#ifndef VIENNA_RNA_PACKAGE_DUPLEX_H
#define VIENNA_RNA_PACKAGE_DUPLEX_H

#include <ViennaRNA/data_structures.h>

/**
 *  @file     duplex.h
 *  @ingroup  cofold
 *  @brief    Functions for simple RNA-RNA duplex interactions
 */


duplexT duplexfold(const char *s1,
                   const char *s2);


duplexT *duplex_subopt(const char *s1,
                       const char *s2,
                       int        delta,
                       int        w);


duplexT aliduplexfold(const char  *s1[],
                      const char  *s2[]);


duplexT *aliduplex_subopt(const char  *s1[],
                          const char  *s2[],
                          int         delta,
                          int         w);


#endif
