%% Peak matching result by SIMA

% in_file = 'sima_mz01_rt75.txt'; % SIMA matching output

[idxPeak, names, idxIdv, massAll, rtAll] = textread(in_file,'%d %s %d %f %f');

nbIdvPeak = numel(names);

runs = zeros(nbIdvPeak,1);

for i = 1:numel(names)

runs(i) = sscanf(names{i}, ['P1_' '%d' '.txt']);

end

idxPeak = idxPeak+1;

idxIdv = idxIdv+1;

nbPeak = idxPeak(end);

uniRuns = unique(runs);

nbRun = numel(uniRuns);

sizePeak = zeros(nbPeak,1);

idxDrop = [];

idxSinSize = [];

for i = 1:nbPeak

tmpIdx = find(idxPeak==i);

sizePeak(i) = numel(tmpIdx);

if numel(tmpIdx)==1

idxDrop = [idxDrop tmpIdx];

idxSinSize = [idxSinSize i];

end

end

idxPeak(idxDrop) = [];

runs(idxDrop) = [];

idxIdv(idxDrop) = [];

massAll(idxDrop) = [];

rtAll(idxDrop) = [];

%% load ground-truth data and evaluate the matching result

load ground_truth_proteomics.mat

for g = 1:numel(ground)

tmpNb = numel(ground(g).idxSamp);

match{g,1} = nan(1,tmpNb);

for p = 1:tmpNb

tmpIdx = find(runs==ground(g).idxSamp(p) & idxIdv==ground(g).idxPeak(p));

if numel(tmpIdx)>1

disp('error');

elseif numel(tmpIdx)==1

match{g,1}(p) = idxPeak(tmpIdx);

end

end

end

prec = 0;

rec = 0;

for g = 1:numel(ground)

nonNan = match{g,1}(~isnan(match{g,1}));

numPR = numel(find(~isnan(match{g,1})));

pk = unique(nonNan);

if numel(pk) ~= 0

denP = sum(sizePeak(pk));

denR = numel(pk)*numel(match{g,1});

prec = prec + numPR/denP;

rec = rec + numPR/denR;

end

end

prec = prec/numel(ground);

rec = rec/numel(ground);