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 =26;
end
% There are a total of 8 entries in each of the rate and state variable arrays.
% There are a total of 35 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_CONSTANTS(:,1) = strpad('RNA_Device1 in component SpeciesInitialConcentrations (nM)');
    LEGEND_CONSTANTS(:,2) = strpad('TF in component SpeciesInitialConcentrations (nM)');
    LEGEND_CONSTANTS(:,3) = strpad('TFS in component SpeciesInitialConcentrations (nM)');
    LEGEND_CONSTANTS(:,4) = strpad('RNA_Device2 in component SpeciesInitialConcentrations (nM)');
    LEGEND_CONSTANTS(:,5) = strpad('IC in component SpeciesInitialConcentrations (nM)');
    LEGEND_CONSTANTS(:,6) = strpad('PhzS in component SpeciesInitialConcentrations (nM)');
    LEGEND_CONSTANTS(:,7) = strpad('PhzM in component SpeciesInitialConcentrations (nM)');
    LEGEND_CONSTANTS(:,8) = strpad('PYO in component SpeciesInitialConcentrations (nM)');
    LEGEND_CONSTANTS(:,35) = strpad('JRNA in component Template_Promoter_Constitutive (nM_per_s)');
    LEGEND_ALGEBRAIC(:,7) = strpad('JGain in component RNA_Device1_interface (nM_per_s)');
    LEGEND_ALGEBRAIC(:,1) = strpad('J in component Template_RxR1P1 (nM_per_s)');
    LEGEND_ALGEBRAIC(:,8) = strpad('J in component Template_ProteinCDS (nM_per_s)');
    LEGEND_ALGEBRAIC(:,13) = strpad('J in component Template_RxR1P1 (nM_per_s)');
    LEGEND_ALGEBRAIC(:,18) = strpad('J in component Template_RxR2P1Rev (nM_per_s)');
    LEGEND_ALGEBRAIC(:,23) = strpad('JGain in component TF_interface (nM_per_s)');
    LEGEND_CONSTANTS(:,9) = strpad('concentration in component S (nM)');
    LEGEND_ALGEBRAIC(:,26) = strpad('JGain in component TFS_interface (nM_per_s)');
    LEGEND_ALGEBRAIC(:,24) = strpad('J in component Template_RxR1P1 (nM_per_s)');
    LEGEND_ALGEBRAIC(:,3) = strpad('JRNA in component Template_Promoter_Inductive (nM_per_s)');
    LEGEND_ALGEBRAIC(:,14) = strpad('JGain in component RNA_Device2_interface (nM_per_s)');
    LEGEND_ALGEBRAIC(:,9) = strpad('J in component Template_RxR1P1 (nM_per_s)');
    LEGEND_ALGEBRAIC(:,10) = strpad('J in component Template_ProteinCDS (nM_per_s)');
    LEGEND_ALGEBRAIC(:,19) = strpad('JGain in component PhzM_interface (nM_per_s)');
    LEGEND_ALGEBRAIC(:,15) = strpad('J in component Template_RxR1P1 (nM_per_s)');
    LEGEND_CONSTANTS(:,10) = strpad('concentration in component PCA (nM)');
    LEGEND_ALGEBRAIC(:,5) = strpad('J in component Template_RxR1P1MM (nM_per_s)');
    LEGEND_ALGEBRAIC(:,20) = strpad('JGain in component IC_interface (nM_per_s)');
    LEGEND_ALGEBRAIC(:,11) = strpad('J in component Template_RxR1P1 (nM_per_s)');
