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 16 entries in each of the rate and state variable arrays.
% There are a total of 55 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 (hour)');
    LEGEND_STATES(:,1) = strpad('MP in component MP (nanomolar)');
    LEGEND_CONSTANTS(:,47) = strpad('vsP in component MP (flux)');
    LEGEND_CONSTANTS(:,1) = strpad('vmP in component MP (flux)');
    LEGEND_CONSTANTS(:,2) = strpad('kdmp in component MP (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,3) = strpad('KAP in component MP (nanomolar)');
    LEGEND_CONSTANTS(:,4) = strpad('KmP in component MP (nanomolar)');
    LEGEND_CONSTANTS(:,5) = strpad('vstot in component model_parameters (flux)');
    LEGEND_CONSTANTS(:,6) = strpad('n in component model_parameters (dimensionless)');
    LEGEND_STATES(:,2) = strpad('BN in component BN (nanomolar)');
    LEGEND_STATES(:,3) = strpad('MC in component MC (nanomolar)');
    LEGEND_CONSTANTS(:,48) = strpad('vsC in component MC (flux)');
    LEGEND_CONSTANTS(:,7) = strpad('vmC in component MC (flux)');
    LEGEND_CONSTANTS(:,8) = strpad('kdmc in component MC (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,9) = strpad('KAC in component MC (nanomolar)');
    LEGEND_CONSTANTS(:,10) = strpad('KmC in component MC (nanomolar)');
    LEGEND_STATES(:,4) = strpad('MB in component MB (nanomolar)');
    LEGEND_CONSTANTS(:,49) = strpad('vsB in component MB (flux)');
    LEGEND_CONSTANTS(:,11) = strpad('vmB in component MB (flux)');
    LEGEND_CONSTANTS(:,12) = strpad('kdmb in component MB (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,13) = strpad('KIB in component MB (nanomolar)');
    LEGEND_CONSTANTS(:,14) = strpad('KmB in component MB (nanomolar)');
    LEGEND_CONSTANTS(:,15) = strpad('m in component model_parameters (dimensionless)');
    LEGEND_STATES(:,5) = strpad('PC in component PC (nanomolar)');
    LEGEND_CONSTANTS(:,50) = strpad('ksP in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,16) = strpad('Kp in component model_parameters (nanomolar)');
    LEGEND_CONSTANTS(:,17) = strpad('Kdp in component model_parameters (nanomolar)');
    LEGEND_CONSTANTS(:,18) = strpad('k3 in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,19) = strpad('k4 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,20) = strpad('kdn in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,51) = strpad('V1P in component model_parameters (flux)');
    LEGEND_CONSTANTS(:,21) = strpad('V2P in component model_parameters (flux)');
    LEGEND_STATES(:,6) = strpad('PCP in component PCP (nanomolar)');
    LEGEND_STATES(:,7) = strpad('PCC in component PCC (nanomolar)');
    LEGEND_STATES(:,8) = strpad('CC in component CC (nanomolar)');
    LEGEND_CONSTANTS(:,52) = strpad('ksC in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,22) = strpad('kdnc in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,23) = strpad('V1C in component model_parameters (flux)');
    LEGEND_CONSTANTS(:,24) = strpad('V2C in component model_parameters (flux)');
    LEGEND_STATES(:,9) = strpad('CCP in component CCP (nanomolar)');
    LEGEND_CONSTANTS(:,25) = strpad('vdPC in component model_parameters (flux)');
    LEGEND_CONSTANTS(:,26) = strpad('Kd in component model_parameters (nanomolar)');
