diff options
| -rw-r--r-- | .SRCINFO | 30 | ||||
| -rw-r--r-- | 0001-corrected-Makefile-in-order-to-work-with-ViennaRNA-2.patch | 46 | ||||
| -rw-r--r-- | 0002-remove-redefinition-of-INF-energies.patch | 81 | ||||
| -rw-r--r-- | 0003-remove-unnecessary-and-deprecated-wrong-declarations.patch | 104 | ||||
| -rw-r--r-- | 0004-make-kinwalker-comply-to-stricter-g.patch | 75 | ||||
| -rw-r--r-- | 0005-remove-all-the-remaining-unnecessary-stuff.patch | 86 | ||||
| -rw-r--r-- | 0006-fix-bug-for-co-transcriptional-folding-with-dangles-.patch | 42 | ||||
| -rw-r--r-- | 0007-Do-not-fail-on-using-B-heuristic.patch | 329 | ||||
| -rw-r--r-- | 0008-Removed-findpath.h-and-cleaned-up-remnants-of-false-.patch | 91 | ||||
| -rw-r--r-- | PKGBUILD | 59 |
10 files changed, 943 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..5ad69240adfb --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,30 @@ +pkgbase = kinwalker + pkgdesc = Compute cotranscriptional folding trajectories of RNAs + pkgver = 2.0 + pkgrel = 1 + url = http://www.bioinf.uni-leipzig.de/Software/Kinwalker/ + arch = x86_64 + arch = i686 + license = Custom + depends = viennarna + source = http://www.bioinf.uni-leipzig.de/Software/Kinwalker/kinwalker.tar.gz + source = 0001-corrected-Makefile-in-order-to-work-with-ViennaRNA-2.patch + source = 0002-remove-redefinition-of-INF-energies.patch + source = 0003-remove-unnecessary-and-deprecated-wrong-declarations.patch + source = 0004-make-kinwalker-comply-to-stricter-g.patch + source = 0005-remove-all-the-remaining-unnecessary-stuff.patch + source = 0006-fix-bug-for-co-transcriptional-folding-with-dangles-.patch + source = 0007-Do-not-fail-on-using-B-heuristic.patch + source = 0008-Removed-findpath.h-and-cleaned-up-remnants-of-false-.patch + md5sums = 7723b173de294ef96b86d94f4f6cbeb9 + md5sums = 2f92e91e58badff10d4fe697bca3abf0 + md5sums = dba93e6fce292b6e9b9e7e0b667e6e6c + md5sums = 9ae628a2c89ac2654813b87a54605966 + md5sums = 73489a3b0f68a5bbfd158b5ea06f422a + md5sums = 39bd8b46857edd134671c30260dcc93c + md5sums = a6bab92d415092d4e47e08564ae9c48e + md5sums = 285cfd82e05b9e0c69d0196089d82e3b + md5sums = 4afda6634ea89393975b953ca7788497 + +pkgname = kinwalker + diff --git a/0001-corrected-Makefile-in-order-to-work-with-ViennaRNA-2.patch b/0001-corrected-Makefile-in-order-to-work-with-ViennaRNA-2.patch new file mode 100644 index 000000000000..75912ca1d530 --- /dev/null +++ b/0001-corrected-Makefile-in-order-to-work-with-ViennaRNA-2.patch @@ -0,0 +1,46 @@ +From f5efd6d09fc7441ee9db14c5fdbe7cb901bbb6f3 Mon Sep 17 00:00:00 2001 +From: Ronny Lorenz <ronny@tbi.univie.ac.at> +Date: Tue, 28 Jan 2014 16:31:16 +0100 +Subject: [PATCH 1/8] corrected Makefile in order to work with ViennaRNA 2.x + +--- + Makefile | 12 +++++++----- + 1 file changed, 7 insertions(+), 5 deletions(-) + +diff --git a/Makefile b/Makefile +index b2276b2..2640e58 100644 +--- a/Makefile ++++ b/Makefile +@@ -10,14 +10,16 @@ CC = gcc + CXX = g++ + LL = g++ + DEFS = +-VRNADIR = ${HOME}/C/ViennaRNA +-INCL = -I. -I$(VRNADIR)/H ++VRNA_INC = $(shell pkg-config --cflags RNAlib2) ++VRNA_LIB = $(shell pkg-config --libs RNAlib2) ++LDFLAGS = ++INCL = -I. $(VRNA_INC) + WARN = -Wall -ansi -pedantic + OPTI = -O3 + #OPTI = -O3 -p -g3 + CFLAGS = $(WARN) $(OPTI) $(DEFS) $(INCL) +-LIBS = -L$(VRNADIR)/lib -lRNA -lm -lstdc++ +-CSRC = options.c findpath.c ++LIBS = ${VRNA_LIB} -lm -lstdc++ ++CSRC = options.c + COBJ = $(foreach file, $(CSRC:.c=.o), $(file)) + CXXSRC = Energy.cpp