INNER CODE UNIT · C++

gap_scaler

refresh-bio/FAMSA · src/msa.cpp:92

		double gap_scaler = log2(n_seqs / (double) params.scaler_log);
		if(n_seqs < (int) params.scaler_log)
			gap_scaler = 1.0;
		else
			gap_scaler = 1.0 + (gap_scaler / params.scaler_div);

		params.gap_ext		 = (score_t) (params.gap_ext       * gap_scaler);
		params.gap_open	 	 = (score_t) (params.gap_open      * gap_scaler);
		params.gap_term_ext  = (score_t) (params.gap_term_ext  * gap_scaler);
		params.gap_term_open = (score_t) (params.gap_term_open * gap_scaler);
	}

	params.score_matrix = score_matrix;
	params.score_vector = score_vector;
}

// *******************************************************************
std::shared_ptr<AbstractTreeGenerator> CFAMSA::createTreeGenerator(const CParams& params) {

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