    LEGEND_CONSTANTS(:,27) = strpad('vdCC in component model_parameters (flux)');
    LEGEND_CONSTANTS(:,28) = strpad('k1 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,29) = strpad('k2 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,53) = strpad('V1PC in component model_parameters (flux)');
    LEGEND_CONSTANTS(:,30) = strpad('V2PC in component model_parameters (flux)');
    LEGEND_STATES(:,10) = strpad('PCCP in component PCCP (nanomolar)');
    LEGEND_STATES(:,11) = strpad('PCN in component PCN (nanomolar)');
    LEGEND_CONSTANTS(:,31) = strpad('k7 in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,32) = strpad('k8 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,54) = strpad('V3PC in component model_parameters (flux)');
    LEGEND_CONSTANTS(:,33) = strpad('V4PC in component model_parameters (flux)');
    LEGEND_STATES(:,12) = strpad('PCNP in component PCNP (nanomolar)');
    LEGEND_STATES(:,13) = strpad('IN in component IN (nanomolar)');
    LEGEND_CONSTANTS(:,34) = strpad('vdPCC in component model_parameters (flux)');
    LEGEND_CONSTANTS(:,35) = strpad('vdPCN in component model_parameters (flux)');
    LEGEND_STATES(:,14) = strpad('BC in component BC (nanomolar)');
    LEGEND_CONSTANTS(:,55) = strpad('ksB in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,36) = strpad('k5 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,37) = strpad('k6 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,38) = strpad('V1B in component model_parameters (flux)');
    LEGEND_CONSTANTS(:,39) = strpad('V2B in component model_parameters (flux)');
    LEGEND_STATES(:,15) = strpad('BCP in component BCP (nanomolar)');
    LEGEND_CONSTANTS(:,40) = strpad('vdBC in component model_parameters (flux)');
    LEGEND_CONSTANTS(:,41) = strpad('V3B in component model_parameters (flux)');
    LEGEND_CONSTANTS(:,42) = strpad('V4B in component model_parameters (flux)');
    LEGEND_STATES(:,16) = strpad('BNP in component BNP (nanomolar)');
    LEGEND_CONSTANTS(:,43) = strpad('vdBN in component model_parameters (flux)');
    LEGEND_CONSTANTS(:,44) = strpad('vdIN in component model_parameters (flux)');
    LEGEND_CONSTANTS(:,45) = strpad('kstot in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,46) = strpad('Vphos in component model_parameters (flux)');
    LEGEND_RATES(:,1) = strpad('d/dt MP in component MP (nanomolar)');
    LEGEND_RATES(:,3) = strpad('d/dt MC in component MC (nanomolar)');
    LEGEND_RATES(:,4) = strpad('d/dt MB in component MB (nanomolar)');
    LEGEND_RATES(:,5) = strpad('d/dt PC in component PC (nanomolar)');
    LEGEND_RATES(:,8) = strpad('d/dt CC in component CC (nanomolar)');
    LEGEND_RATES(:,6) = strpad('d/dt PCP in component PCP (nanomolar)');
    LEGEND_RATES(:,9) = strpad('d/dt CCP in component CCP (nanomolar)');
    LEGEND_RATES(:,7) = strpad('d/dt PCC in component PCC (nanomolar)');
    LEGEND_RATES(:,11) = strpad('d/dt PCN in component PCN (nanomolar)');
    LEGEND_RATES(:,10) = strpad('d/dt PCCP in component PCCP (nanomolar)');
    LEGEND_RATES(:,12) = strpad('d/dt PCNP in component PCNP (nanomolar)');
    LEGEND_RATES(:,14) = strpad('d/dt BC in component BC (nanomolar)');
    LEGEND_RATES(:,15) = strpad('d/dt BCP in component BCP (nanomolar)');
