| 9bdedd5 | Ronny Lorenz | 16 April 2019, 10:18:30 UTC | Prepare for release v2.4.12 | 17 April 2019, 10:34:26 UTC |
| 8ba3b73 | Ronny Lorenz | 16 April 2019, 15:19:20 UTC | Use python3.6 instead of python3.4 for EPEL-7 RPM builds | 17 April 2019, 10:34:26 UTC |
| fb985f1 | Ronny Lorenz | 16 April 2019, 13:29:13 UTC | Revert "SWIG: Add Python stringify method for objects of type duplexT" This reverts commit 580b4d6bbbdda9c1d6a93c74fcc1eb1884e726e3. We hold back this change until we figure out what goes wrong in the perl5 interface... | 17 April 2019, 10:34:26 UTC |
| 6ca4414 | Ronny Lorenz | 16 April 2019, 12:22:11 UTC | SWIG: Add MEA implementation to scripting language interface(s) | 17 April 2019, 10:34:26 UTC |
| 8f4ef97 | Ronny Lorenz | 15 April 2019, 12:00:48 UTC | Refactor RNAheat to support multiple input files and parallel input processing | 15 April 2019, 12:00:48 UTC |
| 6cdc6fb | Ronny Lorenz | 15 April 2019, 11:59:44 UTC | Remove ggo_get_temperature() from ggo_get_m_eval() helper macro | 15 April 2019, 11:59:44 UTC |
| f7f7ae8 | Ronny Lorenz | 15 April 2019, 11:57:51 UTC | Revert removal of vrna_move_apply_db() | 15 April 2019, 11:57:51 UTC |
| 4ffc3b5 | Ronny Lorenz | 12 April 2019, 14:01:01 UTC | Include only what's necessary in landscape/neighbor.h | 12 April 2019, 14:01:01 UTC |
| 1781f09 | Ronny Lorenz | 12 April 2019, 14:00:39 UTC | Include only what's necessary in landscape/move.c | 12 April 2019, 14:00:39 UTC |
| 5e284dc | Ronny Lorenz | 12 April 2019, 14:00:01 UTC | Fix header inclusion in landscape/walk.h (again) | 12 April 2019, 14:00:01 UTC |
| 27661bf | Ronny Lorenz | 12 April 2019, 11:56:50 UTC | Restore backward compatibility for including old header walk.h | 12 April 2019, 11:58:01 UTC |
| ca94166 | Ronny Lorenz | 12 April 2019, 11:56:11 UTC | Reduce old API usage in subopt.c | 12 April 2019, 11:58:01 UTC |
| 14025dd | Ronny Lorenz | 12 April 2019, 11:55:38 UTC | Reduce old API usage in snoop.c | 12 April 2019, 11:58:01 UTC |
| 2c2e3b8 | Ronny Lorenz | 12 April 2019, 11:55:16 UTC | Reduce old API usage in plex_functions.c | 12 April 2019, 11:58:01 UTC |
| acfc15e | Ronny Lorenz | 12 April 2019, 11:54:43 UTC | Reduce old API usage in plex.c | 12 April 2019, 11:58:01 UTC |
| 1fae434 | Ronny Lorenz | 12 April 2019, 11:54:06 UTC | Reduce old API usage in part_func_up.c | 12 April 2019, 11:58:01 UTC |
| 021b350 | Ronny Lorenz | 12 April 2019, 11:53:31 UTC | Reduce old API usage in fold_compound.c | 12 April 2019, 11:58:01 UTC |
| 07fa8c0 | Ronny Lorenz | 12 April 2019, 11:53:02 UTC | Reduce old API usage in eval.c | 12 April 2019, 11:58:01 UTC |
| e763161 | Ronny Lorenz | 12 April 2019, 11:52:35 UTC | Reduce old API usage in equilibrium_probs.c | 12 April 2019, 11:58:01 UTC |
| 2b51cce | Ronny Lorenz | 12 April 2019, 11:51:30 UTC | Reduce old API usage in duplex.c | 12 April 2019, 11:58:01 UTC |
| dc9342c | Ronny Lorenz | 12 April 2019, 11:51:04 UTC | Reduce old API usage in cofold.c | 12 April 2019, 11:58:01 UTC |
