#ifndef __VIENNA_RNA_PACKAGE_RNASTRUCT_H__
#define __VIENNA_RNA_PACKAGE_RNASTRUCT_H__

/**
 *  \file RNAstruct.h
 *  \brief Parsing and Coarse Graining of Structures
 * 
 *   Example:
 *  \verbatim
 *   .((..(((...)))..((..)))).   is the bracket or full tree
 *   becomes expanded:   - expand_Full() -
 *   ((U)(((U)(U)((((U)(U)(U)P)P)P)(U)(U)(((U)(U)P)P)P)P)(U)R)
 *   HIT:                - b2HIT() -
 *   ((U1)((U2)((U3)P3)(U2)((U2)P2)P2)(U1)R)
 *   Coarse:             - b2C() -
 *   ((H)((H)M)R)
 *   becomes expanded:   - expand_Shapiro() -
 *   (((((H)S)((H)S)M)S)R)
 *   weighted Shapiro:   - b2Shapiro() -
 *   ((((((H3)S3)((H2)S2)M4)S2)E2)R)
 *  \endverbatim
 */

#define STRUC     2000

/**
 *  \brief Converts the full structure from bracket notation to the HIT
 *  notation including root.
 * 
 *  \param structure
 *  \return
 */
char *b2HIT(const char *structure);             /* Full   -> HIT    [incl. root] */

/**
 *  \brief Converts the full structure from bracket notation to the a
 *  coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers.
 * 
 *  \param structure
 *  \return
 */
char *b2C(const char *structure);               /* Full   -> Coarse [incl. root] */

/**
 *  \brief Converts the full structure from bracket notation to the
 *  <i>weighted</i> coarse grained notation using the 'H' 'B' 'I' 'M' 'S' 'E' and
 *  'R' identifiers.
 * 
 *  \param structure
 *  \return
 */
char *b2Shapiro(const char *structure);         /* Full -> weighted Shapiro [i.r.] */

/**
 *  \brief Adds a root to an un-rooted tree in any except bracket notation.
 * 
 *  \param  structure
 *  \return
 */
char *add_root(const char *structure);                   /* {Tree} -> ({Tree}R)          */

/**
 *  \brief Inserts missing 'S' identifiers in unweighted coarse grained structures
 *  as obtained from b2C().
 * 
 *  \param coarse
 *  \return
 */
char  *expand_Shapiro(const char *coarse);

/* add S for stacks to coarse struct */
/**
 *  \brief Convert the full structure from bracket notation to the
 *  expanded notation including root.
 * 
 *  \param structure
 *  \return 
 */
char  *expand_Full(const char *structure);      /* Full   -> FFull         */

/**
 *  \brief Restores the bracket notation from an expanded full or HIT tree, that is
 *  any tree using only identifiers 'U' 'P' and 'R'.
 * 
 *  \param ffull
 *  \return 
 */
char  *unexpand_Full(const char *ffull);        /* FFull  -> Full          */

/**
 *  \brief Strip weights from any weighted tree.
 * 
 *  \param wcoarse
 *  \return
 */
char  *unweight(const char *wcoarse);           /* remove weights from coarse struct */

/**
 *  \brief Converts two aligned structures in expanded notation.
 * 
 *  Takes two aligned structures as produced by
 *  tree_edit_distance() function back to bracket notation with '_'
 *  as the gap character. The result overwrites the input.
 * 
 *  \param align
 */
void   unexpand_aligned_F(char *align[2]);

/**
 *  \brief Collects a statistic of structure elements of the full structure in
 *  bracket notation.
 * 
 *  The function writes to the following global variables:
 *  #loop_size, #loop_degree, #helix_size, #loops, #pairs, #unpaired
 * 
 *  \param structure
 *  \return
 */
void   parse_structure(const char *structure);  /* make structure statistics */

/**
 *  \brief contains a list of all loop sizes. loop_size[0] contains the
 *  number of external bases.
 */
extern int    loop_size[STRUC];       /* loop sizes of a structure */

/**
 *  \brief contains a list of all stack sizes.
 */
extern int    helix_size[STRUC];      /* helix sizes of a structure */

/**
 *  \brief contains the corresponding list of loop degrees.
 */
extern int    loop_degree[STRUC];     /* loop degrees of a structure */

/**
 *  \brief contains the number of loops ( and therefore of stacks ).
 */
extern int    loops;                  /* n of loops and stacks */

/**
 *  \brief contains the number of unpaired bases.
 */
extern int    unpaired;

/**
 *  \brief contains the number of base pairs in the last parsed structure.
 */
extern int    pairs;        /* n of unpaired digits and pairs */

#endif