diff options
Diffstat (limited to '0005-remove-all-the-remaining-unnecessary-stuff.patch')
| -rw-r--r-- | 0005-remove-all-the-remaining-unnecessary-stuff.patch | 86 |
1 files changed, 86 insertions, 0 deletions
diff --git a/0005-remove-all-the-remaining-unnecessary-stuff.patch b/0005-remove-all-the-remaining-unnecessary-stuff.patch new file mode 100644 index 000000000000..a1f478b6b92b --- /dev/null +++ b/0005-remove-all-the-remaining-unnecessary-stuff.patch @@ -0,0 +1,86 @@ +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 + |