| 59e1ee6 | Ronny Lorenz | 07 June 2022, 14:20:54 UTC | Update badges/shields in README.md | 07 June 2022, 14:28:56 UTC |
| 56cb0f4 | Ronny Lorenz | 07 June 2022, 13:47:51 UTC | Update Travis-CI config (again) | 07 June 2022, 14:28:36 UTC |
| 2765cc4 | Ronny Lorenz | 02 June 2022, 10:07:06 UTC | Update .travis.yml | 02 June 2022, 10:07:06 UTC |
| 003676e | Ronny Lorenz | 02 June 2022, 07:55:26 UTC | TESTS: Workaround failing inverse folding test | 02 June 2022, 07:55:26 UTC |
| e053e3e | Ronny Lorenz | 02 June 2022, 07:54:54 UTC | Do not remove .la files in RPM packages | 02 June 2022, 07:54:54 UTC |
| 2eea1b2 | Ronny Lorenz | 01 June 2022, 14:04:26 UTC | Prepare for release v2.5.1 | 01 June 2022, 14:27:43 UTC |
| 989bfb9 | Ronny Lorenz | 01 June 2022, 05:49:52 UTC | Revisit generic soft constraints for sliding-windown base pair probability computations | 01 June 2022, 05:49:52 UTC |
| 7d15267 | Ronny Lorenz | 31 May 2022, 14:41:08 UTC | TESTS: Adapt MEA output for RNAfold and RNAalifold G-quadruplex tests | 31 May 2022, 14:41:08 UTC |
| c60b9c4 | Ronny Lorenz | 31 May 2022, 12:53:47 UTC | Fix MEA computation for G-quadruplex predictions Prior to this patch, G-quadruplex probabilities were not properly accounted for in computing the expected accuracy (EA). Now, similar to base pairs, the total number of nucleotides involved in the G-quadruplex are used as contribution to the EA. Along with that, the functions producing pair lists (vrna_ep_t *) keep entries for the quadruplex itself (vrna_ep_t::type == VRNA_PLIST_TYPE_GQUAD) and the individual base triples that for the stacked quartets (vrna_ep_t::type == VRNA_PLIST_TYPE_TRIPLE). | 31 May 2022, 12:53:55 UTC |
| c00a557 | Ronny Lorenz | 19 May 2022, 11:07:02 UTC | Enable to overwrite automatic unpaired probability determination in MEA computation | 24 May 2022, 13:13:20 UTC |
| 98e898a | Ronny Lorenz | 19 May 2022, 11:03:55 UTC | Add VRNA_PLIST_TYPE_UNPAIRED identifier for vrna_ep_t | 19 May 2022, 11:04:15 UTC |
| 569f647 | Ronny Lorenz | 16 May 2022, 08:29:01 UTC | Fix header include for naview.c | 16 May 2022, 08:29:01 UTC |
| 69a1867 | Ronny Lorenz | 04 May 2022, 13:37:36 UTC | Fix memory leak in hard constraints container | 04 May 2022, 13:37:36 UTC |
| 28d0b94 | Ronny Lorenz | 19 October 2021, 15:20:52 UTC | SWIG: Add simple dot-plot file wrapper plot_dp_EPS() | 04 May 2022, 09:18:52 UTC |
| 9d0e8ad | Ronny Lorenz | 27 April 2022, 14:26:45 UTC | SWIG: Add sequence, sequence_encoding and sequence_encoding2 attributes to fold_compound objects | 27 April 2022, 14:26:45 UTC |
| 39e6109 | Ronny Lorenz | 27 April 2022, 12:58:13 UTC | AUTOCONF: Make LaTeX checks more portable | 27 April 2022, 13:39:35 UTC |
| 7ebcbfc | Ronny Lorenz | 26 April 2022, 20:28:21 UTC | SWIG: Fix RNG wrapping | 26 April 2022, 20:28:38 UTC |
| 621f219 | Ronny Lorenz | 26 April 2022, 18:13:05 UTC | SWIG: initialize RNG upon module load and update associated functions | 26 April 2022, 18:14:24 UTC |
| e446189 | Ronny Lorenz | 26 April 2022, 18:13:46 UTC | Add vrna_init_rand_seed() to initialize RNG with seed | 26 April 2022, 18:14:20 UTC |