    LEGEND_RATES(:,2) = strpad('d/dt BN in component BN (nanomolar)');
    LEGEND_RATES(:,16) = strpad('d/dt BNP in component BNP (nanomolar)');
    LEGEND_RATES(:,13) = strpad('d/dt IN in component IN (nanomolar)');
    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) = 0.5;
    CONSTANTS(:,1) = 1.1;
    CONSTANTS(:,2) = 0.01;
    CONSTANTS(:,3) = 0.7;
    CONSTANTS(:,4) = 0.3;
    CONSTANTS(:,5) = 1.0;
    CONSTANTS(:,6) = 4.0;
    STATES(:,2) = 0.1;
    STATES(:,3) = 0.3;
    CONSTANTS(:,7) = 1.0;
    CONSTANTS(:,8) = 0.01;
    CONSTANTS(:,9) = 1.0;
    CONSTANTS(:,10) = 0.4;
    STATES(:,4) = 3.1;
    CONSTANTS(:,11) = 0.2;
    CONSTANTS(:,12) = 0.01;
    CONSTANTS(:,13) = 0.8;
    CONSTANTS(:,14) = 0.4;
    CONSTANTS(:,15) = 4.0;
    STATES(:,5) = 0.1;
    CONSTANTS(:,16) = 0.1;
    CONSTANTS(:,17) = 0.3;
    CONSTANTS(:,18) = 0.8;
    CONSTANTS(:,19) = 0.2;
    CONSTANTS(:,20) = 0.01;
    CONSTANTS(:,21) = 0.3;
    STATES(:,6) = 0.1;
    STATES(:,7) = 0.1;
    STATES(:,8) = 0.1;
    CONSTANTS(:,22) = 0.01;
    CONSTANTS(:,23) = 0.6;
    CONSTANTS(:,24) = 0.1;
    STATES(:,9) = 0.1;
    CONSTANTS(:,25) = 0.7;
    CONSTANTS(:,26) = 0.3;
    CONSTANTS(:,27) = 0.7;
    CONSTANTS(:,28) = 0.8;
    CONSTANTS(:,29) = 0.2;
    CONSTANTS(:,30) = 0.1;
    STATES(:,10) = 0.1;
    STATES(:,11) = 0.1;
    CONSTANTS(:,31) = 0.5;
    CONSTANTS(:,32) = 0.1;
    CONSTANTS(:,33) = 0.1;
    STATES(:,12) = 0.1;
    STATES(:,13) = 0.1;
    CONSTANTS(:,34) = 1.0;
    CONSTANTS(:,35) = 1.0;
    STATES(:,14) = 0.1;
    CONSTANTS(:,36) = 0.4;
    CONSTANTS(:,37) = 0.2;
    CONSTANTS(:,38) = 1.0;
    CONSTANTS(:,39) = 0.1;
    STATES(:,15) = 0.1;
    CONSTANTS(:,40) = 1.0;
    CONSTANTS(:,41) = 1.0;
    CONSTANTS(:,42) = 0.2;
    STATES(:,16) = 0.1;
    CONSTANTS(:,43) = 0.5;
    CONSTANTS(:,44) = 0.8;
    CONSTANTS(:,45) = 1.0;
    CONSTANTS(:,46) = 0.6;
    CONSTANTS(:,47) = CONSTANTS(:,5);
    CONSTANTS(:,48) =  0.800000.*CONSTANTS(:,5);
    CONSTANTS(:,49) =  0.700000.*CONSTANTS(:,5);
    CONSTANTS(:,50) =  0.500000.*CONSTANTS(:,45);
    CONSTANTS(:,51) = CONSTANTS(:,46);
    CONSTANTS(:,52) = CONSTANTS(:,45);
    CONSTANTS(:,53) = CONSTANTS(:,46);
    CONSTANTS(:,54) = CONSTANTS(:,46);
    CONSTANTS(:,55) = CONSTANTS(:,45);
    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(:,47).*(power(STATES(:,2), CONSTANTS(:,6))./(power(CONSTANTS(:,3), CONSTANTS(:,6))+power(STATES(:,2), CONSTANTS(:,6)))) - ( CONSTANTS(:,1).*(STATES(:,1)./(CONSTANTS(:,4)+STATES(:,1)))+ CONSTANTS(:,2).*STATES(:,1));
    RATES(:,3) =  CONSTANTS(:,48).*(power(STATES(:,2), CONSTANTS(:,6))./(power(CONSTANTS(:,9), CONSTANTS(:,6))+power(STATES(:,2), CONSTANTS(:,6)))) - ( CONSTANTS(:,7).*(STATES(:,3)./(CONSTANTS(:,10)+STATES(:,3)))+ CONSTANTS(:,8).*STATES(:,3));
    RATES(:,4) =  CONSTANTS(:,49).*(power(CONSTANTS(:,13), CONSTANTS(:,15))./(power(CONSTANTS(:,13), CONSTANTS(:,15))+power(STATES(:,2), CONSTANTS(:,15)))) - ( CONSTANTS(:,11).*(STATES(:,4)./(CONSTANTS(:,14)+STATES(:,4)))+ CONSTANTS(:,12).*STATES(:,4));
    RATES(:,5) = ( CONSTANTS(:,50).*STATES(:,1)+ CONSTANTS(:,21).*(STATES(:,6)./(CONSTANTS(:,17)+STATES(:,6)))+ CONSTANTS(:,19).*STATES(:,7)) - ( CONSTANTS(:,51).*(STATES(:,5)./(CONSTANTS(:,16)+STATES(:,5)))+ CONSTANTS(:,18).*STATES(:,5).*STATES(:,8)+ CONSTANTS(:,20).*STATES(:,5));