Node.cpp Util.cpp MorganHiggs.cpp main.cpp + CXXOBJ = $(foreach file, $(CXXSRC:.cpp=.o), $(file)) +@@ -35,7 +37,7 @@ $(CXXOBJ): %.o: %.cpp + $(COBJ): %.o: %.c + $(CC) -c $(CFLAGS) $< -o $@ + $(EXE): $(COBJ) $(CXXOBJ) +- $(LL) $(CFLAGS) -o $(EXE) $(COBJ) $(CXXOBJ) $(LIBS) ++ $(LL) $(LDFLAGS) $(CFLAGS) -o $(EXE) $(COBJ) $(CXXOBJ) $(LIBS) + clean: + rm -f $(COBJ) $(CXXOBJ) $(EXE) + backup: clean +-- +2.5.2 + diff --git a/0002-remove-redefinition-of-INF-energies.patch b/0002-remove-redefinition-of-INF-energies.patch new file mode 100644 index 000000000000..08c43cd95efe --- /dev/null +++ b/0002-remove-redefinition-of-INF-energies.patch @@ -0,0 +1,81 @@ +From 9f85164b96b049426705a52b72d1feaedc808b21 Mon Sep 17 00:00:00 2001 +From: Ronny Lorenz <ronny@tbi.univie.ac.at> +Date: Tue, 28 Jan 2014 16:39:49 +0100 +Subject: [PATCH 2/8] remove redefinition of INF energies + +--- + Barrier.cpp | 5 ++++- + MorganHiggs.cpp | 6 +++++- + Node.cpp | 4 ++-- + 3 files changed, 11 insertions(+), 4 deletions(-) + +diff --git a/Barrier.cpp b/Barrier.cpp +index db399e6..6fd2c02 100644 +--- a/Barrier.cpp ++++ b/Barrier.cpp +@@ -12,7 +12,10 @@ + #include "Neighbor.h" + #include "Utils.h" + #include "options.h" +-#define INF 1000000 ++ ++extern "C" { ++#include "energy_const.h" /* defines INF */ ++} + + + /** +diff --git a/MorganHiggs.cpp b/MorganHiggs.cpp +index d4c579f..083fc05 100644 +--- a/MorganHiggs.cpp ++++ b/MorganHiggs.cpp +@@ -3,14 +3,18 @@ + $Id: MorganHiggs.cpp,v 1.13 2007/10/21 21:01:35 Kinwalker Exp $ + */ + ++#include <cstring> + #include "MorganHiggs.h" + #define BP_ADD_CONST 10000 +-#define INF 1000000 + using std::cout; + using std::endl; + + extern short * pair_table; + ++extern "C" { ++#include "energy_const.h" /* defines INF */ ++} ++ + bool MHS_debug=false; + int min_stack_size=1; + +diff --git a/Node.cpp b/Node.cpp +index 94ce681..3ddcb0f 100644 +--- a/Node.cpp ++++ b/Node.cpp +@@ -2,12 +2,12 @@ + Last changed Time-stamp: <2007-07-10 19:27:22 xtof> + $Id: Node.cpp,v 1.35 2007/11/03 16:45:58 Kinwalker Exp $ + */ +-#include "Node.h" + + #include <algorithm> + #include <iostream> + #include <iterator> + #include <utility> ++#include "Node.h" + + #include "template_utils.c" + +@@ -16,7 +16,7 @@ + #define EPSILON .00000000001 + + #define MIN_ENERGY_DIFF .01 +-#define INF 1000000 ++ + double BARRIER_TOO_HIGH=10000;//std::numeric_limits<int>::max(); + // class variables + int Node::verbose; +-- +2.5.2 + diff --git a/0003-remove-unnecessary-and-deprecated-wrong-declarations.patch b/0003-remove-unnecessary-and-deprecated-wrong-declarations.patch new file mode 100644 index 000000000000..dd95530cce9b --- /dev/null +++ b/0003-remove-unnecessary-and-deprecated-wrong-declarations.patch @@ -0,0 +1,104 @@ +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 + diff --git a/0004-make-kinwalker-comply-to-stricter-g.patch b/0004-make-kinwalker-comply-to-stricter-g.patch new file mode 100644 index 000000000000..e73893a0d3ae --- /dev/null +++ b/0004-make-kinwalker-comply-to-stricter-g.patch @@ -0,0 +1,75 @@ +From 561039364ab627c332e4debef3c3cc78a571e608 Mon Sep 17 00:00:00 2001 +From: Ronny Lorenz <ronny@tbi.univie.ac.at> +Date: Tue, 28 Jan 2014 16:56:01 +0100 +Subject: [PATCH 4/8] make kinwalker comply to stricter g++ + +--- + Energy.cpp | 3 ++- + MorganHiggs.h | 4 ++-- + Node.h | 1 + + Util.h | 3 +++ + 4 files changed, 8 insertions(+), 3 deletions(-) + +diff --git a/Energy.cpp b/Energy.cpp +index 67659de..ae72679 100644 +--- a/Energy.cpp ++++ b/Energy.cpp +@@ -2,9 +2,10 @@ + Last changed Time-stamp: <2006-10-13 22:34:37 xtof> + $Id: Energy.cpp,v 1.12 2007/11/03 16:45:58 Kinwalker Exp $ + */ ++#include <cstdlib> + #include <iostream> + #include <string> +- ++#include <cstring> + #include "Energy.h" + + +diff --git a/MorganHiggs.h b/MorganHiggs.h +index 76a15f3..f069429 100644 +--- a/MorganHiggs.h ++++ b/MorganHiggs.h +@@ -133,9 +133,9 @@ public: + + void AddInside(std::pair<int,int> bp,char first,char second); + +- void AddOutside(int first,int second,char first,char second); ++ void AddOutside(int first,int second,char cfirst,char csecond); + +- void AddInside(int first,int second,char first,char second); ++ void AddInside(int first,int second,char cfirst,char csecond); + + + static bool IsGCPair(char first,char second); +diff --git a/Node.h b/Node.h +index 3f99d23..43b2a3f 100644 +--- a/Node.h ++++ b/Node.h +@@ -25,6 +25,7 @@ + #include <iomanip> + #include <limits> + #include <string> ++#include <cstring> + #include <vector> + + +diff --git a/Util.h b/Util.h +index 5511ea0..a60f7c4 100644 +--- a/Util.h ++++ b/Util.h +@@ -1,8 +1,11 @@ + #include <string> ++#include <cstring> + #include <vector> + #include <sstream> + #include <cstdarg> + #include <iostream> ++#include <cstdlib> ++#include <algorithm> + + void Cout(std::string s); + +-- +2.5.2 + 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 + 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 + diff --git a/0007-Do-not-fail-on-using-B-heuristic.patch b/0007-Do-not-fail-on-using-B-heuristic.patch new file mode 100644 index 000000000000..a6e35db8a4f6 --- /dev/null +++ b/0007-Do-not-fail-on-using-B-heuristic.patch @@ -0,0 +1,329 @@ +From 5757202e85a95f7931dab6a0caaadd18aa4fa1c1 Mon Sep 17 00:00:00 2001 +From: Ronny Lorenz <ronny@tbi.univie.ac.at> +Date: Fri, 19 Jun 2015 19:17:46 +0200 +Subject: [PATCH 7/8] Do not fail on using 'B' heuristic! + +The 'B' heuristic (a.k.a. findpath) NEVER actually worked but caused the +program to terminate with segfaults. This has finally been fixed now! +--- + Node.cpp | 132 ++++++++++++++++++++++++++++++++------------------------------- + 1 file changed, 67 insertions(+), 65 deletions(-) + +diff --git a/Node.cpp b/Node.cpp +index bdc092c..bc53207 100644 +--- a/Node.cpp ++++ b/Node.cpp +@@ -182,10 +182,10 @@ void Node::GetMorganHiggsPath(std::string target){ + int t=Node::transcribed; + + Node::path = MorganHiggsEnergy(Node::sequence.substr(0,t), +- Node::front_structure.substr(0,t), +- target.substr(0,t), +- Node::front_energy+Node::energy_barrier, +- Node::lookahead,Node::grouping);//,Node::interrupt_trajectory); ++ Node::front_structure.substr(0,t), ++ target.substr(0,t), ++ Node::front_energy+Node::energy_barrier, ++ Node::lookahead,Node::grouping);//,Node::interrupt_trajectory); + } + + void Node::GetMorganHiggsStudlaPath(std::string target){ +@@ -193,10 +193,10 @@ void Node::GetMorganHiggsStudlaPath(std::string target){ + int t=Node::transcribed; + + Node::path = MorganHiggsStudlaEnergy(Node::sequence.substr(0,t), +- Node::front_structure.substr(0,t), +- target.substr(0,t), +- Node::front_energy+Node::energy_barrier, +- Node::lookahead,Node::grouping);//,Node::interrupt_trajectory); ++ Node::front_structure.substr(0,t), ++ target.substr(0,t), ++ Node::front_energy+Node::energy_barrier, ++ Node::lookahead,Node::grouping);//,Node::interrupt_trajectory); + } + + /** +@@ -254,7 +254,7 @@ void Node::GetSaddleFromPath(std::pair<double,std::string> & saddle,std::pair<do + //if we have increased to the size of the path, it means there is no structure that is lower, in that case retrun the front structure, + //as this trajectory is worthless, even when the energy barrier is higher + if(last_idx_of_partial_path>path_size){ +- final_structure=std::make_pair(Node::front_energy,Node::front_structure); ++ final_structure=std::make_pair(Node::front_energy,Node::front_structure); + return; + } + } +@@ -295,25 +295,27 @@ void Node::CalculateFoldingPath(Node* extremum,std::string integrated_structure) + 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); ++ 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; +- for (int i=0; i<p_len; i++) { +- // memorize idx of structure with highest energy seen so far +- if (!barrier_exceeded && 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)); ++ 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) { ++ maxE = p[i].en; ++ maxE_idx = i+1; ++ //barrier_exceeded=true; ++ } ++ v.push_back(std::make_pair(p[i].en, p[i].s)); + } + // add dummy entry with idx of structure with highest energy + v.push_back(std::make_pair(maxE_idx, "")); + /* clean up space of path */ +- for (int i=0; i<p_len; i++) free(p[i].s); ++ for (int i=0; p[i].s != NULL; i++) free(p[i].s); + free(p); + Node::path = v; ++ + } + + if(verbose>=3) { +@@ -436,6 +438,7 @@ Node::FindExtremum(){ + //only if everything is transcribed and we are moving towards the mfE + //done by the function CalculateFoldingPath + skip=false; ++ + if(!Node::interrupt_trajectory){ + if(node_substructure==Node::front_structure || Evaluate(node_substructure)>Node::front_energy) skip=true; + } +@@ -452,17 +455,18 @@ Node::FindExtremum(){ + barrier=barrier2; + combined_structure=final_structure.second; + if(debug) Cout("Have valid front extension with\n"+combined_structure+" "+Str(barrier)); +- } ++ } + } + } + if(debug) Cout("Current combined structure and barrier\n"+combined_structure+" "+Str(barrier)); + if(verbose>=3) Cout("Actually obtained combination:\n"+combined_structure+"\n"); + extension_cost.push_back(barrier); ++ + + if(verbose>=2) { + std::cout<<"Node "+Print(extrema[i])+" has extension cost "+Str(extension_cost.back())+" ("+Str(Node::energy_barrier)+" "+Str(Node::transcribed)+")\n"; + } +- if ( barrier <=Node::energy_barrier ) { ++ if ( barrier <= Node::energy_barrier ) { + //1.First structure if that is suitable. + //2.Otherwise seconds structure, if suitable, or we won't get here + extrema[i]->AddToFront(combined_structure,barrier); +@@ -488,69 +492,68 @@ static int front_count=1; + void + Node::AddToFront(std::string new_front_structure,double barrier){ + this->Reeligify(Node::front_structure,new_front_structure); +- + double new_front_energy =Evaluate(new_front_structure); + if ( verbose >= 1 ) { +- std::cout<<"Add Node ("+Print(this)+" "+Str(extension_cost.back())+" ("+Str(Node::energy_barrier)+" "+Str(Node::transcribed)+")\n"; ++ std::cout<<"Add Node ("+Print(this)+" "+Str(extension_cost.back())+" ("+Str(Node::energy_barrier)+" "+Str(Node::transcribed)+")\n"; + std::cout<<"src:"+Node::front_structure+" "+Str(Node::front_energy)+"\n"; + std::cout<<"tgt:"+new_front_structure+" "+Str(new_front_energy)+"\n"; + } + + //add the extremum to the front +- for (int i=this->i; i<=this->j; i++) { +- for (int j=i; j<=this->j; j++) front[i][j] = true; ++ for (int i=this->i; i<=this->j; i++) { ++ for (int