965568e | Ronny Lorenz | 08 October 2015, 14:05:18 UTC | Bumped submodule RNAforester | 08 October 2015, 14:05:18 UTC |
d0c4340 | Ronny Lorenz | 08 October 2015, 12:29:50 UTC | Bump RNAforester to version 2.0 | 08 October 2015, 12:29:50 UTC |
7654701 | Ronny Lorenz | 08 October 2015, 12:28:44 UTC | Added Perl submodules in interfaces/Perl/RNA to distribution | 08 October 2015, 12:28:44 UTC |
0360de9 | Ronny Lorenz | 21 September 2015, 10:52:32 UTC | Fixed memory leak in cofold.c | 21 September 2015, 10:52:32 UTC |
3d0c290 | Ronny Lorenz | 21 September 2015, 10:52:05 UTC | Fixed memory leak in backward compatibility of eval.c | 21 September 2015, 10:52:05 UTC |
5e5e7b2 | Ronny Lorenz | 05 September 2015, 22:54:17 UTC | Fixed compilation error in RNALalifold.c due to removed pf functionality (cherry picked from commit 4bdc6f6e010d2152f5160c6f77f5503ed87d03db) Signed-off-by: Ronny Lorenz <ronny@tbi.univie.ac.at> | 05 September 2015, 23:00:25 UTC |
0611eb5 | Ronny Lorenz | 05 September 2015, 22:53:23 UTC | Fixed soft constraint error in multibanch loops (pf version) (cherry picked from commit 54746fff96da13a354c30576d885d13e09decc64) Signed-off-by: Ronny Lorenz <ronny@tbi.univie.ac.at> | 05 September 2015, 23:00:13 UTC |
3585e07 | Ronny Lorenz | 03 September 2015, 16:06:33 UTC | Merge branch 'dev_sc_func_fix' into 'development' Fixed most of the generalized soft constraint features in MFE and PF recursions - duplicated code to make loops faster - moved QB forward recursions into header files - merged QB forward recursions for single, and hybrid structures - made RNAcofold able to omit base pair probability computations (-p0) - fixed G-Quad exterior loops in pf_linear() See merge request !24 | 03 September 2015, 16:06:33 UTC |
5db75ae | Ronny Lorenz | 24 August 2015, 15:38:26 UTC | Fixed most of the generalized soft constraint features in MFE and PF recursions - duplicated code to make loops faster - moved QB forward recursions into header files - merged QB forward recursions for single, and hybrid structures - made RNAcofold able to omit base pair probability computations (-p0) - fixed G-Quad exterior loops in pf_linear() | 03 September 2015, 16:00:02 UTC |
a213ed8 | Ronny Lorenz | 27 August 2015, 12:46:45 UTC | Removed partition function option from RNALalifold since it is NOT IMPLEMENTED Thanks to Roman to figure this bug out! | 27 August 2015, 12:46:45 UTC |
a1098ec | Ronny Lorenz | 04 August 2015, 16:56:02 UTC | Fixed 'prohibit base pair' case for hard constraint via input file | 04 August 2015, 16:56:02 UTC |
65771e9 | Ronny Lorenz | 04 August 2015, 16:55:35 UTC | Obey hard constraints in stochastic backtracking | 04 August 2015, 16:55:35 UTC |
0a3b92b | Ronny Lorenz | 04 August 2015, 16:54:04 UTC | Do not compute base pair probabilities when stochastic backtracking in RNAsubopt is requested! | 04 August 2015, 16:54:04 UTC |
8aa4001 | Ronny Lorenz | 03 August 2015, 09:50:15 UTC | Fixed some minor issues that made the compiler complain... | 03 August 2015, 09:50:15 UTC |
112107b | Ronny Lorenz | 30 July 2015, 10:08:26 UTC | Merge branch 'dev_vrna-perl' into 'development' new RNA::Design functions See merge request !23 | 30 July 2015, 10:08:26 UTC |
cb0cc4b | Stefan Badelt | 30 June 2015, 16:42:10 UTC | bugfix for cofold input | 30 June 2015, 16:42:10 UTC |
65ebed4 | Stefan Badelt | 30 June 2015, 15:24:10 UTC | new RNA::Design functions | 30 June 2015, 15:24:10 UTC |
82945b6 | Stefan Badelt | 18 June 2015, 14:22:53 UTC | merge pairtable typo-fix in RNA::Design | 18 June 2015, 14:22:53 UTC |
