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

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

diff --git a/binaries/src/ViennaRNA/H/dist_vars.h b/binaries/src/ViennaRNA/H/dist_vars.h
new file mode 100644 (file)
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+++ b/binaries/src/ViennaRNA/H/dist_vars.h
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+#ifndef __VIENNA_RNA_PACKAGE_DIST_VARS_H__
+#define __VIENNA_RNA_PACKAGE_DIST_VARS_H__
+
+/**
+ *  \file dist_vars.h
+ *  \brief Global variables for Distance-Package
+ */
+
+/**
+ *  \brief Produce an alignment of the two structures being compared by
+ *  tracing the editing path giving the minimum distance.
+ * 
+ *  set to 1 if you want backtracking
+ */
+extern int   edit_backtrack;
+
+/**
+ *  \brief Contains the two aligned structures after a call to one of the distance
+ *  functions with #edit_backtrack set to 1.
+ */
+extern char *aligned_line[4];
+
+/**
+ *  \brief Specify the cost matrix to be used for distance calculations
+ * 
+ *  if 0, use the default cost matrix (upper matrix in example), otherwise
+ *  use Shapiro's costs (lower matrix).
+ */
+extern int  cost_matrix;
+
+/*  Global type defs for Distance-Package */
+
+typedef struct {
+                 int  type;
+                 int  weight;
+                 int  father;
+                 int  sons;
+                 int  leftmostleaf;
+               } Postorder_list;
+
+typedef struct {
+                 Postorder_list *postorder_list;
+                 int            *keyroots;
+               } Tree;
+
+typedef struct {
+                 int    type;
+                 int    sign;
+                 float  weight;
+               } swString;
+#endif