j=i; j<=this->j; j++) front[i][j] = true; + } + front_extrema.push_back(this); + Node::front_structure=new_front_structure; + Node::front_energy=new_front_energy; + + if(barrier>0.0) Node::IncreaseTime(TimePassedFolding(barrier)); +- std::string trajectory_entry=std::string(); ++ std::string trajectory_entry=std::string(); + trajectory_entry+=Node::front_structure+" "; +- trajectory_entry+=Str(Node::front_energy)+" "; ++ trajectory_entry+=Str(Node::front_energy)+" "; + trajectory_entry+=Str(Node::time)+" "; + trajectory_entry+=Str(barrier)+" "; + trajectory_entry+=Str(Node::energy_barrier)+" "; + trajectory_entry+=Str(Node::transcribed)+" "; +- trajectory.push_back(trajectory_entry); ++ trajectory.push_back(trajectory_entry); + + //and remove it and the extrema it dominates from the extrema vector +- int count=0; ++ int count=0; + for(size_t i=0;i<extrema.size();i++){ + if(!extrema[i]->is_included && extrema[i]->i>=this->i && extrema[i]->j<=this->j){ + if(extrema[i]->IsMfE()) continue; + extrema[i]->SetIncluded(true); + extrema[i]->SetIneligible(); +- count++; +- } +- } +- ++ count++; ++ } ++ } ++ + //print new front + if ( verbose >= 1 ) { + std::cout<<"Path to new front:\n"; + std::cout<<FoldingPathToString(this->path)<<std::endl; +- Cout("New Front\n"); ++ Cout("New Front\n"); + std::cout<<front_structure+" "+Str(front_energy)<<std::endl; +- } ++ } + +- if ( verbose >= 5 ) Cout(Node::PrintFront()+"\n"); ++ if ( verbose >= 5 ) Cout(Node::PrintFront()+"\n"); + //make all extrema eligible again. + if(Node::print_front_trajectory) { +- std::vector<std::pair<int,int> > ext= std::vector<std::pair<int,int> >(); ++ std::vector<std::pair<int,int> > ext= std::vector<std::pair<int,int> >(); + for(size_t k=0;k<front_extrema.size();k++)ext.push_back(std::pair<int,int> (front_extrema[k]->i,front_extrema[k]->j)); +- Node::front_trajectory_ps+=PSFrontPlot(Node::sequence,ext); ++ Node::front_trajectory_ps+=PSFrontPlot(Node::sequence,ext); + +- // /* ++ // /* + Node::front_trajectory_ps=PSFrontPlot(Node::sequence,ext); + Node::front_trajectory_ps+="end \n"; +- std::string filename="front_trajectory"+Str(front_count)+".ps"; ++ std::string filename="front_trajectory"+Str(front_count)+".ps"; + std::ofstream outfile(filename.c_str()); + outfile << Node::front_trajectory_ps; + outfile.close(); +- front_count++; +- //*/ ++ front_count++; ++ //*/ + +- } ++ } + } + + +@@ -574,7 +577,7 @@ Node::ExtendFront() + + extern "C" { + void export_fold_arrays(int **f5_p, int **c_p, int **fML_p, int **fM1_p, +- int **indx_p, char **ptype_p); ++ int **indx_p, char **ptype_p); + } + void + Node::FindLocalExtrema() +@@ -588,8 +591,8 @@ Node::FindLocalExtrema() + double val = c[indx[j]+i]; + //i and j pair AND no lonely pair + if(val < INF) { +- //Node node=Node(i, j,val); +- extrema.push_back(new Node(i, j,val)); ++ //Node node=Node(i, j,val); ++ extrema.push_back(new Node(i, j,val)); + if(verbose>=2) Cout(Print(extrema.back())+" "+Str(val)+"\n"); + } + } +@@ -807,11 +810,11 @@ void Node::BacktrackFront(std::pair<double,std::string> & ret,std::string node_s + //do nothing if the base pair is already part of basepairs + if(find(basepairs.begin(),basepairs.end(),bp_node[i])!