e0b29e8 | Ronny Lorenz | 17 June 2015, 12:46:12 UTC | Tell MakeMaker to include tests in interfaces/Perl/RNA/t upon 'make check' | 17 June 2015, 12:46:12 UTC |
4f86e56 | Ronny Lorenz | 17 June 2015, 11:23:33 UTC | Use latest version of ViennaRNA-perl | 17 June 2015, 11:23:33 UTC |
4686334 | Ronny Lorenz | 21 May 2015, 10:17:07 UTC | Use new API partition function calls in RNApdist.c | 21 May 2015, 10:17:07 UTC |
b1a84ac | Ronny Lorenz | 18 May 2015, 12:42:59 UTC | Merge branch 'dev_perlinterface' into 'development' Integrate additional collection of useful perl modules into the ViennaRNA Package and its "RNA" namespace See merge request !22 | 18 May 2015, 12:42:59 UTC |
06b4ea1 | Ronny Lorenz | 18 May 2015, 12:37:26 UTC | Adapted Makefile.PL.in for Perl interface to include additional ViennaRNA-perl modules collection | 18 May 2015, 12:37:26 UTC |
834f9c0 | Ronny Lorenz | 18 May 2015, 12:28:04 UTC | Added ViennaRNA-perl submodule that augments the Perl interface to RNAlib | 18 May 2015, 12:28:04 UTC |
8a8977a | Ronny Lorenz | 15 May 2015, 09:03:09 UTC | Fixed hard constraints bug: revert accidental enforcement of base pairs although calling hc_weak_enforce_pair() | 15 May 2015, 09:03:09 UTC |
9204338 | Ronny Lorenz | 11 May 2015, 15:13:30 UTC | Provide RNAcofold with an '--enforceConstraint' flag - Also allow pipe-symbol in pseudo-dot-bracket constraint for RNAcofold and RNAsubopt | 11 May 2015, 15:13:30 UTC |
567fa1d | Ronny Lorenz | 11 May 2015, 15:11:27 UTC | Obey hard constraints in base pair probability computation for multibranch loops in part_func.c - This part may require some additional checks to assess whether hard-constraints for unpaired nucleotides in multibranch loops is implemented correctly. | 11 May 2015, 15:11:27 UTC |
12b2119 | Ronny Lorenz | 11 May 2015, 15:10:12 UTC | Fixed minimal multiloop-part size in backtracking of multibranch_loops.h | 11 May 2015, 15:10:12 UTC |
5328fa8 | Ronny Lorenz | 11 May 2015, 15:08:17 UTC | Fixed mixup of upstream/downstream pair in dot-bracket hard constraint - Also allow for enforcing upstream/downstream/both pairing state for dot-bracket constraints | 11 May 2015, 15:08:17 UTC |
e4bc14c | Ronny Lorenz | 11 May 2015, 08:52:27 UTC | Some restructuring of the code base to put deprecated code into consecutive blocks Here, we also moved the energy parameter update related functions to data_structures.c, and applied a small renaming of pre-released new API functions... | 11 May 2015, 08:52:27 UTC |
fbe62bf | Ronny Lorenz | 11 May 2015, 08:50:38 UTC | Fixed hard-constraint related bug in base pair prob computation of part_func.c | 11 May 2015, 08:50:38 UTC |
2e878d6 | Ronny Lorenz | 07 May 2015, 11:02:29 UTC | Fixed multi loop parts backtracking for dangles==3 again! This time for real! | 07 May 2015, 11:02:29 UTC |
b23f08e | Ronny Lorenz | 06 May 2015, 17:07:56 UTC | Fixed subopt with dangles!=2|0 Using odd dangles (1,3), vrna_subopt() did the wrong decisions for dangling end energy contributions. This is fixed now! | 06 May 2015, 17:07:56 UTC |
7e97693 | Ronny Lorenz | 06 May 2015, 17:07:01 UTC | Fixed multiloop backtracing error on dangles==3 in fold.c and cofold.c | 06 May 2015, 17:07:01 UTC |
075b3a5 | Ronny Lorenz | 05 May 2015, 13:09:31 UTC | Added maxBPspan, enforceCosntraint, and SHAPE reactivity data input flags to commandline parameters of RNAsubopt | 05 May 2015, 13:09:31 UTC |
