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

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

diff --git a/binaries/src/ViennaRNA/H/Lfold.h b/binaries/src/ViennaRNA/H/Lfold.h
new file mode 100644 (file)
index 0000000..1becbaa
--- /dev/null
+++ b/binaries/src/ViennaRNA/H/Lfold.h
@@ -0,0 +1,81 @@
+#ifndef __VIENNA_RNA_PACKAGE_LFOLD_H__
+#define __VIENNA_RNA_PACKAGE_LFOLD_H__
+
+/**
+ */
+
+/**
+ *  \addtogroup local_fold
+ *
+ *  Local structures can be predicted by a modified version of the
+ *  fold() algorithm that restricts the span of all base pairs.
+ *  @{
+ *    \file Lfold.h
+ *    \brief Predicting local MFE structures of large sequences
+ *
+ *  @}
+ */
+
+/**
+ *  \addtogroup local_mfe_fold
+ *  @{
+ *
+ *  @}
+ */
+
+/**
+ *  \brief The local analog to fold().
+ * 
+ *  Computes the minimum free energy structure including only base pairs
+ *  with a span smaller than 'maxdist'
+ *
+ *  \ingroup local_mfe_fold
+ * 
+ *  \param string
+ *  \param structure
+ *  \param maxdist
+ */
+float Lfold(const char *string,
+            char *structure,
+            int maxdist);
+
+/**
+ *  \brief
+ * 
+ *  \ingroup local_mfe_fold
+ * 
+ *  \param string
+ *  \param structure
+ *  \param maxdist
+ *  \param zsc
+ *  \param min_z
+ */
+float Lfoldz( const char *string,
+              char *structure,
+              int maxdist,
+              int zsc,
+              double min_z);
+
+
+/**
+ *  \addtogroup local_consensus_fold
+ *  @{
+ *
+ *  @}
+ */
+
+/**
+ *  \brief
+ *
+ *  \ingroup local_consensus_fold
+ * 
+ *  \param strings
+ *  \param structure
+ *  \param maxdist
+ *  \return
+ */
+float aliLfold( const char **strings,
+                char *structure,
+                int maxdist);
+
+#endif