    RATES(:,8) = ( CONSTANTS(:,52).*STATES(:,3)+ CONSTANTS(:,24).*(STATES(:,9)./(CONSTANTS(:,17)+STATES(:,9)))+ CONSTANTS(:,19).*STATES(:,7)) - ( CONSTANTS(:,23).*(STATES(:,8)./(CONSTANTS(:,16)+STATES(:,8)))+ CONSTANTS(:,18).*STATES(:,5).*STATES(:,8)+ CONSTANTS(:,22).*STATES(:,8));
    RATES(:,6) =  CONSTANTS(:,51).*(STATES(:,5)./(CONSTANTS(:,16)+STATES(:,5))) - ( CONSTANTS(:,21).*(STATES(:,6)./(CONSTANTS(:,17)+STATES(:,6)))+ CONSTANTS(:,25).*(STATES(:,6)./(CONSTANTS(:,26)+STATES(:,6)))+ CONSTANTS(:,20).*STATES(:,6));
    RATES(:,9) =  CONSTANTS(:,23).*(STATES(:,8)./(CONSTANTS(:,16)+STATES(:,8))) - ( CONSTANTS(:,24).*(STATES(:,9)./(CONSTANTS(:,17)+STATES(:,9)))+ CONSTANTS(:,27).*(STATES(:,9)./(CONSTANTS(:,26)+STATES(:,9)))+ CONSTANTS(:,20).*STATES(:,9));
    RATES(:,7) = ( CONSTANTS(:,30).*(STATES(:,10)./(CONSTANTS(:,17)+STATES(:,10)))+ CONSTANTS(:,18).*STATES(:,5).*STATES(:,8)+ CONSTANTS(:,29).*STATES(:,11)) - ( CONSTANTS(:,53).*(STATES(:,7)./(CONSTANTS(:,16)+STATES(:,7)))+ CONSTANTS(:,19).*STATES(:,7)+ CONSTANTS(:,28).*STATES(:,7)+ CONSTANTS(:,20).*STATES(:,7));
    RATES(:,11) = ( CONSTANTS(:,33).*(STATES(:,12)./(CONSTANTS(:,17)+STATES(:,12)))+ CONSTANTS(:,28).*STATES(:,7)+ CONSTANTS(:,32).*STATES(:,13)) - ( CONSTANTS(:,54).*(STATES(:,11)./(CONSTANTS(:,16)+STATES(:,11)))+ CONSTANTS(:,29).*STATES(:,11)+ CONSTANTS(:,31).*STATES(:,2).*STATES(:,11)+ CONSTANTS(:,20).*STATES(:,11));
    RATES(:,10) =  CONSTANTS(:,53).*(STATES(:,7)./(CONSTANTS(:,16)+STATES(:,7))) - ( CONSTANTS(:,30).*(STATES(:,10)./(CONSTANTS(:,17)+STATES(:,10)))+ CONSTANTS(:,34).*(STATES(:,10)./(CONSTANTS(:,26)+STATES(:,10)))+ CONSTANTS(:,20).*STATES(:,10));
    RATES(:,12) =  CONSTANTS(:,54).*(STATES(:,11)./(CONSTANTS(:,16)+STATES(:,11))) - ( CONSTANTS(:,33).*(STATES(:,12)./(CONSTANTS(:,17)+STATES(:,12)))+ CONSTANTS(:,35).*(STATES(:,12)./(CONSTANTS(:,26)+STATES(:,12)))+ CONSTANTS(:,20).*STATES(:,12));
    RATES(:,14) = ( CONSTANTS(:,39).*(STATES(:,15)./(CONSTANTS(:,17)+STATES(:,15)))+ CONSTANTS(:,37).*STATES(:,2)+ CONSTANTS(:,55).*STATES(:,4)) - ( CONSTANTS(:,38).*(STATES(:,14)./(CONSTANTS(:,16)+STATES(:,14)))+ CONSTANTS(:,36).*STATES(:,14)+ CONSTANTS(:,20).*STATES(:,14));
    RATES(:,15) =  CONSTANTS(:,38).*(STATES(:,14)./(CONSTANTS(:,16)+STATES(:,14))) - ( CONSTANTS(:,39).*(STATES(:,15)./(CONSTANTS(:,17)+STATES(:,15)))+ CONSTANTS(:,40).*(STATES(:,15)./(CONSTANTS(:,26)+STATES(:,15)))+ CONSTANTS(:,20).*STATES(:,15));
    RATES(:,2) = ( CONSTANTS(:,42).*(STATES(:,16)./(CONSTANTS(:,17)+STATES(:,16)))+ CONSTANTS(:,36).*STATES(:,14)+ CONSTANTS(:,32).*STATES(:,13)) - ( CONSTANTS(:,41).*(STATES(:,2)./(CONSTANTS(:,16)+STATES(:,2)))+ CONSTANTS(:,37).*STATES(:,2)+ CONSTANTS(:,31).*STATES(:,2).*STATES(:,11)+ CONSTANTS(:,20).*STATES(:,2));
    RATES(:,16) =  CONSTANTS(:,41).*(STATES(:,2)./(CONSTANTS(:,16)+STATES(:,2))) - ( CONSTANTS(:,42).*(STATES(:,16)./(CONSTANTS(:,17)+STATES(:,16)))+ CONSTANTS(:,43).*(STATES(:,16)./(CONSTANTS(:,26)+STATES(:,16)))+ CONSTANTS(:,20).*STATES(:,16));
    RATES(:,13) =  CONSTANTS(:,31).*STATES(:,2).*STATES(:,11) - ( CONSTANTS(:,32).*STATES(:,13)+ CONSTANTS(:,44).*(STATES(:,13)./(CONSTANTS(:,26)+STATES(:,13)))+ CONSTANTS(:,20).*STATES(:,13));
   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