9fd113a | Ronny Lorenz | 05 May 2015, 11:04:14 UTC | Added Fix for setup.py refusing to build Python extension on OS X, using clang compiler The fix was taken from BioPython setup.py and adds a compiler flag to warn instead of error-out on compilation with CFLAGS that the OS X version of clang does not understand. Thanks to Kevin Allen to bring up this issue and bugfix | 05 May 2015, 11:04:14 UTC |
a13c1ab | Ronny Lorenz | 04 May 2015, 10:56:27 UTC | Merge branch 'dev_sc_backtrack' into 'development' Re-use main parts of MFe backtracking in fold.c, cofold.c, and alifold.c Major parts of the backtracking routines were moved to hairpin_loops.h, interior_loops.h, multibranch_loops.h, and exterior_loops.h. This finally allows to share the backtracking code among multiple implementations, therefore making changes in the backtracking code easilty affect multiple implementations... See merge request !21 | 04 May 2015, 10:56:27 UTC |
00dec8e | Ronny Lorenz | 03 May 2015, 18:02:22 UTC | Moved remaining backtracking parts from cofold.c to multibranch_loops.h | 03 May 2015, 18:02:22 UTC |
8238053 | Ronny Lorenz | 30 April 2015, 14:32:59 UTC | Added an option to really enforce base pairs given in dot-bracket constraint string RNAfold already exposes this feature as commandline parameter "--enforceConstraint" | 30 April 2015, 14:32:59 UTC |
2e83c32 | Ronny Lorenz | 30 April 2015, 12:05:25 UTC | Moved backtracking of split point for multiloops to multibranch_loops.h | 30 April 2015, 12:05:25 UTC |
88ce010 | Ronny Lorenz | 30 April 2015, 09:57:46 UTC | Do backtracking of fake multi loops in multibranch_loops.h as well | 30 April 2015, 09:57:46 UTC |
c63e78a | Ronny Lorenz | 29 April 2015, 15:39:03 UTC | Use the same f5 backtracking in fold.c and cofold.c | 29 April 2015, 15:39:03 UTC |
46fcbaa | Ronny Lorenz | 28 April 2015, 13:31:53 UTC | Use polymorphic Hairpin-loop evaluation and backtracking in alifold.c | 28 April 2015, 13:31:53 UTC |
8bdb78e | Ronny Lorenz | 28 April 2015, 13:29:06 UTC | Moved major backtracking related code into corresponding loop-type header files - This enables to share even more code between cofold.c and fold.c, as well as future application to alifold.c, once the backtracking procedures have been made polymorphic | 28 April 2015, 13:29:06 UTC |
f370aaf | Ronny Lorenz | 27 April 2015, 13:23:50 UTC | Moved backtracking of hairpins and interior loops to their respective header files - This enables to re-use the backtracking routines at least in cofold. Implementation of polymorphism to deal with consensus structures may be worthwile too. | 27 April 2015, 13:23:50 UTC |
732e45e | Ronny Lorenz | 22 April 2015, 16:05:47 UTC | Added user-defined backtracking function via soft constraint feature for hairpin loops and interior loops. For now, this feature is only present in vrna_fold(), and vrna_cofold() but should be possible for vrna_ali_fold() as well... | 27 April 2015, 10:44:15 UTC |
debdcd4 | Ronny Lorenz | 17 April 2015, 21:11:49 UTC | Added user-defined backtracking to soft constraint feature | 17 April 2015, 21:11:49 UTC |
09663bb | Ronny Lorenz | 17 April 2015, 20:04:12 UTC | Made energy_of_xxx() in eval.c fast again! Successive old API calls to energy_of_xxx() functions in the library were usually horribly slow, compared to ViennaRNA 1.x. This has been fixed now by recycling of data structures generated in previous calls. | 17 April 2015, 20:04:12 UTC |
2dbd0f4 | Ronny Lorenz | 16 April 2015, 10:41:33 UTC | Rearranged parameters for vrna_TwoD_backtrack5() | 16 April 2015, 10:41:33 UTC |
