3) = ALGEBRAIC(:,10) - ALGEBRAIC(:,11);
    ALGEBRAIC(:,1) =  rem(VOI, 1000.00);
    ALGEBRAIC(:,3) = piecewise({ALGEBRAIC(:,1) - 1.20000<=0.00000, 0.00000 }, ALGEBRAIC(:,1) - 1.20000);
    ALGEBRAIC(:,4) =  CONSTANTS(:,21).*power(1.00000 - exp( - ALGEBRAIC(:,3)./CONSTANTS(:,18)), CONSTANTS(:,20)).*exp( - ALGEBRAIC(:,3)./CONSTANTS(:,19));
    ALGEBRAIC(:,2) = CONSTANTS(:,17)+ CONSTANTS(:,16).*power(1.00000 - exp( - ALGEBRAIC(:,1)./CONSTANTS(:,13)), CONSTANTS(:,15)).*exp( - ALGEBRAIC(:,1)./CONSTANTS(:,14));
    ALGEBRAIC(:,5) =  (CONSTANTS(:,42)./( (power(CONSTANTS(:,23), 3.00000)+power(CONSTANTS(:,10), 3.00000)).*(CONSTANTS(:,24)+CONSTANTS(:,9)).*(1.00000+ CONSTANTS(:,25).*exp(( (CONSTANTS(:,26) - 1.00000).*ALGEBRAIC(:,2).*CONSTANTS(:,4))./( CONSTANTS(:,6).*CONSTANTS(:,5)))))).*( exp(( CONSTANTS(:,26).*ALGEBRAIC(:,2).*CONSTANTS(:,4))./( CONSTANTS(:,6).*CONSTANTS(:,5))).*power(CONSTANTS(:,22), 3.00000).*CONSTANTS(:,9) -  exp(( (CONSTANTS(:,26) - 1.00000).*ALGEBRAIC(:,2).*CONSTANTS(:,4))./( CONSTANTS(:,6).*CONSTANTS(:,5))).*power(CONSTANTS(:,10), 3.00000).*STATES(:,1));
    ALGEBRAIC(:,14) =  CONSTANTS(:,40).*STATES(:,1).*(CONSTANTS(:,39) - STATES(:,4)) -  CONSTANTS(:,41).*STATES(:,4);
    ALGEBRAIC(:,12) = power(1.00000+( CONSTANTS(:,7).*CONSTANTS(:,8))./power(CONSTANTS(:,8)+STATES(:,1), 2.00000),  - 1.00000);
    RATES(:,1) =  ALGEBRAIC(:,12).*(((( ALGEBRAIC(:,5).*CONSTANTS(:,1).*CONSTANTS(:,3))./( 2.00000.*CONSTANTS(:,2).*CONSTANTS(:,4)) - ALGEBRAIC(:,10))+CONSTANTS(:,12)+ALGEBRAIC(:,4)) - ALGEBRAIC(:,14));
   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(:,6) =  (CONSTANTS(:,31)+( CONSTANTS(:,32).*CONSTANTS(:,30).*STATES(:,2))./1.00000).*(1.00000+ 0.270000.*CONSTANTS(:,28));
    ALGEBRAIC(:,8) =  power(ALGEBRAIC(:,6), 2.00000).*CONSTANTS(:,44);
    ALGEBRAIC(:,10) =  CONSTANTS(:,45).*power(STATES(:,1), 2.00000).*(CONSTANTS(:,27) - STATES(:,3)) -  ALGEBRAIC(:,8).*STATES(:,3);
    ALGEBRAIC(:,7) = CONSTANTS(:,33) - ( CONSTANTS(:,34).*CONSTANTS(:,30).*STATES(:,2))./1.00000;
    ALGEBRAIC(:,9) = CONSTANTS(:,38)./power(ALGEBRAIC(:,7), 2.00000);
    ALGEBRAIC(:,11) =  CONSTANTS(:,43).*STATES(:,3) -  ALGEBRAIC(:,9).*power(CONSTANTS(:,11), 2.00000).*(CONSTANTS(:,27) - STATES(:,3));
    ALGEBRAIC(:,1) =  rem(VOI, 1000.00);
    ALGEBRAIC(:,3) = piecewise({ALGEBRAIC(:,1) - 1.20000<=0.00000, 0.00000 }, ALGEBRAIC(:,1) - 1.20000);
    ALGEBRAIC(:,4) =  CONSTANTS(:,21).*power(1.00000 - exp( - ALGEBRAIC(:,3)./CONSTANTS(:,18)), CONSTANTS(:,20)).*exp( - ALGEBRAIC(:,3)./CONSTANTS(:,19));
    ALGEBRAIC(:,2) = CONSTANTS(:,17)+ CONSTANTS(:,16).*power(1.00000 - exp( - ALGEBRAIC(:,1)./CONSTANTS(:,13)), CONSTANTS(:,15)).*exp( - ALGEBRAIC(:,1)./CONSTANTS(:,14));
    ALGEBRAIC(:,5) =  (CONSTANTS(:,42)./( (power(CONSTANTS(:,23), 3.00000)+power(CONSTANTS(:,10), 3.00000)).*(CONSTANTS(:,24)+CONSTANTS(:,9)).*(1.00000+ CONSTANTS(:,25).*exp(( (CONSTANTS(:,26) - 1.00000).*ALGEBRAIC(:,2).*CONSTANTS(:,4))./( CONSTANTS(:,6).*CONSTANTS(:,5)))))).*( exp(( CONSTANTS(:,26).*ALGEBRAIC(:,2).*CONSTANTS(:,4))./( CONSTANTS(:,6).*CONSTANTS(:,5))).*power(CONSTANTS(:,22), 3.00000).*CONSTANTS(:,9) -  exp(( (CONSTANTS(:,26) - 1.00000).*ALGEBRAIC(:,2).*CONSTANTS(:,4))./( CONSTANTS(:,6).*CONSTANTS(:,5))).*power(CONSTANTS(:,10), 3.00000).*STATES(:,1));
    ALGEBRAIC(:,14) =  CONSTANTS(:,40).*STATES(:,1).*(CONSTANTS(:,39) - STATES(:,4)) -  CONSTANTS(:,41).*STATES(:,4);
    ALGEBRAIC(:,12) = power(1.00000+( CONSTANTS(:,7).*CONSTANTS(:,8))./power(CONSTANTS(:,8)+STATES(:,1), 2.00000),  - 1.00000);
    ALGEBRAIC(:,13) = ALGEBRAIC(:,10) - ALGEBRAIC(:,11);
end

% Compute result of a piecewise function
function x = piecewise(cases, default)
    set = [0];
    for i = 1:2:length(cases)
        if (length(cases{i+1}) == 1)
            x(cases{i} & ~set,:) = cases{i+1};
        else
            x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set);
        end
        set = set | cases{i};
        if(set), break, end
    end
    if (length(default) == 1)
        x(~set,:) = default;
    else
        x(~set,:) = default(~set);
    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