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author | Ronny Lorenz | 2015-09-19 15:44:46 +0200 |
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committer | Ronny Lorenz | 2015-09-19 15:44:46 +0200 |
commit | 7ff3896d2b4ac53e1650c3766eaa9b9d245814a8 (patch) | |
tree | 2906fe1b78dad906dd63193a66188323f20f5fd8 /0006-fix-bug-for-co-transcriptional-folding-with-dangles-.patch | |
download | aur-kinwalker.tar.gz |
Initial commit featuring several bugfixes and linking agains ViennaRNA Package 2.x
Diffstat (limited to '0006-fix-bug-for-co-transcriptional-folding-with-dangles-.patch')
-rw-r--r-- | 0006-fix-bug-for-co-transcriptional-folding-with-dangles-.patch | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/0006-fix-bug-for-co-transcriptional-folding-with-dangles-.patch b/0006-fix-bug-for-co-transcriptional-folding-with-dangles-.patch new file mode 100644 index 000000000000..b386599ea2e3 --- /dev/null +++ b/0006-fix-bug-for-co-transcriptional-folding-with-dangles-.patch @@ -0,0 +1,42 @@ +From 02ebdb357913d9c07021e156768e504ef5e27950 Mon Sep 17 00:00:00 2001 +From: Ronny Lorenz <ronny@tbi.univie.ac.at> +Date: Tue, 28 Jan 2014 17:00:00 +0100 +Subject: [PATCH 6/8] fix bug for co-transcriptional folding with dangles != 0 + +--- + Node.cpp | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/Node.cpp b/Node.cpp +index 3f33123..bdc092c 100644 +--- a/Node.cpp ++++ b/Node.cpp +@@ -581,6 +581,7 @@ Node::FindLocalExtrema() + { + int *f5, *c, *fML, *fM1, *indx; char *ptype; + export_fold_arrays(&f5,&c,&fML,&fM1,&indx,&ptype); ++ if(verbose>=2) Cout("#extrema: "+Str((int)extrema.size())+"\n"); + int n = matrix_size; + for (int i=1; i<=n-TURN-1; i++) { + for (int j=i+TURN+1; j<=n; j++) { +@@ -598,8 +599,8 @@ Node::FindLocalExtrema() + // (1,n) is in general not a pair. You can't include it in the list + //Node node2=Node(1,n,energy); + extrema.push_back(new Node(1,n,energy));//& node2); +- sort(extrema.begin(), extrema.end(), Node::LessThan); + if(verbose>=3) Cout("#extrema: "+Str((int)Node::extrema.size())+"\n"); ++ stable_sort(extrema.begin(), extrema.end(), Node::LessThan); + } + + +@@ -941,6 +942,7 @@ void Node::Transcribe(){ + pair_table[0]=Node::transcribed; + Node::front_structure+="."; + MakePairTableFromFrontStructure(); ++ Node::front_energy=Evaluate(Node::front_structure); + } + + bool Node::IsTranscribed(){ +-- +2.5.2 + |