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

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

diff --git a/binaries/src/ViennaRNA/H/RNAstruct.h b/binaries/src/ViennaRNA/H/RNAstruct.h
new file mode 100644 (file)
index 0000000..aa65e26
--- /dev/null
+++ b/binaries/src/ViennaRNA/H/RNAstruct.h
@@ -0,0 +1,152 @@
+#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