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

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

diff --git a/binaries/src/ViennaRNA/H/subopt.h b/binaries/src/ViennaRNA/H/subopt.h
new file mode 100644 (file)
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+++ b/binaries/src/ViennaRNA/H/subopt.h
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+/* subopt.h */
+#ifndef __VIENNA_RNA_PACKAGE_SUBOPT_H__
+#define __VIENNA_RNA_PACKAGE_SUBOPT_H__
+
+#include "data_structures.h"
+
+#define MAXDOS 1000
+
+/**
+ *  \addtogroup subopt_fold Enumerating Suboptimal Structures
+ *  \ingroup folding_routines
+ *  @{
+ *    \file subopt.h
+ *    \brief RNAsubopt and density of states declarations
+ *
+ *  @}
+ */
+
+/**
+ *  \addtogroup subopt_wuchty
+ *  @{
+ *
+ *  @}
+ */
+
+/**
+ *  \brief Returns list of subopt structures or writes to fp
+ * 
+ *  This function produces <b>all</b> suboptimal secondary structures within
+ *  'delta' * 0.01 kcal/mol of the optimum. The results are either
+ *  directly written to a 'fp' (if 'fp' is not NULL), or
+ *  (fp==NULL) returned in a #SOLUTION * list terminated
+ *  by an entry were the 'structure' pointer is NULL.
+ *
+ *  \ingroup subopt_wuchty
+ *
+ *  \param  seq
+ *  \param  structure
+ *  \param  delta
+ *  \param  fp
+ *  \return
+ */
+SOLUTION *subopt (char *seq,
+                  char *structure,
+                  int delta,
+                  FILE *fp);
+
+/**
+ *  \brief Returns list of subopt structures or writes to fp
+ * 
+ *  \ingroup subopt_wuchty
+ */
+SOLUTION *subopt_par( char *seq,
+                      char *structure,
+                      paramT *parameters,
+                      int delta,
+                      int is_constrained,
+                      int is_circular,
+                      FILE *fp);
+
+/**
+ *  \brief Returns list of circular subopt structures or writes to fp
+ * 
+ *  This function is similar to subopt() but calculates secondary structures
+ *  assuming the RNA sequence to be circular instead of linear
+ * 
+ *  \ingroup subopt_wuchty
+ *
+ *  \param  seq
+ *  \param  sequence
+ *  \param  delta
+ *  \param  fp
+ *  \return
+ */
+SOLUTION *subopt_circ ( char *seq,
+                        char *sequence,
+                        int delta,
+                        FILE *fp);
+
+/**
+ *  \brief Sort output by energy
+ * 
+ *  \ingroup subopt_wuchty
+ *
+ */
+extern  int     subopt_sorted;
+
+
+/**
+ *  \brief printing threshold for use with logML
+ * 
+ *  \ingroup subopt_wuchty
+ *
+ */
+extern  double  print_energy;
+
+/**
+ *  \addtogroup dos
+ *  @{
+ */
+
+/**
+ *  \brief The Density of States
+ *
+ *  This array contains the density of states for an RNA sequences after a call to subopt_par(),
+ *  subopt() or subopt_circ().
+ *
+ *  \pre  Call one of the functions subopt_par(), subopt() or subopt_circ() prior accessing the contents
+ *        of this array
+ *  \see  subopt_par(), subopt(), subopt_circ()
+ *
+ */
+extern  int     density_of_states[MAXDOS+1];
+
+/** @} */ /* End of group dos */
+
+#endif