    LEGEND_ALGEBRAIC(:,16) = strpad('J in component Template_RxR1P1MM (nM_per_s)');
    LEGEND_ALGEBRAIC(:,12) = strpad('J in component Template_ProteinCDS (nM_per_s)');
    LEGEND_ALGEBRAIC(:,21) = strpad('JGain in component PhzS_interface (nM_per_s)');
    LEGEND_ALGEBRAIC(:,17) = strpad('J in component Template_RxR1P1 (nM_per_s)');
    LEGEND_ALGEBRAIC(:,25) = strpad('JGain in component PYO_interface (nM_per_s)');
    LEGEND_ALGEBRAIC(:,22) = strpad('J in component Template_RxR1P1 (nM_per_s)');
    LEGEND_CONSTANTS(:,11) = strpad('cellVolume in component Chassis_EColi (femtoliter)');
    LEGEND_VOI = strpad('time in component Time (second)');
    LEGEND_CONSTANTS(:,12) = strpad('k in component ElectrEcoBluDevice1_Promoter (PoPs)');
    LEGEND_STATES(:,1) = strpad('concentration in component Template_Species (nM)');
    LEGEND_CONSTANTS(:,13) = strpad('kDecay in component Bioenvironment_Degradation_ElectrEcoBluDevice1RNA (per_s)');
    LEGEND_ALGEBRAIC(:,2) = strpad('RNARiPs in component Template_RBS (RiPsInAttoMoles)');
    LEGEND_CONSTANTS(:,14) = strpad('k in component ElectrEcoBluDevice1_RBS (RiPs)');
    LEGEND_STATES(:,2) = strpad('concentration in component Template_Species (nM)');
    LEGEND_CONSTANTS(:,15) = strpad('kDecay in component Bioenvironment_Degradation_TF (per_s)');
    LEGEND_CONSTANTS(:,16) = strpad('kf in component Bioenvironment_RxR2P1Rev_TFSFormation (per_nM_per_s)');
    LEGEND_CONSTANTS(:,17) = strpad('kb in component Bioenvironment_RxR2P1Rev_TFSFormation (per_s)');
    LEGEND_STATES(:,3) = strpad('concentration in component Template_Species (nM)');
    LEGEND_CONSTANTS(:,18) = strpad('kDecay in component Bioenvironment_Degradation_TFS (per_s)');
    LEGEND_CONSTANTS(:,19) = strpad('k in component ElectrEcoBluDevice2_Promoter (PoPs)');
    LEGEND_CONSTANTS(:,20) = strpad('Km in component ElectrEcoBluDevice2_Promoter (nM)');
    LEGEND_CONSTANTS(:,21) = strpad('n in component ElectrEcoBluDevice2_Promoter (dimensionless)');
    LEGEND_STATES(:,4) = strpad('concentration in component Template_Species (nM)');
    LEGEND_CONSTANTS(:,22) = strpad('kDecay in component Bioenvironment_Degradation_ElectrEcoBluDevice2RNA (per_s)');
    LEGEND_ALGEBRAIC(:,4) = strpad('RNARiPs in component Template_RBS (RiPsInAttoMoles)');
    LEGEND_CONSTANTS(:,23) = strpad('k in component ElectrEcoBluDevice2_RBS_PhzM (RiPs)');
    LEGEND_ALGEBRAIC(:,6) = strpad('RNARiPs in component Template_RBS (RiPsInAttoMoles)');
    LEGEND_CONSTANTS(:,24) = strpad('k in component ElectrEcoBluDevice2_RBS_PhzS (RiPs)');
