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