ed67d5d | Ronny Lorenz | 15 April 2015, 16:41:35 UTC | Made Python interface building the default for autoconf | 15 April 2015, 16:41:35 UTC |
9715c5a | Ronny Lorenz | 15 April 2015, 16:34:10 UTC | Fixed Issue #15, "Do not allo too many non-canonical base pairs upon hard costraint application | 15 April 2015, 16:34:10 UTC |
da574c0 | Ronny Lorenz | 03 April 2015, 12:54:27 UTC | Fixed RNAup error mentioned in Issue#16 | 03 April 2015, 12:54:27 UTC |
8c07b60 | Ronny Lorenz | 03 April 2015, 12:51:40 UTC | Prefill vrna_mx_pf_t.q1k and vrna_mx_pf_t.qln while computing bppm These arrays are allocated anyway, and they are needed for RNAup | 03 April 2015, 12:51:40 UTC |
b9295fa | Ronny Lorenz | 01 April 2015, 15:39:13 UTC | Merge branch 'dev_dox' into 'development' Cleanups for generated reference manual and automake processes | 01 April 2015, 15:39:13 UTC |
01921ee | Ronny Lorenz | 01 April 2015, 15:23:01 UTC | Hacked Makefiles to enable a proper 'make distcheck' even with activated SWIG Perl interface | 01 April 2015, 15:28:36 UTC |
4d85807 | Ronny Lorenz | 01 April 2015, 08:13:20 UTC | Added generic SWIG part for Makefiles in 'interfaces' | 01 April 2015, 15:28:36 UTC |
66854aa | Ronny Lorenz | 31 March 2015, 17:24:50 UTC | Update head of submodule 'Kinfold' | 01 April 2015, 15:28:35 UTC |
c5c218e | Ronny Lorenz | 31 March 2015, 17:20:00 UTC | Fixed makedist for python interface Perl interface still needs some way for target 'uninstall' to behave as it should do upon calling 'make uninstall'. However, MakeMaker is not able to do that out of the box... | 01 April 2015, 15:28:35 UTC |
9e07c0d | Ronny Lorenz | 30 March 2015, 23:43:47 UTC | Fixed out-of-tree building for SWIG generated interfaces and unit tests | 01 April 2015, 15:28:35 UTC |
b0ad882 | Ronny Lorenz | 30 March 2015, 23:42:34 UTC | Fixed constantly rebuilding of RNAlib Reference Manual | 01 April 2015, 15:28:35 UTC |
f4aeee2 | Ronny Lorenz | 27 March 2015, 15:45:36 UTC | Several changes to prepare a working 'make distcheck' Still, the swig interfaces won't build upon make distcheck, but the rest does... | 01 April 2015, 15:28:34 UTC |
fe4bbe8 | Ronny Lorenz | 27 March 2015, 15:42:06 UTC | Subsitute perl command in shebang line in perl utilities only after install Perl scripts are modified by an install-hook in src/Utils/Makefile.am instead of make-time modification. This helps to modify these files inplace even when srcdir and builddir differ from each other. | 01 April 2015, 15:28:34 UTC |
6b884b3 | Ronny Lorenz | 27 March 2015, 02:06:04 UTC | Fixed automake rules for installing html and pdf reference manual Also obey user-defined htmldir path passed to configure script | 01 April 2015, 15:28:34 UTC |
627607c | Ronny Lorenz | 25 March 2015, 15:34:17 UTC | Added doc/refman.include to EXTRA_DIST in doc/Makefile.am | 01 April 2015, 15:28:33 UTC |
a43406f | Ronny Lorenz | 25 March 2015, 14:51:25 UTC | Set dot image file format to SVG Note, that since we do not name the html reference manual pages .xhtml but .html, IE9+ browser will not display SVG images. But who is using Microsoft browser anyway???!!! | 01 April 2015, 15:28:33 UTC |
842dd16 | Ronny Lorenz | 25 March 2015, 12:57:55 UTC | Split mainpage.dox into smaller files | 01 April 2015, 15:28:33 UTC |
2f8c8ac | Ronny Lorenz | 24 March 2015, 16:38:12 UTC | Added page about v3.0 API features to reference manual | 01 April 2015, 15:28:32 UTC |
70a071f | Ronny Lorenz | 21 March 2015, 12:01:52 UTC | Fixed generation of PDF documentation | 01 April 2015, 15:28:32 UTC |