=basepairs.end()) continue; + if(!Conflict(basepairs,bp_node[i])) { +- //if (debug) { ++ //if (debug) { + if(debug_pt) Cout("added bp "+PrintBasePair(bp_node[i])+"\n");//} +- basepairs.push_back(bp_node[i]); ++ basepairs.push_back(bp_node[i]); + int first=bp_node[i].first; +- int second=bp_node[i].second; ++ int second=bp_node[i].second; + pair_table[first]=second; + pair_table[second]=first; + //manually change front_structure to circumvent a call to BasePairListToStructure1 +@@ -846,23 +849,23 @@ void Node::BacktrackFront(std::pair<double,std::string> & ret,std::string node_s + if(ConformationHasPair(basepairs,stack[j])) stack.erase(stack.begin()+j); + } + +- std::vector<std::pair<double,std::string> > front_resolutions= std::vector<std::pair<double,std::string> >(); ++ std::vector<std::pair<double,std::string> > front_resolutions= std::vector<std::pair<double,std::string> >(); + //std::vector<std::pair<double,std::vector<std::pair<int,int> > > > front_resolutions= std::vector<std::pair<double,std::vector<std::pair<int,int> > > >(); + + //front_resolutions.push_back(make_pair(front_energy,basepairs)); + front_resolutions.push_back(make_pair(front_energy,front_structure));//basepairs)); + + //ensure that the base pair in front at first_idx_stack does not come from the node that stack is constructued from. +- std::string resolved_structure=front_structure; ++ std::string resolved_structure=front_structure; + for(size_t j=0;j<stack.size();j++){ +- //last_insertion=j; +- //double resolution_energy= ++ //last_insertion=j; ++ //double resolution_energy= + ConstructFrontResolution(resolved_structure,new_basepairs,stack[j]); + front_resolutions.push_back(make_pair(FastEvaluate(),resolved_structure)); +- //front_resolutions.push_back(make_pair(resolution_energy,BasePairListToStructure1(Node::transcribed,new_basepairs))); +- } ++ //front_resolutions.push_back(make_pair(resolution_energy,BasePairListToStructure1(Node::transcribed,new_basepairs))); ++ } + //revert changes in pair_table: remove stack and add those elts of basepairs back that were removed because they conflicted with elements in stack +- MakePairTable(const_cast<char*>(front_structure.substr(0,Node::transcribed).c_str())); ++ MakePairTable(const_cast<char*>(front_structure.substr(0,Node::transcribed).c_str())); + if(debug_pt) std::cout<<"Pairtable after reverting changes of outside in "+PrintPairTable(); + //add stack back to front as much as possible + new_basepairs=basepairs; +@@ -876,15 +879,15 @@ void Node::BacktrackFront(std::pair<double,std::string> & ret,std::string node_s + //now accept the best solution in front_resolutions and update structure, energy and bp + front_energy=INF; + front_structure=std::string(Node::transcribed,'.'); +- for(std::vector<std::pair<double,std::string> >::iterator it=front_resolutions.begin();it!=front_resolutions.end();it++){ ++ for(std::vector<std::pair<double,std::string> >::iterator it=front_resolutions.begin();it!=front_resolutions.end();it++){ + if(it->first<front_energy){ + front_energy=it->first; +- front_structure=it->second; +- } ++ front_structure=it->second; ++ } + } + basepairs=MakeBasePairList1(front_structure); + //sync pair_table with latest front unless this was the last iteration or the latest front is already in pair_table +- if(i<bp_node_conflict_stacks.size()-1){ ++ if(i<bp_node_conflict_stacks.size()-1){ + MakePairTable(const_cast<char*>(front_structure.substr(0,Node::transcribed).c_str())); + if(debug_pt) std::cout<<"Pairtable after syncing with front resolution "+PrintPairTable(); + if(debug_pt) std::cout<<"Basepairs "+PrintBasePairList(basepairs); +@@ -905,7 +908,7 @@ std::string Node::BacktrackNode(Node* n){ + } + else { + char *s = backtrack_fold_from_pair(const_cast<char*>(Node::sequence.c_str()), +- n->i, n->j); ++ n->i, n->j); + std::string ss(s); + free(s); + return (ss.substr(0,Node::transcribed)); +@@ -970,7 +973,7 @@ double Node::MinimalExtensionCost(){ + void Node::RaiseEnergyBarrier(){ + Node::energy_barrier += 1.0; + double minimial_extension_cost=MinimalExtensionCost(); +- if(Node::energy_barrier<minimial_extension_cost && minimial_extension_cost>=0.0) Node::energy_barrier = ceil(minimial_extension_cost); ++ if(Node::energy_barrier < minimial_extension_cost && minimial_extension_cost>=0.0) Node::energy_barrier = ceil(minimial_extension_cost); + Node * n; + int count=0; + for(size_t i=0;i<extrema.size();i++){ +@@ -1111,7 +1114,6 @@ void Node::Reeligify(std::string old_structure,std::string new_structure){ + count++; + } + } +- //Cout("Reeligified "+Str(count)+" extrema after adding "+Node::Print(this)+"\n"); + } + + void Node::SetIneligible(){ +-- +2.5.2 + diff --git a/0008-Removed-findpath.h-and-cleaned-up-remnants-of-false-.patch b/0008-Removed-findpath.h-and-cleaned-up-remnants-of-false-.patch new file mode 100644 index 000000000000..7139c931a318 --- /dev/null +++ b/0008-Removed-findpath.h-and-cleaned-up-remnants-of-false-.patch @@ -0,0 +1,91 @@ +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 + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..958559604596 --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,59 @@ +# Maintainer: Ronny Lorenz <ronny at tbi dot univie dot ac dot at> + +pkgname=kinwalker +pkgver=2.0 +pkgrel=1 +pkgdesc="Compute cotranscriptional folding trajectories of RNAs" +arch=('x86_64' 'i686') +license=('Custom') +url="http://www.bioinf.uni-leipzig.de/Software/Kinwalker/" +depends=('viennarna') +optdepends=() +makedepends=() +provides=() +source=(http://www.bioinf.uni-leipzig.de/Software/Kinwalker/kinwalker.tar.gz + 0001-corrected-Makefile-in-order-to-work-with-ViennaRNA-2.patch + 0002-remove-redefinition-of-INF-energies.patch + 0003-remove-unnecessary-and-deprecated-wrong-declarations.patch + 0004-make-kinwalker-comply-to-stricter-g.patch + 0005-remove-all-the-remaining-unnecessary-stuff.patch + 0006-fix-bug-for-co-transcriptional-folding-with-dangles-.patch + 0007-Do-not-fail-on-using-B-heuristic.patch + 0008-Removed-findpath.h-and-cleaned-up-remnants-of-false-.patch +) +md5sums=( '7723b173de294ef96b86d94f4f6cbeb9' + '2f92e91e58badff10d4fe697bca3abf0' + 'dba93e6fce292b6e9b9e7e0b667e6e6c' + '9ae628a2c89ac2654813b87a54605966' + '73489a3b0f68a5bbfd158b5ea06f422a' + '39bd8b46857edd134671c30260dcc93c' + 'a6bab92d415092d4e47e08564ae9c48e' + '285cfd82e05b9e0c69d0196089d82e3b' + '4afda6634ea89393975b953ca7788497' + ) + +prepare() { + cd "${srcdir}/kinwalker" + + patch -p1 < ../0001-corrected-Makefile-in-order-to-work-with-ViennaRNA-2.patch + patch -p1 < ../0002-remove-redefinition-of-INF-energies.patch + patch -p1 < ../0003-remove-unnecessary-and-deprecated-wrong-declarations.patch + patch -p1 < ../0004-make-kinwalker-comply-to-stricter-g.patch + patch -p1 < ../0005-remove-all-the-remaining-unnecessary-stuff.patch + patch -p1 < ../0006-fix-bug-for-co-transcriptional-folding-with-dangles-.patch + patch -p1 < ../0007-Do-not-fail-on-using-B-heuristic.patch + patch -p1 < ../0008-Removed-findpath.h-and-cleaned-up-remnants-of-false-.patch +} + +build() { + cd "${srcdir}/kinwalker" + make || return 1 +} + +package() { + cd "${srcdir}/kinwalker" + + install -Dm755 kinwalker "${pkgdir}/usr/bin/kinwalker" + install -Dm644 man/kinwalker.1 "${pkgdir}/usr/share/man/man1/kinwalker.1" +} + |