| 03764fb | Ronny Lorenz | 12 April 2019, 11:50:31 UTC | Reduce old API usage in boltzmann_sampling.c | 12 April 2019, 11:58:01 UTC |
| b29ba11 | Ronny Lorenz | 12 April 2019, 11:50:03 UTC | Reduce old API usage in ali_plex.c | 12 April 2019, 11:58:01 UTC |
| 3f79ca9 | Ronny Lorenz | 12 April 2019, 11:49:12 UTC | Reduce old API usage in LPfold.c | 12 April 2019, 11:58:01 UTC |
| b46a2f9 | Ronny Lorenz | 12 April 2019, 11:48:14 UTC | Reduce old API usage in 2Dpfold.c | 12 April 2019, 11:58:01 UTC |
| e9abd3e | Ronny Lorenz | 12 April 2019, 11:48:04 UTC | Reduce old API usage in 2Dfold.c | 12 April 2019, 11:58:01 UTC |
| 0366e2a | Ronny Lorenz | 12 April 2019, 11:47:05 UTC | Reduce old API usage in utils/msa_utils.c | 12 April 2019, 11:58:01 UTC |
| 0caf4d8 | Ronny Lorenz | 12 April 2019, 11:46:24 UTC | Reduce old API usage in plotting/structures.c | 12 April 2019, 11:58:01 UTC |
| 1bd22dc | Ronny Lorenz | 12 April 2019, 11:45:53 UTC | Reduce old API usage in plotting/alignments.c | 12 April 2019, 11:58:01 UTC |
| d63d253 | Ronny Lorenz | 12 April 2019, 11:44:58 UTC | Fix header inclusion in plotting/RNApuzzler/includes | 12 April 2019, 11:58:01 UTC |
| 152d0c1 | Ronny Lorenz | 12 April 2019, 11:44:11 UTC | Reduce old API usage in loops/multibranch*.c | 12 April 2019, 11:58:01 UTC |
| 082f1dc | Ronny Lorenz | 12 April 2019, 11:43:29 UTC | Reduce old API usage in loops/hairpin*.c | 12 April 2019, 11:57:49 UTC |
| d8ffae8 | Ronny Lorenz | 12 April 2019, 11:43:11 UTC | Reduce old API usage in loops/external*.c | 12 April 2019, 11:43:11 UTC |
| bdf39df | Ronny Lorenz | 12 April 2019, 11:42:15 UTC | Fix header inclusion in landscape/walk.h | 12 April 2019, 11:42:15 UTC |
| 0aca2c2 | Ronny Lorenz | 12 April 2019, 11:41:24 UTC | Reduce old API usage in constraints/SHAPE.c | 12 April 2019, 11:41:24 UTC |
| 5bb8515 | Ronny Lorenz | 12 April 2019, 07:35:53 UTC | Remove old API dependencies in RNAalifold | 12 April 2019, 07:35:53 UTC |
| 0054c87 | Ronny Lorenz | 12 April 2019, 07:35:21 UTC | Remove old API dependencies in RNALalifold | 12 April 2019, 07:35:21 UTC |
| f7be3b0 | Ronny Lorenz | 12 April 2019, 06:48:27 UTC | Remove deprecated API calls from RNAheat | 12 April 2019, 06:48:27 UTC |
| 30ebe03 | Ronny Lorenz | 12 April 2019, 06:47:32 UTC | Update exp_params model details as well when calling vrna_params_reset() | 12 April 2019, 06:47:32 UTC |
| ba6a82e | Ronny Lorenz | 10 April 2019, 07:40:34 UTC | Fix typo in Makefile.am | 10 April 2019, 07:40:34 UTC |
| 580b4d6 | Ronny Lorenz | 09 April 2019, 15:47:52 UTC | SWIG: Add Python stringify method for objects of type duplexT | 09 April 2019, 15:48:40 UTC |
| 8cc1576 | Ronny Lorenz | 09 April 2019, 13:28:57 UTC | Restore backward compatibility for inclusion of neighbor.h | 09 April 2019, 13:28:57 UTC |
| e071227 | Ronny Lorenz | 09 April 2019, 13:27:23 UTC | Merge branch 'dev_fastneighbors' into 'development' Add faster local neighborhood update functions and min-heap based gradient descent walk See merge request rna/viennarna!81 | 09 April 2019, 13:27:23 UTC |
