% SUPPLEMENTARY MATERIAL "Source S1": Simulating acquired spectra.
%
% Example source code for “Method for assessing the reliability of 
% molecular diagnostics based on multiplexed SERS-coded nanoparticles.”
% (Manuscript #PONE-D-13-01484)

% Load reference spectra
s440 = load('s440 ref.asc');
    spectra_maxvalue = max([s440(:,2)]);
    length_s440 = 601;
    
% Load acquired set of background noise at a particular condition
bkglist = load('AFglass,water2000acqat100msbkgcorrectedtoroomlightsat10mWlaserpower.asc');

% Simulate 50000 acquisition trials and 10 different S440 concentrations
num_trials = 50000;
num_points = 10;

% Pre-allocate space for noise vector
noise = zeros(length_s440,1);

for  i = 1:num_trials
    for j = 1:num_points

        % First, generate noise using the 'randn' function to ensure the
        % noise is normally-distributed
        
        noise = (10/100)*spectra_maxvalue*randn(length_s440,1);
        
        % From the list of experimentally-acquired background acqusitions,
        % randomly choose one to add to the simulated spectrum.
        bkg_index = round(2 + (2000-2).*rand);
        bkg = bkglist(:,bkgindex);
        
        % The simulated spectrum 'test' is composed of S440, background,
        % and noise.
        test = j*s440 + bkg + noise;
    end
end