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 =15;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 29 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 (millisecond)');
    LEGEND_CONSTANTS(:,1) = strpad('A_iso in component parameters (mN_per_mm2_per_mM)');
    LEGEND_CONSTANTS(:,2) = strpad('k_off in component parameters (per_msec)');
    LEGEND_CONSTANTS(:,3) = strpad('k_on in component parameters (per_mM_per_msec)');
    LEGEND_CONSTANTS(:,4) = strpad('k_onI in component parameters (per_msec)');
    LEGEND_CONSTANTS(:,5) = strpad('k_offi in component parameters (per_msec)');
    LEGEND_CONSTANTS(:,6) = strpad('k_OFF in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,7) = strpad('k_xboff in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,8) = strpad('k_tmoff in component parameters (per_msec)');
    LEGEND_CONSTANTS(:,9) = strpad('k_tmonc in component parameters (per_msec)');
    LEGEND_CONSTANTS(:,10) = strpad('k_tmRU in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,11) = strpad('k_tmxb in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,12) = strpad('k_12 in component parameters (per_mM_per_msec)');
    LEGEND_CONSTANTS(:,13) = strpad('k_minus12 in component parameters (per_msec)');
    LEGEND_CONSTANTS(:,14) = strpad('k_Titin in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,15) = strpad('k_3c in component parameters (per_msec)');
    LEGEND_CONSTANTS(:,16) = strpad('k_3f in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,17) = strpad('k_3xb in component parameters (dimensionless)');
    LEGEND_CONSTANTS(:,18) = strpad('k_minus3 in component parameters (per_msec)');
    LEGEND_CONSTANTS(:,19) = strpad('k_4 in component parameters (per_msec)');
    LEGEND_CONSTANTS(:,20) = strpad('k_minus4 in component parameters (per_msec)');
    LEGEND_CONSTANTS(:,21) = strpad('k_5 in component parameters (per_msec)');
    LEGEND_ALGEBRAIC(:,1) = strpad('F_b in component active_force (mN_per_mm2)');
    LEGEND_STATES(:,1) = strpad('RUA_MADPPi in component RU_species (mM)');
    LEGEND_STATES(:,2) = strpad('RUA_MADP in component RU_species (mM)');
    LEGEND_ALGEBRAIC(:,6) = strpad('Q_CaB in component Ca_binding_rate (mM_per_msec)');
    LEGEND_ALGEBRAIC(:,4) = strpad('RUNA in component RU_species (mM)');
    LEGEND_STATES(:,3) = strpad('Ca in component RU_species (mM)');
    LEGEND_STATES(:,4) = strpad('RUTCa_off in component RU_species (mM)');
    LEGEND_ALGEBRAIC(:,12) = strpad('Q_TCaA in component TnI_conf_change_rate (mM_per_msec)');
    LEGEND_ALGEBRAIC(:,10) = strpad('k_offI in component TnI_conf_change_rate (per_msec)');
    LEGEND_STATES(:,5) = strpad('RUTCa_on in component RU_species (mM)');
    LEGEND_ALGEBRAIC(:,8) = strpad('RUA in component RU_species (mM)');
    LEGEND_CONSTANTS(:,22) = strpad('RU_total in component RU_species (mM)');
    LEGEND_ALGEBRAIC(:,3) = strpad('Q_TMA in component Tm_conf_change_rate (mM_per_msec)');
    LEGEND_ALGEBRAIC(:,2) = strpad('k_tmon in component Tm_conf_change_rate (per_msec)');
    LEGEND_STATES(:,6) = strpad('RUTM_on in component RU_species (mM)');
    LEGEND_ALGEBRAIC(:,11) = strpad('Q_MB in component myosin_binding_rate (mM_per_msec)');
    LEGEND_CONSTANTS(:,29) = strpad('KTitin in component KTitin (dimensionless)');
    LEGEND_CONSTANTS(:,25) = strpad('L in component length (mmeter)');