| e0acda8 | Ronny Lorenz | 09 April 2019, 13:22:47 UTC | Use fast heap-based gradient descent implementation in vrna_path_gradient() | 09 April 2019, 13:24:07 UTC |
| 034b9cc | Ronny Lorenz | 09 April 2019, 13:07:30 UTC | Finalize API for vrna_move_neighbor_diff*() functions | 09 April 2019, 13:24:07 UTC |
| bd43315 | Ronny Lorenz | 09 April 2019, 11:12:48 UTC | Remove vrna_move_apply_db() and rename vrna_move_is_deletion() to vrna_move_is_removal() | 09 April 2019, 13:24:07 UTC |
| e52bd13 | Ronny Lorenz | 09 April 2019, 11:11:10 UTC | REFMAN: Add ViennaRNA/landscape to doxygen input directories | 09 April 2019, 13:24:07 UTC |
| 62d46fa | Ronny Lorenz | 08 April 2019, 16:57:03 UTC | Use abstract heap data structure type in fast gradient walk implementation | 08 April 2019, 17:23:02 UTC |
| d727c9e | Ronny Lorenz | 08 April 2019, 16:54:16 UTC | Add pair table argument to vrna_move_compare() function - This is required for future support of shift moves | 08 April 2019, 17:23:02 UTC |
| b625da3 | Ronny Lorenz | 08 April 2019, 15:53:31 UTC | Add an abstract heap implementation with some cool extra features | 08 April 2019, 17:22:55 UTC |
| bb4413b | Ronny Lorenz | 05 April 2019, 16:58:43 UTC | Refactor min-heap based gradient walk | 08 April 2019, 16:59:22 UTC |
| 5fe9957 | Ronny Lorenz | 06 April 2019, 14:28:58 UTC | Start min-heap based neighbor callback implementation for fast gradient walks | 08 April 2019, 16:59:21 UTC |
| f167f1b | Ronny Lorenz | 05 April 2019, 16:58:02 UTC | Fix remaining issues in neighbor callback generation | 08 April 2019, 16:59:21 UTC |
| 9afc779 | Ronny Lorenz | 06 February 2019, 20:38:01 UTC | Report 3 distinct cases for local neighbor generation callback | 08 April 2019, 16:59:20 UTC |
| c1679aa | Ronny Lorenz | 06 April 2019, 14:04:28 UTC | Fix vrna_path() lexicographical ordering | 08 April 2019, 16:59:20 UTC |
| 3ceca35 | Ronny Lorenz | 05 April 2019, 16:57:12 UTC | Add helper functions for vrna_move_t | 08 April 2019, 16:59:20 UTC |
| 01730e1 | Ronny Lorenz | 05 February 2019, 22:25:25 UTC | Move landscape implementations into separate subdirectory - Move the common structure landscape implementations and corresponding header files into subdirectory ViennaRNA/landscape/ - Move vrna_move_t related functions into separate source and header files ViennaRNA/landscape/move.[c,h] | 08 April 2019, 16:59:19 UTC |
| feca39d | Ronny Lorenz | 05 February 2019, 22:31:50 UTC | Start implementing fast structure move application with callback-based local neighbor update | 08 April 2019, 16:59:19 UTC |
| 9ede85e | Ronny Lorenz | 03 April 2019, 13:43:51 UTC | Mark old API of RNA secondary structure layout implementation as deprecated | 03 April 2019, 13:43:51 UTC |
| cbe3c50 | Ronny Lorenz | 03 April 2019, 12:51:07 UTC | Update CHANGELOG.md | 03 April 2019, 12:51:07 UTC |
| c992e60 | Ronny Lorenz | 03 April 2019, 11:58:25 UTC | Merge branch 'dev_rnapuzzler' into 'development' RNApuzzler secondary structure layout algorithm See merge request rna/viennarna!80 | 03 April 2019, 11:58:25 UTC |