| f617980 | Ronny Lorenz | 26 April 2022, 15:52:52 UTC | AUTOCONF: Check whether we can build the swig interface when SVM support is deactivated | 26 April 2022, 15:54:43 UTC |
| 9876e5d | Ronny Lorenz | 26 April 2022, 12:51:20 UTC | Update dlib to version 19.23 | 26 April 2022, 15:54:43 UTC |
| 554e131 | Ronny Lorenz | 26 April 2022, 12:34:03 UTC | AUTOCONF: Update latex packages to check for Reference Manual build | 26 April 2022, 15:54:34 UTC |
| 14e727d | Ronny Lorenz | 26 April 2022, 12:33:51 UTC | AUTOCONF: Update latex packages to check for Tutorial build | 26 April 2022, 15:54:28 UTC |
| 36bef89 | Ronny Lorenz | 26 April 2022, 12:33:41 UTC | AUTOCONF: Update latex packages to check for CLA build | 26 April 2022, 15:54:20 UTC |
| 400669b | Ronny Lorenz | 06 April 2022, 13:28:04 UTC | Allow for deactivating the Naview layout algorithm at configure-time This may become useful for installing or distributing the package without the Naview layout algorithm of Bruccoleri 1988 | 12 April 2022, 11:28:14 UTC |
| b97abb7 | Ronny Lorenz | 06 April 2022, 13:00:49 UTC | Use vrna_plot_coords_pt() instead of naview_xy_coordinates() | 12 April 2022, 11:28:14 UTC |
| e0c2b57 | Ronny Lorenz | 12 April 2022, 11:10:12 UTC | Increase size of hard constraints matrix by 1 We don't actually require that, but it seems necessary for the swig generated wrappers | 12 April 2022, 11:11:55 UTC |
| 0186819 | Ronny Lorenz | 12 April 2022, 11:11:24 UTC | SWIG: Even more simplification and cleanup for var_arrays.i | 12 April 2022, 11:11:55 UTC |
| 506a112 | Ronny Lorenz | 12 April 2022, 10:59:28 UTC | SWIG: More cleanup in var_arrays.i | 12 April 2022, 10:59:28 UTC |
| 574f6c2 | Ronny Lorenz | 07 April 2022, 15:17:01 UTC | SWIG: Add input value checks for inputs of var_array<short>-derived types | 07 April 2022, 15:17:01 UTC |
| 9273a36 | Ronny Lorenz | 07 April 2022, 13:40:50 UTC | SWIG: Use var_array<short> for ptable in structure_utils.i | 07 April 2022, 13:40:50 UTC |
| 6a532ac | Ronny Lorenz | 07 April 2022, 13:40:22 UTC | SWIG: Use var_array<short> in walk.i | 07 April 2022, 13:40:22 UTC |
| ce2ad46 | Ronny Lorenz | 07 April 2022, 13:39:57 UTC | SWIG: Use var_array<short> for ptable in eval.i | 07 April 2022, 13:39:57 UTC |
| f016bb0 | Ronny Lorenz | 07 April 2022, 08:15:31 UTC | SWIG: Draft pair_table wrappers | 07 April 2022, 08:15:31 UTC |
| d27e2b7 | Ronny Lorenz | 07 April 2022, 08:15:15 UTC | SWIG: More extension of var_array<T> wrapper | 07 April 2022, 08:15:15 UTC |
| 6246d8c | Ronny Lorenz | 15 March 2022, 13:24:20 UTC | DOC: fix argument parameter names in eval.dox | 06 April 2022, 22:01:31 UTC |
| 3689833 | Ronny Lorenz | 15 March 2022, 13:22:03 UTC | DOC: Remove ambiguous double paramter description in fold_compound.h | 06 April 2022, 22:01:31 UTC |
| 9dfe410 | Ronny Lorenz | 15 March 2022, 13:21:26 UTC | DOC: Add more documentation to dp_matrices.h | 06 April 2022, 22:01:31 UTC |
