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From e54e50a1f35b5636d92baef536d78fd844267ca2 Mon Sep 17 00:00:00 2001
From: Ronny Lorenz <ronny@tbi.univie.ac.at>
Date: Tue, 28 Jan 2014 16:57:04 +0100
Subject: [PATCH 5/8] remove all the remaining unnecessary stuff
---
Node.cpp | 7 ++++---
Util.cpp | 27 +--------------------------
2 files changed, 5 insertions(+), 29 deletions(-)
diff --git a/Node.cpp b/Node.cpp
index 3ddcb0f..3f33123 100644
--- a/Node.cpp
+++ b/Node.cpp
@@ -291,12 +291,13 @@ void Node::CalculateFoldingPath(Node* extremum,std::string integrated_structure)
int maxE_idx = -1;
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,
- &p_len);
+ Node::OptS->maxkeep);
bool barrier_exceeded=false;
for (int i=0; i<p_len; i++) {
// memorize idx of structure with highest energy seen so far
diff --git a/Util.cpp b/Util.cpp
index d0a9ecb..592a303 100644
--- a/Util.cpp
+++ b/Util.cpp
@@ -57,16 +57,6 @@ std::string PrintPairTable(){
return s;
}
-void
-PrettyPrint(char *fmt, ...)
-{
- va_list args;
-
- va_start(args, fmt);
- vfprintf(stdout, fmt, args);
- fflush(stdout);
- va_end(args);
-}
std::string PrintBasePair(std::pair<int,int> bp){
return "("+Str(bp.first)+","+Str(bp.second)+")";
@@ -283,21 +273,6 @@ ConformationToStacks(std::vector<std::vector<std::pair<int,int> > > & stacks, st
}
}
-void *MG_space(unsigned size) {
- void *pointer;
-
- if ( (pointer = (void *) calloc(1, (size_t) size)) == NULL) {
-#ifdef EINVAL
- if (errno==EINVAL) {
- fprintf(stderr,"SPACE: requested size: %d\n", size);
- printf("SPACE allocation failure -> EINVAL");
- }
- if (errno==ENOMEM)
-#endif
- printf("SPACE allocation failure -> no memory");
- }
- return pointer;
-}
#ifdef WITH_DMALLOC
#define MG_space(S) calloc(1,(S))
@@ -314,7 +289,7 @@ void *MG_space(unsigned size) {
// short *table;
length = (short) strlen(structure);
- stack = (short *) MG_space(sizeof(short)*(length+1));
+ stack = (short *) space(sizeof(short)*(length+1));
//table = (short *) space(sizeof(short)*(length+2));
pair_table[0] = length;
--
2.5.2
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