7fd51d1 | Ronny Lorenz | 21 March 2015, 11:14:12 UTC | Modified m4/package.m4 to use user-specified PerlCmd and PythonCmd in favor of system default This helps for situations, where for instance /usr/bin/python points to Python 3 instead of Python 2 as it is the case in ArchLinux | 01 April 2015, 15:28:32 UTC |
48767b7 | Ronny Lorenz | 21 March 2015, 10:57:50 UTC | Added examples directory | 01 April 2015, 15:28:32 UTC |
e40ac3b | Ronny Lorenz | 13 March 2015, 12:30:42 UTC | Added "Supported File Formats" page to doxygen documentation This moves the huge documentation from file_formats.h to a separate .dox file in the doc/ directory | 01 April 2015, 15:28:31 UTC |
423c6f8 | Ronny Lorenz | 26 March 2015, 20:44:07 UTC | Fix bug in sequence composition determination for Lfoldz Unfortunalety, the z-scoring mechanism was limited to sequence lengths up to 2^16 nucelotides. All sequence input above resulted in unpredicted behavior of the programs. This is fixed now! (cherry picked from commit f714824204cfa3635076dc877fc0fbac51a5e7a0) | 26 March 2015, 20:49:31 UTC |
1b8da2b | Ronny Lorenz | 23 March 2015, 13:53:45 UTC | Enabled client-side (javascript) search engine for doxygen documentation | 23 March 2015, 13:53:45 UTC |
66c0181 | Ronny Lorenz | 23 March 2015, 13:36:11 UTC | Small correction in interior loop energy parameter files | 23 March 2015, 13:36:11 UTC |
4873717 | Ronny Lorenz | 23 March 2015, 13:19:27 UTC | Fixed mismatch and dangle contributions in extra energy parameter files Also non-canonical pairs and non-canonical bases are treated the same in DNA parameter files as they are for RNA. | 23 March 2015, 13:19:27 UTC |
b3abeb8 | Ronny Lorenz | 20 March 2015, 12:15:59 UTC | Bump to v2.2.0-RC2 | 20 March 2015, 12:15:59 UTC |
d02b422 | Ronny Lorenz | 20 March 2015, 09:38:37 UTC | Use memcmp() instead of wrong memcpy() in findpath.c | 20 March 2015, 09:38:37 UTC |
de783fd | Ronny Lorenz | 20 March 2015, 09:25:56 UTC | Fixed names for backtracking functions in 2Dfold headers | 20 March 2015, 09:25:56 UTC |
a8b9ce1 | Ronny Lorenz | 20 March 2015, 09:20:12 UTC | Merge branch 'dev_2Dfold' into 'development' Updated interface to 2Dfold functions | 20 March 2015, 09:20:12 UTC |
8d69738 | Ronny Lorenz | 20 March 2015, 09:17:20 UTC | Fixed crosslink functions in 2Dfold.c and 2Dpfold.c for the sake of backward compatibility | 20 March 2015, 09:17:20 UTC |
4a18047 | Ronny Lorenz | 20 March 2015, 09:12:01 UTC | Applied more consistent naming scheme to new API functions in 2Dfold Updated the documentation as well... | 20 March 2015, 09:12:01 UTC |
45e9263 | Ronny Lorenz | 19 March 2015, 17:22:26 UTC | Fixed usage of ptype array in 2Dpfold.c Now we have a working version of RNA2Dfold that uses vrna_fold_compound... The backward compatibility feature needs attention now, testing was not done on it yet. | 19 March 2015, 17:22:26 UTC |
0f2539f | Ronny Lorenz | 19 March 2015, 16:56:46 UTC | Fixed wrong usage of ptype in 2Dfold.c | 19 March 2015, 16:56:46 UTC |
a9b56e0 | Ronny Lorenz | 19 March 2015, 11:28:34 UTC | Removed old API calls in RNA2Dfold.c | 19 March 2015, 11:28:34 UTC |
842f07b | Ronny Lorenz | 19 March 2015, 11:20:48 UTC | Removed dependency of pair_mat.h from 2Dfold.c and 2Dpfold.c | 19 March 2015, 11:20:48 UTC |
df3bb49 | Ronny Lorenz | 19 March 2015, 10:51:44 UTC | Minor cleanup of documentation in 2Dpfold.h | 19 March 2015, 10:51:44 UTC |