    LEGEND_CONSTANTS(:,23) = strpad('L_0 in component length (mmeter)');
    LEGEND_CONSTANTS(:,24) = strpad('MADPPi in component RU_species (mM)');
    LEGEND_ALGEBRAIC(:,9) = strpad('RUTM_on_eff in component RU_species (mM)');
    LEGEND_STATES(:,7) = strpad('RUAMADPPi in component RU_species (mM)');
    LEGEND_CONSTANTS(:,26) = strpad('f_titinNormal in component KTitin (dimensionless)');
    LEGEND_CONSTANTS(:,28) = strpad('f_titinDamaged in component KTitin (dimensionless)');
    LEGEND_ALGEBRAIC(:,15) = strpad('Q_Fgen in component Force_Generating_rate (mM_per_msec)');
    LEGEND_ALGEBRAIC(:,14) = strpad('k_3 in component Force_Generating_rate (per_msec)');
    LEGEND_ALGEBRAIC(:,13) = strpad('RUTCa_on_eff in component RU_species (mM)');
    LEGEND_ALGEBRAIC(:,5) = strpad('Q_PiR in component Pi_release_rate (mM_per_msec)');
    LEGEND_ALGEBRAIC(:,7) = strpad('Q_ADPR in component ADP_release_rate (mM_per_msec)');
    LEGEND_CONSTANTS(:,27) = strpad('alpha in component alpha (dimensionless)');
    LEGEND_RATES(:,4) = strpad('d/dt RUTCa_off in component RU_species (mM)');
    LEGEND_RATES(:,5) = strpad('d/dt RUTCa_on in component RU_species (mM)');
    LEGEND_RATES(:,6) = strpad('d/dt RUTM_on in component RU_species (mM)');
    LEGEND_RATES(:,7) = strpad('d/dt RUAMADPPi in component RU_species (mM)');
    LEGEND_RATES(:,1) = strpad('d/dt RUA_MADPPi in component RU_species (mM)');
    LEGEND_RATES(:,2) = strpad('d/dt RUA_MADP in component RU_species (mM)');
    LEGEND_RATES(:,3) = strpad('d/dt Ca in component RU_species (mM)');
    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) = 9000;
    CONSTANTS(:,2) = 0.2;
    CONSTANTS(:,3) = 17.3;
    CONSTANTS(:,4) = 0.2;
    CONSTANTS(:,5) = 0.075;
    CONSTANTS(:,6) = -0.32;
    CONSTANTS(:,7) = -1.37;
    CONSTANTS(:,8) = 0.067;
    CONSTANTS(:,9) = 0.014;
    CONSTANTS(:,10) = 10;
    CONSTANTS(:,11) = -1.86;
    CONSTANTS(:,12) = 2;
    CONSTANTS(:,13) = 0.6;
    CONSTANTS(:,14) = 0.2;
    CONSTANTS(:,15) = 0.025;
    CONSTANTS(:,16) = 50;
    CONSTANTS(:,17) = -1.23;
    CONSTANTS(:,18) = 0.008;
    CONSTANTS(:,19) = 0.077;
    CONSTANTS(:,20) = 0.001;
    CONSTANTS(:,21) = 0.03723;
    STATES(:,1) = 0;
    STATES(:,2) = 0;
    STATES(:,3) = 0.01;
    STATES(:,4) = 0;
    STATES(:,5) = 0;
    CONSTANTS(:,22) = 0.0726;
    STATES(:,6) = 0;
    CONSTANTS(:,23) = 0.001;
    CONSTANTS(:,24) = 0.1375;
    STATES(:,7) = 0;
    CONSTANTS(:,25) = CONSTANTS(:,23);
    CONSTANTS(:,26) =  CONSTANTS(:,14).*(9.96630./(1.00000+exp((CONSTANTS(:,25)./CONSTANTS(:,23)+1.06390)./0.0696000)));
    CONSTANTS(:,27) = piecewise({CONSTANTS(:,25)<1.00000,  1.50000.*(CONSTANTS(:,25)./CONSTANTS(:,23)) - 0.500000 , 1.00000<=CONSTANTS(:,25)&CONSTANTS(:,25)<1.10000, 1.00000 },   - 1.60000.*(CONSTANTS(:,25)./CONSTANTS(:,23))+2.76000);
    CONSTANTS(:,28) =  CONSTANTS(:,14).*(  - 31.0000.*(CONSTANTS(:,25)./CONSTANTS(:,23))+40.0000);
    CONSTANTS(:,29) = piecewise({CONSTANTS(:,25)<=1.10000, CONSTANTS(:,26) }, 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
    ALGEBRAIC(:,5) =  CONSTANTS(:,19).*STATES(:,1) -  CONSTANTS(:,20).*STATES(:,2);
    ALGEBRAIC(:,7) =  CONSTANTS(:,21).*STATES(:,2);
    RATES(:,2) = ALGEBRAIC(:,5) - ALGEBRAIC(:,7);
    ALGEBRAIC(:,4) = CONSTANTS(:,22) - (STATES(:,4)+STATES(:,5)+STATES(:,6)+STATES(:,7)+STATES(:,1)+STATES(:,2));
