H/plex.h

#ifndef __VIENNA_RNA_PACKAGE_PLEX_H__
#define __VIENNA_RNA_PACKAGE_PLEX_H__

#include "data_structures.h"


extern int subopt_sorted;

duplexT** Lduplexfold(const char *s1,
                      const char *s2,
                      const int threshold,
                      const int extension_cost,
                      const int alignment_length,
                      const int delta,
                      const int fast,
                      const int il_a,
                      const int il_b,
                      const int b_a,
                      const int b_b);

duplexT** Lduplexfold_XS( const char*s1,
                          const char* s2,
                          const int **access_s1,
                          const int **access_s2,
                          const int threshold,
                          const int delta,
                          const int alignment_length,
                          const int fast,
                          const int il_a,
                          const int il_b,
                          const int b_a,
                          const int b_b);//, const int target_dead, const int query_dead);

duplexT** Lduplexfold_C(const char *s1,
                        const char *s2,
                        const int threshold,
                        const int extension_cost,
                        const int alignment_length,
                        const int delta,
                        const int fast,
                        const char* structure,
                        const int il_a,
                        const int il_b,
                        const int b_a,
                        const int b_b);

duplexT** Lduplexfold_CXS(const char*s1,
                          const char* s2,
                          const int **access_s1,
                          const int **access_s2,
                          const int threshold,
                          const int delta,
                          const int alignment_length,
                          const int fast,
                          const char* structure,
                          const int il_a,
                          const int il_b,
                          const int b_a,
                          const int b_b);//, const int target_dead, const int query_dead);




int      arraySize(duplexT** array);
void     freeDuplexT(duplexT** array);

#endif

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