| def12c4 | Ronny Lorenz | 15 March 2022, 13:20:56 UTC | DOC: Fix argument list for doxygen parameter list in boltzmann_sampling.h | 06 April 2022, 22:01:31 UTC |
| 4d15d0d | Ronny Lorenz | 15 March 2022, 13:20:18 UTC | Remove stale return argument from doxygen comments in RNAstruct.h | 06 April 2022, 22:01:31 UTC |
| 2a82ba2 | Ronny Lorenz | 15 March 2022, 13:19:32 UTC | DOC: Fix argument list for doxygen parameter list in utils/structures.h | 06 April 2022, 22:01:31 UTC |
| e2c84cd | Ronny Lorenz | 15 March 2022, 13:18:04 UTC | DOC: Fix doxygen commands in constraints/ligand.h | 06 April 2022, 22:01:31 UTC |
| 80f1734 | Ronny Lorenz | 03 April 2022, 09:52:27 UTC | GIT: Add generated PDF files to .gitignore | 06 April 2022, 22:01:31 UTC |
| 3b1afd7 | Ronny Lorenz | 03 April 2022, 09:52:03 UTC | GIT: add more files to .gitignore | 06 April 2022, 22:01:31 UTC |
| cd7b309 | Ronny Lorenz | 29 March 2022, 13:13:15 UTC | SWIG: Expose hard constraints in fold_compound objects | 29 March 2022, 13:13:15 UTC |
| 3a174a5 | Ronny Lorenz | 29 March 2022, 09:43:24 UTC | SWIG: Enable access for more fold_compound member arrays | 29 March 2022, 09:43:24 UTC |
| 6e536d0 | Ronny Lorenz | 29 March 2022, 09:42:44 UTC | SWIG: Even more simplification for variable-sized arrays | 29 March 2022, 09:42:44 UTC |
| 4186e45 | Ronny Lorenz | 28 March 2022, 22:57:24 UTC | SWIG: Simplify variable length array wrapper by using templated structures | 28 March 2022, 22:57:24 UTC |
| abbe2f9 | Ronny Lorenz | 28 March 2022, 22:04:32 UTC | SWIG: Add exp_E_ext_stem() method to fold_compound objects | 28 March 2022, 22:04:32 UTC |
| 728eb16 | Ronny Lorenz | 28 March 2022, 22:03:09 UTC | SWIG: Expose DP matrices within fold_compound objects | 28 March 2022, 22:03:09 UTC |
| ebcf4f9 | Ronny Lorenz | 14 March 2022, 16:38:29 UTC | Add vrna_zsc_compute_raw() to obtain mean and sd for Z-score computation | 14 March 2022, 22:13:30 UTC |
| 058dd75 | Ronny Lorenz | 21 February 2022, 08:15:38 UTC | Change URL to https:// in configure.ac | 14 March 2022, 22:11:57 UTC |
| 4969dd3 | Ronny Lorenz | 28 January 2022, 08:26:42 UTC | Merge branch 'rnapuzzler-fix' into 'development' rnapuzzler fix See merge request rna/viennarna!85 | 28 January 2022, 08:26:42 UTC |
| 1c593bb | Daniel Wiegreffe | 27 January 2022, 14:57:42 UTC | rnapuzzler fix | 27 January 2022, 14:57:42 UTC |
| 560121e | Ronny Lorenz | 19 January 2022, 11:19:30 UTC | Add verbose info for ct2db that states the number of base pairs removed upon PK removal | 19 January 2022, 11:19:30 UTC |
| 3a5aa5d | Ronny Lorenz | 03 January 2022, 13:45:47 UTC | Refactor ct2db program to allow for pseudoknots in output structure | 03 January 2022, 13:46:46 UTC |
| 0c9230f | Ronny Lorenz | 03 January 2022, 13:44:59 UTC | Add vrna_file_connect_read_record() function to parse .ct files | 03 January 2022, 13:46:46 UTC |
| d01c76f | Ronny Lorenz | 03 January 2022, 13:44:04 UTC | Fix potential use of unitialized value in vrna_strtrim() | 03 January 2022, 13:46:46 UTC |
| 6221bbc | Ronny Lorenz | 03 January 2022, 08:15:08 UTC | Fix invalid memory access in vrna_strjoin() | 03 January 2022, 13:46:46 UTC |