    ALGEBRAIC(:,6) =  CONSTANTS(:,3).*ALGEBRAIC(:,4).*STATES(:,3) -  CONSTANTS(:,2).*STATES(:,4);
    RATES(:,3) =  - ALGEBRAIC(:,6);
    ALGEBRAIC(:,2) =  CONSTANTS(:,9).*(STATES(:,5)./CONSTANTS(:,22)).*power(1.00000+ CONSTANTS(:,10).*(STATES(:,6)./CONSTANTS(:,22)), 2.00000).*power(1.00000+ CONSTANTS(:,11).*((STATES(:,1)+STATES(:,2))./CONSTANTS(:,22)), 2.00000);
    ALGEBRAIC(:,3) =  ALGEBRAIC(:,2).*STATES(:,5) -  CONSTANTS(:,8).*STATES(:,6);
    ALGEBRAIC(:,9) =  CONSTANTS(:,27).*STATES(:,6);
    ALGEBRAIC(:,11) =  CONSTANTS(:,12).*CONSTANTS(:,29).*CONSTANTS(:,24).*ALGEBRAIC(:,9) -  CONSTANTS(:,13).*STATES(:,7);
    RATES(:,6) = (ALGEBRAIC(:,3) - ALGEBRAIC(:,11))+ALGEBRAIC(:,7);
    ALGEBRAIC(:,8) = STATES(:,5)+STATES(:,6)+STATES(:,7)+STATES(:,1)+STATES(:,2);
    ALGEBRAIC(:,10) =  CONSTANTS(:,5).*power(1.00000+ CONSTANTS(:,6).*(ALGEBRAIC(:,8)./CONSTANTS(:,22)), 2.00000).*power(1.00000+ CONSTANTS(:,7).*((STATES(:,1)+STATES(:,2))./CONSTANTS(:,22)), 4.40000);
    ALGEBRAIC(:,12) =  CONSTANTS(:,4).*STATES(:,4) -  ALGEBRAIC(:,10).*STATES(:,5);
    RATES(:,4) = ALGEBRAIC(:,6) - ALGEBRAIC(:,12);
    RATES(:,5) = ALGEBRAIC(:,12) - ALGEBRAIC(:,3);
    ALGEBRAIC(:,13) =  CONSTANTS(:,27).*STATES(:,5);
    ALGEBRAIC(:,14) =  CONSTANTS(:,15).*power(1.00000+( CONSTANTS(:,16).*(ALGEBRAIC(:,13)+ALGEBRAIC(:,9)+STATES(:,7)))./CONSTANTS(:,22), 2.00000).*power(1.00000+( CONSTANTS(:,17).*(STATES(:,1)+STATES(:,2)))./CONSTANTS(:,22), 2.00000);
    ALGEBRAIC(:,15) =  ALGEBRAIC(:,14).*STATES(:,7) -  CONSTANTS(:,18).*STATES(:,1);
    RATES(:,7) = ALGEBRAIC(:,11) - ALGEBRAIC(:,15);
    RATES(:,1) = ALGEBRAIC(:,15) - ALGEBRAIC(:,5);
   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(:,5) =  CONSTANTS(:,19).*STATES(:,1) -  CONSTANTS(:,20).*STATES(:,2);
    ALGEBRAIC(:,7) =  CONSTANTS(:,21).*STATES(:,2);
    ALGEBRAIC(:,4) = CONSTANTS(:,22) - (STATES(:,4)+STATES(:,5)+STATES(:,6)+STATES(:,7)+STATES(:,1)+STATES(:,2));
    ALGEBRAIC(:,6) =  CONSTANTS(:,3).*ALGEBRAIC(:,4).*STATES(:,3) -  CONSTANTS(:,2).*STATES(:,4);
    ALGEBRAIC(:,2) =  CONSTANTS(:,9).*(STATES(:,5)./CONSTANTS(:,22)).*power(1.00000+ CONSTANTS(:,10).*(STATES(:,6)./CONSTANTS(:,22)), 2.00000).*power(1.00000+ CONSTANTS(:,11).*((STATES(:,1)+STATES(:,2))./CONSTANTS(:,22)), 2.00000);
    ALGEBRAIC(:,3) =  ALGEBRAIC(:,2).*STATES(:,5) -  CONSTANTS(:,8).*STATES(:,6);
    ALGEBRAIC(:,9) =  CONSTANTS(:,27).*STATES(:,6);
    ALGEBRAIC(:,11) =  CONSTANTS(:,12).*CONSTANTS(:,29).*CONSTANTS(:,24).*ALGEBRAIC(:,9) -  CONSTANTS(:,13).*STATES(:,7);
    ALGEBRAIC(:,8) = STATES(:,5)+STATES(:,6)+STATES(:,7)+STATES(:,1)+STATES(:,2);
    ALGEBRAIC(:,10) =  CONSTANTS(:,5).*power(1.00000+ CONSTANTS(:,6).*(ALGEBRAIC(:,8)./CONSTANTS(:,22)), 2.00000).*power(1.00000+ CONSTANTS(:,7).*((STATES(:,1)+STATES(:,2))./CONSTANTS(:,22)), 4.40000);
    ALGEBRAIC(:,12) =  CONSTANTS(:,4).*STATES(:,4) -  ALGEBRAIC(:,10).*STATES(:,5);
    ALGEBRAIC(:,13) =  CONSTANTS(:,27).*STATES(:,5);
    ALGEBRAIC(:,14) =  CONSTANTS(:,15).*power(1.00000+( CONSTANTS(:,16).*(ALGEBRAIC(:,13)+ALGEBRAIC(:,9)+STATES(:,7)))./CONSTANTS(:,22), 2.00000).*power(1.00000+( CONSTANTS(:,17).*(STATES(:,1)+STATES(:,2)))./CONSTANTS(:,22), 2.00000);
    ALGEBRAIC(:,15) =  ALGEBRAIC(:,14).*STATES(:,7) -  CONSTANTS(:,18).*STATES(:,1);
    ALGEBRAIC(:,1) =  CONSTANTS(:,1).*(STATES(:,1)+STATES(:,2));
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