#ifndef __VIENNA_RNA_PACKAGE_MEA_H__
#define __VIENNA_RNA_PACKAGE_MEA_H__

#include "data_structures.h"

/**
 *  \file MEA.h
 *  \brief Computes a MEA (maximum expected accuracy) structure.
 */

/**
 *  \brief Computes a MEA (maximum expected accuracy) structure.
 * 
 *  The algorithm maximizes the expected accuracy
 *  \f[ A(S) = \sum_{(i,j) \in S} 2 \gamma p_{ij} + \sum_{i \notin S} p^u_i \f]
 *  Higher values of \f$\gamma\f$ result in more base pairs of lower
 *  probability and thus higher sensitivity. Low values of \f$\gamma\f$ result in structures
 *  containing only highly likely pairs (high specificity).
 *  The code of the MEA function also demonstrates the use of sparse dynamic
 *  programming scheme to reduce the time and memory complexity of folding.
 */
float MEA(plist *p,
          char *structure,
          double gamma);

#endif