public void calcAveragesOfEvalScoreTPRandFPR() {
		// average evaluation-score
		Double avgEvlScr = 0.0;
		// average TPR:
		Double avgTruePosRate = 0.0;
		// average FPR:
		Double avgFalsePosRate = 0.0;
		for (Protein p : getProteins().values()) {
			EvaluationScoreCalculator e = p.getEvaluationScoreCalculator();
			if (e != null) {
				if (e.getEvalScoreMinBestCompScore() != null)
					avgEvlScr += e.getEvalScoreMinBestCompScore();
				if (e.getTruePositivesRate() != null)
					avgTruePosRate += e.getTruePositivesRate();
				if (e.getFalsePositivesRate() != null)
					avgFalsePosRate += e.getFalsePositivesRate();
			}
		}
		// average each number:
		Double numberOfProts = new Double(getProteins().size());
		if (avgEvlScr > 0.0)
			avgEvlScr = avgEvlScr / numberOfProts;
		if (avgTruePosRate > 0.0)
			avgTruePosRate = avgTruePosRate / numberOfProts;
		if (avgFalsePosRate > 0.0)
			avgFalsePosRate = avgFalsePosRate / numberOfProts;
		// done:
		getSettings().setAvgEvaluationScore(avgEvlScr);
		getSettings().setAvgTruePositivesRate(avgTruePosRate);
		getSettings().setAvgFalsePositivesRate(avgFalsePosRate);
	}