    LEGEND_STATES(:,5) = strpad('concentration in component Template_Species (nM)');
    LEGEND_CONSTANTS(:,25) = strpad('kDecay in component Bioenvironment_Degradation_PhzM (per_s)');
    LEGEND_CONSTANTS(:,26) = strpad('k in component Bioenvironment_RxR1P1MM_ICFormation (per_s)');
    LEGEND_CONSTANTS(:,27) = strpad('Km in component Bioenvironment_RxR1P1MM_ICFormation (nM)');
    LEGEND_STATES(:,6) = strpad('concentration in component Template_Species (nM)');
    LEGEND_CONSTANTS(:,28) = strpad('kDecay in component Bioenvironment_Degradation_IC (per_s)');
    LEGEND_STATES(:,7) = strpad('concentration in component Template_Species (nM)');
    LEGEND_CONSTANTS(:,29) = strpad('kDecay in component Bioenvironment_Degradation_PhzS (per_s)');
    LEGEND_CONSTANTS(:,30) = strpad('k in component Bioenvironment_RxR1P1MM_PYOFormation (per_s)');
    LEGEND_CONSTANTS(:,31) = strpad('Km in component Bioenvironment_RxR1P1MM_PYOFormation (nM)');
    LEGEND_STATES(:,8) = strpad('concentration in component Template_Species (nM)');
    LEGEND_CONSTANTS(:,32) = strpad('kDecay in component Bioenvironment_Degradation_PYO (per_s)');
    LEGEND_CONSTANTS(:,33) = strpad('avogadrosConstant in component Template_Promoter_Constitutive (per_mole)');
    LEGEND_CONSTANTS(:,34) = strpad('avogadrosConstant in component Template_Promoter_Inductive (per_mole)');
    LEGEND_RATES(:,1) = strpad('d/dt concentration in component Template_Species (nM)');
    LEGEND_RATES(:,2) = strpad('d/dt concentration in component Template_Species (nM)');
    LEGEND_RATES(:,3) = strpad('d/dt concentration in component Template_Species (nM)');
    LEGEND_RATES(:,4) = strpad('d/dt concentration in component Template_Species (nM)');
    LEGEND_RATES(:,5) = strpad('d/dt concentration in component Template_Species (nM)');
    LEGEND_RATES(:,6) = strpad('d/dt concentration in component Template_Species (nM)');
    LEGEND_RATES(:,7) = strpad('d/dt concentration in component Template_Species (nM)');
    LEGEND_RATES(:,8) = strpad('d/dt concentration in component Template_Species (nM)');
    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;
    CONSTANTS(:,2) = 8621;
    CONSTANTS(:,3) = 0;
    CONSTANTS(:,4) = 0;
    CONSTANTS(:,5) = 0;
    CONSTANTS(:,6) = 0;
    CONSTANTS(:,7) = 0;
    CONSTANTS(:,8) = 0;
    CONSTANTS(:,9) = 5000;
    CONSTANTS(:,10) = 2;
    CONSTANTS(:,11) = 1;
    CONSTANTS(:,12) = 1.085;
    CONSTANTS(:,13) = 0.05;
    CONSTANTS(:,14) = 1.4;
    CONSTANTS(:,15) = 5.8e-3;
    CONSTANTS(:,16) = 1e3;
    CONSTANTS(:,17) = 4e6;
    CONSTANTS(:,18) = 3.851e-4;
    CONSTANTS(:,19) = 89;
    CONSTANTS(:,20) = 15000;