60bf1f6 | Ronny Lorenz | 19 March 2015, 10:47:46 UTC | Made 2Dfold partition function operate on vrna_fold_compound | 19 March 2015, 10:47:46 UTC |
7e0a57c | Ronny Lorenz | 19 March 2015, 01:00:30 UTC | Added function to retrieve vrna_fold_compound for Distance Class Partitioning and ported MFE version of 2Dfold MFE version of 2Dfold now internally operates on vrna_fold_compound structure. Porting definetely broke compatibility to pairmat.h, so we need to remove this include next and replace everything with corresponding calls via new API. Next step also needs to be PF version of 2Dfold, so that the RNA2Dfold executable can be finished. | 19 March 2015, 01:00:30 UTC |
da52f0f | Ronny Lorenz | 18 March 2015, 21:50:36 UTC | Implemented memory free() 2Dfold matrices in polymorphic vrna_mx_mfe_t and vrna_mx_pf_t | 18 March 2015, 21:50:36 UTC |
bad2541 | Ronny Lorenz | 18 March 2015, 20:55:29 UTC | Implemented memory allocation for 2Dfold matrices in polymorphic vrna_mx_pf_t | 18 March 2015, 20:55:29 UTC |
ad2f062 | Ronny Lorenz | 18 March 2015, 17:22:01 UTC | Implemented memory allocation for 2Dfold matrices in polymorphic vrna_mx_mfe_t | 18 March 2015, 17:22:01 UTC |
ce3b61b | Ronny Lorenz | 18 March 2015, 14:25:01 UTC | More changes toward 2Dfold integration into polymorphic vrna_fold_compound | 18 March 2015, 14:25:01 UTC |
6b57a5c | Ronny Lorenz | 18 March 2015, 12:59:34 UTC | Added 2Dfold MFE matrices to vrna_mx_mfe_t The new data fields are encapsulated in an unnamed union/struct, together with the default MFE matrices. However, this feature is only exploited when using a C11 capable compiler. Otherwise, the data fields just extend the default data fields of vrna_mx_mfe_t. Also changed the vrna_fold_compound.type fields from unsigned int to enum type. | 18 March 2015, 12:59:34 UTC |
aec5131 | Ronny Lorenz | 18 March 2015, 11:20:51 UTC | Use unnamed unions/structs only if compiler understands C11 standard | 18 March 2015, 11:20:51 UTC |
ce9bd98 | Ronny Lorenz | 17 March 2015, 16:58:12 UTC | Made old API functions in findpath.c fast again Using a global static backward_compat structure to keep all previously computed data in memory, consecutive calls of the old API functions using the same input sequence and the same model details is very fast again... | 17 March 2015, 16:58:12 UTC |
056fd20 | Ronny Lorenz | 17 March 2015, 16:23:44 UTC | Make (at least the new API ) functions of findpath.c fast again! Still, the old API functions are horribly slow, since they always create the vrna_fold_compound first, before doing the analysis. So calling the old API functions say a million times, induces calling vrna_get_fold_compound() a million times, too. The best way is to use the new API in 3rd party projects, but maybe, we can implement a backward_compatibility approach as used in fold.c to circumvent constant re-creation of the fold compound using the old API... | 17 March 2015, 16:23:44 UTC |
134c188 | Ronny Lorenz | 16 March 2015, 12:08:28 UTC | Bump RC1 of 2.2 version | 16 March 2015, 12:08:28 UTC |
9bc1f4d | Ronny Lorenz | 16 March 2015, 11:33:23 UTC | Changed default value of sigma-tau ratio in RNApvmin - Fixed bug in SHAPE reactivity derived soft constraints with Deigan et al. method | 16 March 2015, 11:33:23 UTC |
a2ad1b0 | Ronny Lorenz | 13 March 2015, 14:40:38 UTC | Fixed bug in soft constraints for exterior loops of eval.c | 13 March 2015, 14:40:38 UTC |
03f5f44 | Ronny Lorenz | 12 March 2015, 10:25:07 UTC | Merge branch 'dev_refman' into 'development' Reference Manual Update | 12 March 2015, 10:25:07 UTC |