| 9f97f85 | Ronny Lorenz | 03 April 2019, 11:50:55 UTC | Update RNAfold/RNAplot help output regarding structure plot layout algorithm | 03 April 2019, 11:50:55 UTC |
| 502a6e3 | Ronny Lorenz | 03 April 2019, 11:34:33 UTC | Add v3.0 API for Naview RNA secondary structure layout algorithm | 03 April 2019, 11:37:11 UTC |
| 200cfbd | Ronny Lorenz | 03 April 2019, 11:34:08 UTC | REFMAN: Add documentation for RNApuzzler implementation | 03 April 2019, 11:37:03 UTC |
| 8d6c2cb | Ronny Lorenz | 03 April 2019, 10:18:04 UTC | Rename vrna_figure_* symbols to vrna_plot_* for consistent v3.0 API | 03 April 2019, 10:18:04 UTC |
| e22a5a0 | Ronny Lorenz | 03 April 2019, 09:40:05 UTC | Create v3.0 API for RNApuzzler/RNAturtle implementation | 03 April 2019, 09:54:07 UTC |
| 9498974 | Ronny Lorenz | 02 April 2019, 17:23:18 UTC | Refactor RNApuzzler sources (again) - Now, all auxiliary implementation files for the RNApuzzler implementation resides in separate .inc files. This finally ensures proper hiding of unnecessary symbols and avoids confusion regarding the inclusion of corresponding header files | 02 April 2019, 18:11:10 UTC |
| 9769a69 | Ronny Lorenz | 02 April 2019, 16:26:41 UTC | Refactor plotting/layouts.c and revert API change to vrna_file_PS_rnaplot_a()... ... which was introduced with the RNApuzzler layout algorithm. - This patch provides a new v3.0 API for most of the RNA secondary structure layout algorithms. Most notably, functions that compute nucleotide coordinates now allocate the required memory themselves to ensure that enough memory is available. | 02 April 2019, 16:26:41 UTC |
| 99ef97b | Ronny Lorenz | 01 April 2019, 15:38:11 UTC | CLEANUP: Uncrustify changed RNApuzzler sources | 02 April 2019, 09:29:58 UTC |
| 62b0751 | Ronny Lorenz | 01 April 2019, 15:04:22 UTC | Rename RNApuzzler .c files to .inc | 02 April 2019, 09:29:52 UTC |
| 64a34d0 | Ronny Lorenz | 11 March 2019, 14:40:27 UTC | Hide unnecessary symbols in RNApuzzler implementation | 02 April 2019, 09:29:48 UTC |
| 1ddeb56 | Ronny Lorenz | 11 March 2019, 14:03:17 UTC | CLEANUP: Uncrustify RNApuzzler implementation | 02 April 2019, 09:29:41 UTC |
| 3233532 | Ronny Lorenz | 11 March 2019, 13:26:07 UTC | Fix allocation of puzzleroptions in structures.c | 02 April 2019, 09:29:40 UTC |
| 2486abd | Daniel Wiegreffe | 04 March 2019, 11:56:03 UTC | bugfix circle calculation, changed some const | 02 April 2019, 09:29:39 UTC |
| efbb747 | Daniel Wiegreffe | 28 February 2019, 19:32:26 UTC | code cleanup and bugfix | 02 April 2019, 09:29:38 UTC |
| 6344a9f | Daniel Wiegreffe | 27 February 2019, 10:55:59 UTC | renamed cfgreader to drawingconfig | 02 April 2019, 09:29:38 UTC |
| bf2ae00 | Daniel Wiegreffe | 27 February 2019, 10:33:33 UTC | removed unnecessary debug stuff and outputs | 02 April 2019, 09:29:37 UTC |
| 91dc573 | Daniel Wiegreffe | 22 February 2019, 14:58:22 UTC | draw modified loops as circles | 02 April 2019, 09:29:36 UTC |
| b0959bc | Daniel Wiegreffe | 17 January 2019, 15:45:01 UTC | update help message | 02 April 2019, 09:29:35 UTC |