    CONSTANTS(:,21) = 1;
    CONSTANTS(:,22) = 8e-6;
    CONSTANTS(:,23) = 40;
    CONSTANTS(:,24) = 1;
    CONSTANTS(:,25) = 8e-1;
    CONSTANTS(:,26) = 0.2;
    CONSTANTS(:,27) = 0.1;
    CONSTANTS(:,28) = 5e-5;
    CONSTANTS(:,29) = 8e-1;
    CONSTANTS(:,30) = 1;
    CONSTANTS(:,31) = 0.1;
    CONSTANTS(:,32) = 5e-1;
    CONSTANTS(:,33) = 6.0221415e23;
    CONSTANTS(:,34) = 6.0221415e23;
    CONSTANTS(:,35) =  CONSTANTS(:,12).*1.00000e+09./( CONSTANTS(:,11).*1.00000e-15.*CONSTANTS(:,33));
    STATES(:,1) = CONSTANTS(:,1);
    STATES(:,2) = CONSTANTS(:,2);
    STATES(:,3) = CONSTANTS(:,3);
    STATES(:,4) = CONSTANTS(:,4);
    STATES(:,5) = CONSTANTS(:,7);
    STATES(:,6) = CONSTANTS(:,5);
    STATES(:,7) = CONSTANTS(:,6);
    STATES(:,8) = CONSTANTS(:,8);
    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);
    else
        statesRowCount = statesSize(1);
        ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
        RATES = zeros(statesRowCount, statesColumnCount);
    end
    ALGEBRAIC(:,1) =  CONSTANTS(:,13).*STATES(:,1);
    ALGEBRAIC(:,7) = CONSTANTS(:,35) - ALGEBRAIC(:,1);
    RATES(:,1) = ALGEBRAIC(:,7);
    ALGEBRAIC(:,3) =   CONSTANTS(:,19).*STATES(:,3) .^ CONSTANTS(:,21)./(CONSTANTS(:,20) .^ CONSTANTS(:,21)+STATES(:,3) .^ CONSTANTS(:,21)).*1.00000e+09./( CONSTANTS(:,11).*1.00000e-15.*CONSTANTS(:,34));
    ALGEBRAIC(:,9) =  CONSTANTS(:,22).*STATES(:,4);
    ALGEBRAIC(:,14) = ALGEBRAIC(:,3) - ALGEBRAIC(:,9);
    RATES(:,4) = ALGEBRAIC(:,14);
    ALGEBRAIC(:,4) =  1.00000e+09.*CONSTANTS(:,23).*STATES(:,4).*CONSTANTS(:,11).*1.00000e-15;
    ALGEBRAIC(:,10) =  1.00000e+06.*ALGEBRAIC(:,4)./CONSTANTS(:,11);
    ALGEBRAIC(:,15) =  CONSTANTS(:,25).*STATES(:,5);
    ALGEBRAIC(:,19) = ALGEBRAIC(:,10) - ALGEBRAIC(:,15);
    RATES(:,5) = ALGEBRAIC(:,19);
    ALGEBRAIC(:,5) =  CONSTANTS(:,26).*STATES(:,5).*CONSTANTS(:,10)./(CONSTANTS(:,10)+CONSTANTS(:,27));
    ALGEBRAIC(:,11) =  CONSTANTS(:,28).*STATES(:,6);
    ALGEBRAIC(:,16) =  CONSTANTS(:,30).*STATES(:,7).*STATES(:,6)./(STATES(:,6)+CONSTANTS(:,31));
    ALGEBRAIC(:,20) = ALGEBRAIC(:,5) - ALGEBRAIC(:,11) - ALGEBRAIC(:,16);
    RATES(:,6) = ALGEBRAIC(:,20);
    ALGEBRAIC(:,6) =  1.00000e+09.*CONSTANTS(:,24).*STATES(:,4).*CONSTANTS(:,11).*1.00000e-15;
    ALGEBRAIC(:,12) =  1.00000e+06.*ALGEBRAIC(:,6)./CONSTANTS(:,11);
    ALGEBRAIC(:,17) =  CONSTANTS(:,29).*STATES(:,7);
    ALGEBRAIC(:,21) = ALGEBRAIC(:,12) - ALGEBRAIC(:,17);
    RATES(:,7) = ALGEBRAIC(:,21);
    ALGEBRAIC(:,2) =  1.00000e+09.*CONSTANTS(:,14).*STATES(:,1).*CONSTANTS(:,11).*1.00000e-15;
    ALGEBRAIC(:,8) =  1.00000e+06.*ALGEBRAIC(:,2)./CONSTANTS(:,11);
