WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / H / MEA.h

diff --git a/binaries/src/ViennaRNA/H/MEA.h b/binaries/src/ViennaRNA/H/MEA.h
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+++ b/binaries/src/ViennaRNA/H/MEA.h
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+#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);
+
+float MEA_seq(plist *p,
+              const char *sequence,
+              char *structure,
+              double gamma,
+              pf_paramT *pf);
+
+#endif