| 135a234 | Ronny Lorenz | 31 December 2021, 11:43:07 UTC | Update sanity checks for input in vrna_pbacktrack_sub*() | 03 January 2022, 13:46:46 UTC |
| 7ddf326 | Ronny Lorenz | 31 December 2021, 11:41:40 UTC | Add VRNA_TRIM_SUBST_BY_FIRST flag for vrna_strtrim() | 03 January 2022, 13:46:46 UTC |
| 55bff27 | Ronny Lorenz | 08 December 2021, 08:12:09 UTC | EXAMPLES: Add Python examples for vrna_pbacktrack_sub*() functions | 03 January 2022, 13:46:46 UTC |
| 9310d01 | Ronny Lorenz | 08 December 2021, 08:11:35 UTC | DOC: Add description of SWIG interfaces for vrna_pbacktrack_sub*() functions | 03 January 2022, 13:46:46 UTC |
| a744e32 | Ronny Lorenz | 02 December 2021, 16:26:18 UTC | SWIG: Add wrapper for vrna_strtrim() | 03 January 2022, 13:46:46 UTC |
| dd9a06d | Ronny Lorenz | 02 December 2021, 16:24:30 UTC | Add vrna_strtrim() function | 03 January 2022, 13:46:45 UTC |
| 3045a0d | Ronny Lorenz | 26 November 2021, 16:48:30 UTC | DOC: Update doxygen.conf for version 1.9.2 | 26 November 2021, 16:48:30 UTC |
| 736b333 | Ronny Lorenz | 26 November 2021, 16:39:52 UTC | AUTOCONF: Fix condition check for CLA build | 26 November 2021, 16:39:52 UTC |
| 1f455f2 | Ronny Lorenz | 25 November 2021, 19:15:41 UTC | SWIG: Fix memory leak in wrapper for vrna_db_from_ptable() | 25 November 2021, 19:15:41 UTC |
| 505dd38 | Ronny Lorenz | 25 November 2021, 19:15:04 UTC | Allow for pseudo-knots in vrna_db_from_ptable | 25 November 2021, 19:15:04 UTC |
| 1a8e25c | Ronny Lorenz | 24 November 2021, 16:31:15 UTC | Do not use min_loop_size=0 for multi strand interaction prediction | 24 November 2021, 16:31:15 UTC |
| ef49a16 | Ronny Lorenz | 24 November 2021, 16:30:15 UTC | Remove unnecessary uses of min_loop_size in loops/*.c | 24 November 2021, 16:30:15 UTC |
| 4f779b8 | Ronny Lorenz | 24 November 2021, 16:29:12 UTC | Remove unnecessary uses of min_loop_size in constraints/soft.c | 24 November 2021, 16:29:12 UTC |
| 91daa42 | Ronny Lorenz | 24 November 2021, 16:29:02 UTC | Remove unnecessary uses of min_loop_size in constraints/hard.c | 24 November 2021, 16:29:02 UTC |
| 481412b | Ronny Lorenz | 24 November 2021, 16:26:42 UTC | Remove min_loop_size from utils/msa_utils.c | 24 November 2021, 16:26:42 UTC |
| 81663a7 | Ronny Lorenz | 24 November 2021, 16:25:52 UTC | Remove min_loop_size from centroid.c | 24 November 2021, 16:25:52 UTC |
| 852ae9f | Ronny Lorenz | 24 November 2021, 16:25:32 UTC | Remove min_loop_size from LPfold.c | 24 November 2021, 16:25:32 UTC |
| cfa62ee | Ronny Lorenz | 18 November 2021, 09:35:34 UTC | Remove min_loop_size from index loops in subopt.c | 24 November 2021, 16:24:27 UTC |
| b161f74 | Ronny Lorenz | 18 November 2021, 09:25:44 UTC | Remove min_loop_size from index loops in subopt_zuker.c | 24 November 2021, 16:24:22 UTC |
| 6d81777 | Ronny Lorenz | 18 November 2021, 08:48:12 UTC | Remove min_loop_size from index loops in equilibrium_probs.c | 24 November 2021, 16:24:18 UTC |
| 4a9bfcf | Ronny Lorenz | 18 November 2021, 08:47:57 UTC | Remove min_loop_size from index loops in part_func.c | 24 November 2021, 16:24:12 UTC |