    ALGEBRAIC(:,13) =  CONSTANTS(:,15).*STATES(:,2);
    ALGEBRAIC(:,18) =  STATES(:,2).*CONSTANTS(:,9).*CONSTANTS(:,16) -  CONSTANTS(:,17).*STATES(:,3);
    ALGEBRAIC(:,23) = ALGEBRAIC(:,8) - ALGEBRAIC(:,13) - ALGEBRAIC(:,18);
    RATES(:,2) = ALGEBRAIC(:,23);
    ALGEBRAIC(:,22) =  CONSTANTS(:,32).*STATES(:,8);
    ALGEBRAIC(:,25) = ALGEBRAIC(:,16) - ALGEBRAIC(:,22);
    RATES(:,8) = ALGEBRAIC(:,25);
    ALGEBRAIC(:,24) =  CONSTANTS(:,18).*STATES(:,3);
    ALGEBRAIC(:,26) = ALGEBRAIC(:,18) - ALGEBRAIC(:,24);
    RATES(:,3) = ALGEBRAIC(:,26);
   RATES = RATES';
end

% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
    ALGEBRAIC(:,1) =  CONSTANTS(:,13).*STATES(:,1);
    ALGEBRAIC(:,7) = CONSTANTS(:,35) - ALGEBRAIC(:,1);
    ALGEBRAIC(:,3) =   CONSTANTS(:,19).*STATES(:,3) .^ CONSTANTS(:,21)./(CONSTANTS(:,20) .^ CONSTANTS(:,21)+STATES(:,3) .^ CONSTANTS(:,21)).*1.00000e+09./( CONSTANTS(:,11).*1.00000e-15.*CONSTANTS(:,34));
    ALGEBRAIC(:,9) =  CONSTANTS(:,22).*STATES(:,4);
    ALGEBRAIC(:,14) = ALGEBRAIC(:,3) - ALGEBRAIC(:,9);
    ALGEBRAIC(:,4) =  1.00000e+09.*CONSTANTS(:,23).*STATES(:,4).*CONSTANTS(:,11).*1.00000e-15;
    ALGEBRAIC(:,10) =  1.00000e+06.*ALGEBRAIC(:,4)./CONSTANTS(:,11);
    ALGEBRAIC(:,15) =  CONSTANTS(:,25).*STATES(:,5);
    ALGEBRAIC(:,19) = ALGEBRAIC(:,10) - ALGEBRAIC(:,15);
    ALGEBRAIC(:,5) =  CONSTANTS(:,26).*STATES(:,5).*CONSTANTS(:,10)./(CONSTANTS(:,10)+CONSTANTS(:,27));
    ALGEBRAIC(:,11) =  CONSTANTS(:,28).*STATES(:,6);
    ALGEBRAIC(:,16) =  CONSTANTS(:,30).*STATES(:,7).*STATES(:,6)./(STATES(:,6)+CONSTANTS(:,31));
    ALGEBRAIC(:,20) = ALGEBRAIC(:,5) - ALGEBRAIC(:,11) - ALGEBRAIC(:,16);
    ALGEBRAIC(:,6) =  1.00000e+09.*CONSTANTS(:,24).*STATES(:,4).*CONSTANTS(:,11).*1.00000e-15;
    ALGEBRAIC(:,12) =  1.00000e+06.*ALGEBRAIC(:,6)./CONSTANTS(:,11);
    ALGEBRAIC(:,17) =  CONSTANTS(:,29).*STATES(:,7);
    ALGEBRAIC(:,21) = ALGEBRAIC(:,12) - ALGEBRAIC(:,17);
    ALGEBRAIC(:,2) =  1.00000e+09.*CONSTANTS(:,14).*STATES(:,1).*CONSTANTS(:,11).*1.00000e-15;
    ALGEBRAIC(:,8) =  1.00000e+06.*ALGEBRAIC(:,2)./CONSTANTS(:,11);
    ALGEBRAIC(:,13) =  CONSTANTS(:,15).*STATES(:,2);
    ALGEBRAIC(:,18) =  STATES(:,2).*CONSTANTS(:,9).*CONSTANTS(:,16) -  CONSTANTS(:,17).*STATES(:,3);
    ALGEBRAIC(:,23) = ALGEBRAIC(:,8) - ALGEBRAIC(:,13) - ALGEBRAIC(:,18);
    ALGEBRAIC(:,22) =  CONSTANTS(:,32).*STATES(:,8);
    ALGEBRAIC(:,25) = ALGEBRAIC(:,16) - ALGEBRAIC(:,22);
    ALGEBRAIC(:,24) =  CONSTANTS(:,18).*STATES(:,3);
    ALGEBRAIC(:,26) = ALGEBRAIC(:,18) - ALGEBRAIC(:,24);
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