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From fa8d5c6b78cebee3d2df987150375d415e46593a Mon Sep 17 00:00:00 2001
From: Ronny Lorenz <ronny@tbi.univie.ac.at>
Date: Tue, 28 Jan 2014 16:46:51 +0100
Subject: [PATCH 3/8] remove unnecessary and deprecated/wrong declarations of
stuff from RNAlib
---
Energy.cpp | 2 --
Node.h | 7 +------
Util.cpp | 4 ++++
findpath.h | 33 ++++++++++++++++++++++++---------
4 files changed, 29 insertions(+), 17 deletions(-)
diff --git a/Energy.cpp b/Energy.cpp
index 6cb9455..67659de 100644
--- a/Energy.cpp
+++ b/Energy.cpp
@@ -13,8 +13,6 @@ extern "C" {
#include "fold_vars.h"
#include "utils.h"
#include "pair_mat.h"
-extern int
-energy_of_struct_pt (char *string, short * ptable, short *s, short *s1);
}
extern short * S;
extern short * S1;
diff --git a/Node.h b/Node.h
index b1d090c..3f99d23 100644
--- a/Node.h
+++ b/Node.h
@@ -33,12 +33,7 @@ extern "C" {
#include "fold.h"
#include "energy_const.h"
#include "utils.h"
- extern float fold(const char* sequence, char* structure);
- extern void export_fold_arrays(int **f5_p, int **c_p, int **fML_p,
- int **fM1_p, int **indx_p, char **ptype_p);
- extern char * backtrack_fold_from_pair(char* seq,int i,int j);
- extern void free_arrays(void);
- extern int fold_constrained;
+ #include "fold_vars.h"
}
#include "Energy.h"
#include "MorganHiggs.h"
diff --git a/Util.cpp b/Util.cpp
index 75cdec5..d0a9ecb 100644
--- a/Util.cpp
+++ b/Util.cpp
@@ -5,6 +5,10 @@ extern short *pair_table;
/*@exits@*/
//extern void nrerror(const char message[]);
+extern "C" {
+#include "utils.h"
+}
+
void Cout(std::string s){std::cout<<s;}
std::string Str(double x)
diff --git a/findpath.h b/findpath.h
index a0b3e4e..2e27237 100644
--- a/findpath.h
+++ b/findpath.h
@@ -1,13 +1,28 @@
-#ifndef FIND_PATH_H
-#define FIND_PATH_H
+/*
+* file borrowed from ViennaRNA Package 2.0.4
+* (this file may be removed completely since it is also present in the ViennaRNA includes
+*/
+#ifndef __VIENNA_RNA_PACKAGE_FIND_PATH_H__
+#define __VIENNA_RNA_PACKAGE_FIND_PATH_H__
-typedef struct path {
- double en;
- char *s;
-} path_t;
+#include "data_structures.h"
-extern int find_saddle (char *seq, char *struc1, char *struc2, int max);
-extern path_t* get_path(char *seq, char *s1, char* s2,
- int maxkeep, int *num_entry);
+/**
+ * \file findpath.h
+ * \brief Compute direct refolding paths between two secondary structures
+ */
+
+int find_saddle(char *seq,
+ char *struc1,
+ char *struc2,
+ int max);
+
+
+path_t* get_path( char *seq,
+ char *s1,
+ char* s2,
+ int maxkeep);
+
+void free_path(path_t *path);
#endif
--
2.5.2
|