| 0511fbd | Ronny Lorenz | 18 November 2021, 08:56:13 UTC | Remove min_loop_size from index loops in mfe.c | 24 November 2021, 16:24:08 UTC |
| a1c5f26 | Ronny Lorenz | 18 November 2021, 08:11:58 UTC | Deprecate cutpoint member of vrna_fold_compound_t and prepare for 5'/3' encoding | 18 November 2021, 08:11:58 UTC |
| 4600674 | Ronny Lorenz | 18 November 2021, 08:10:55 UTC | Refactor sequence addition/preparation for vrna_fold_compound | 18 November 2021, 08:10:55 UTC |
| bfc8a70 | Ronny Lorenz | 16 November 2021, 10:59:06 UTC | Move covariance energy evaluation to separate object | 16 November 2021, 10:59:06 UTC |
| b01e290 | Ronny Lorenz | 16 November 2021, 10:58:26 UTC | CLEANUP: tidy-up eval_wrappers.c and guard public functions against missing input | 16 November 2021, 10:58:26 UTC |
| f5ddefc | Ronny Lorenz | 16 November 2021, 10:00:33 UTC | CLEANUP: Tidy-up eval.c | 16 November 2021, 10:00:33 UTC |
| 691a06e | Ronny Lorenz | 16 November 2021, 08:33:53 UTC | Remove unused code in eval.c | 16 November 2021, 08:33:53 UTC |
| 0c57590 | Ronny Lorenz | 15 November 2021, 21:42:08 UTC | Start to merge en_corr_of_loop_gquad() for single seq and MSA eval | 15 November 2021, 21:42:08 UTC |
| f58f58a | Ronny Lorenz | 01 November 2021, 10:38:42 UTC | Prepare for release v2.5.0 | 11 November 2021, 06:45:22 UTC |
| e69037d | Ronny Lorenz | 11 November 2021, 06:45:08 UTC | SWIG: Add remaining Perl 5/Python 2.x wrappers for subsequence Boltzmann sampling | 11 November 2021, 06:45:22 UTC |
| 2bd7955 | Ronny Lorenz | 11 November 2021, 05:32:46 UTC | TESTS: Make command line program checks more portable | 11 November 2021, 05:33:09 UTC |
| 1055687 | Ronny Lorenz | 11 November 2021, 05:31:17 UTC | Add C++11 requirement to the autoconf/automake build process (needed by dlib) | 11 November 2021, 05:33:09 UTC |
| 2e525e1 | Ronny Lorenz | 09 November 2021, 21:30:15 UTC | Add RNAmultifold.1.gz to installed manpages in viennarna.spec | 10 November 2021, 07:13:07 UTC |
| 6697162 | Ronny Lorenz | 10 November 2021, 06:52:19 UTC | CLEANUP: Uncrustify src/ViennaRNA/utils/utils.c | 10 November 2021, 07:13:07 UTC |
| e5b57b3 | Ronny Lorenz | 10 November 2021, 06:52:19 UTC | CLEANUP: Uncrustify src/ViennaRNA/utils/svm_utils.c | 10 November 2021, 07:13:07 UTC |
| d50285b | Ronny Lorenz | 10 November 2021, 06:52:18 UTC | CLEANUP: Uncrustify src/ViennaRNA/utils/structure_utils.c | 10 November 2021, 07:13:07 UTC |
| 0d61983 | Ronny Lorenz | 10 November 2021, 06:52:18 UTC | CLEANUP: Uncrustify src/ViennaRNA/utils/msa_utils.c | 10 November 2021, 07:13:07 UTC |
| e72f640 | Ronny Lorenz | 10 November 2021, 06:52:18 UTC | CLEANUP: Uncrustify src/ViennaRNA/utils/higher_order_functions.c | 10 November 2021, 07:13:07 UTC |
| 91b4df5 | Ronny Lorenz | 10 November 2021, 06:52:12 UTC | CLEANUP: Uncrustify src/ViennaRNA/search/BoyerMoore.c | 10 November 2021, 07:13:07 UTC |
| 2fde562 | Ronny Lorenz | 10 November 2021, 06:51:55 UTC | CLEANUP: Uncrustify src/ViennaRNA/params/convert.c | 10 November 2021, 07:13:07 UTC |
