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From 9b30c38b2abfc7b6db04290aef96cee9a4c40aeb Mon Sep 17 00:00:00 2001
From: Ronny Lorenz <ronny@tbi.univie.ac.at>
Date: Fri, 19 Jun 2015 19:37:25 +0200
Subject: [PATCH 8/8] Removed findpath.h and cleaned up remnants of false usage
of get_path()
---
Node.cpp | 14 ++++++--------
findpath.h | 28 ----------------------------
2 files changed, 6 insertions(+), 36 deletions(-)
delete mode 100644 findpath.h
diff --git a/Node.cpp b/Node.cpp
index bc53207..36d122d 100644
--- a/Node.cpp
+++ b/Node.cpp
@@ -11,6 +11,10 @@
#include "template_utils.c"
+extern "C" {
+#include "findpath.h"
+}
+
#define MS_PER_TIME_UNIT .0001
#define TIME_VS_DELTAG_DY_DX (8.0/11.0)
#define EPSILON .00000000001
@@ -288,24 +292,18 @@ void Node::CalculateFoldingPath(Node* extremum,std::string integrated_structure)
path_t *p;
int p_len = 0;
double maxE = -INF;//std::numeric_limits<double>::max();
- int maxE_idx = -1;
+ int maxE_idx = 0;
int t = Node::transcribed;
std::vector<std::pair<double,std::string> > v;
- /* length of path always is the base pair distance + 1 */
- p_len = bp_distance(const_cast<char*>(sequence.substr(0,t).c_str()),
- const_cast<char*>(Node::front_structure.c_str())) + 1;
p = get_path(const_cast<char*>(sequence.substr(0,t).c_str()),
const_cast<char*>(Node::front_structure.c_str()),
const_cast<char*>(integrated_structure.substr(0,t).c_str()),
Node::OptS->maxkeep);
- bool barrier_exceeded=false;
- maxE_idx = 0;
for (int i=0; p[i].s != NULL; i++) {
// memorize idx of structure with highest energy seen so far
- if (!barrier_exceeded && p[i].en > maxE) {
+ if(p[i].en > maxE){
maxE = p[i].en;
maxE_idx = i+1;
- //barrier_exceeded=true;
}
v.push_back(std::make_pair(p[i].en, p[i].s));
}
diff --git a/findpath.h b/findpath.h
deleted file mode 100644
index 2e27237..0000000
--- a/findpath.h
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
-* 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__
-
-#include "data_structures.h"
-
-/**
- * \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
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