| 0cc5814 | Daniel Wiegreffe | 17 January 2019, 15:44:38 UTC | build default puzzleroptions if drawing function is not called by RNAplot | 02 April 2019, 09:29:34 UTC |
| bfe0618 | Daniel Wiegreffe | 17 January 2019, 14:00:03 UTC | fixed binding creation, modified drawing call | 02 April 2019, 09:29:34 UTC |
| 7489927 | Daniel Wiegreffe | 16 January 2019, 10:43:33 UTC | full integration of rnapuzzler | 02 April 2019, 09:29:33 UTC |
| fc24f20 | Daniel Wiegreffe | 15 January 2019, 17:06:50 UTC | wip commit, lots of change due refactoring of the wrapper classes | 02 April 2019, 09:29:32 UTC |
| 6b15907 | Daniel Wiegreffe | 11 January 2019, 14:09:06 UTC | initial rnapuzzler commit, moved code to repo, compiles without interfaces | 02 April 2019, 09:29:31 UTC |
| 4dea939 | Ronny Lorenz | 16 March 2019, 10:09:12 UTC | TESTS: Adapt expected postscript output files to changes in library functions | 02 April 2019, 09:29:30 UTC |
| 59f4e76 | Ronny Lorenz | 15 March 2019, 16:16:21 UTC | Refactor general EPS file structure for plotting functions - The new helper functions in plotting/ps_helpers.inc now allow for a cleaner structure of the EPS output. The header always specifies the necessary things first, followd by some auxiliary comment(s). Then, a dictionary is created and filled with the prolog functions. After that, arbitrary commands may follow. The footer finally closes the dictionary again... | 02 April 2019, 09:29:24 UTC |
| 2c9f93f | Ronny Lorenz | 15 March 2019, 16:12:18 UTC | Rename vrna_annotate_covar_struct() to vrna_annotate_covar_db() - This also adds a new function vrna_annotate_covar_db_extended() that allows for parsing additional bracket types from the consensus structure dot-bracket string. | 02 April 2019, 09:29:24 UTC |
| 8fdccef | Ronny Lorenz | 15 March 2019, 11:07:49 UTC | SWIG: Sanitize alignment plot scripting language interface | 02 April 2019, 09:29:24 UTC |
| 2c58e2c | Ronny Lorenz | 14 March 2019, 11:03:48 UTC | Refactor Alignment plotting implementation - This replaces the function vrna_file_PS_aln_sub() by something that actually displays sub-alignments, the new function vrna_file_PS_aln_slice() that enables one to display a slice of an alignment. Not only doesn't it require to be passed an already sliced alignment, it also allows for adding an offset value that is used to shift the numbers of the ruler. - This commit also deprecates the 'old' API | 02 April 2019, 09:29:23 UTC |
| 5a95b6d | Ronny Lorenz | 11 March 2019, 15:22:52 UTC | Refactor PostScript plotting implementations | 02 April 2019, 09:29:23 UTC |
| 56c201d | Ronny Lorenz | 01 April 2019, 15:36:54 UTC | Update uncrustify.cfg | 01 April 2019, 15:42:19 UTC |
| b4008ad | Ronny Lorenz | 30 March 2019, 09:40:29 UTC | Fix viennarna.spec for OpenSUSE RPM builds | 30 March 2019, 09:40:29 UTC |
| 343787e | Ronny Lorenz | 28 March 2019, 16:14:04 UTC | SWIG: Use SP macro instead of lower-case sp in Perl callback wrappers | 28 March 2019, 16:14:04 UTC |
| 79a459c | Ronny Lorenz | 28 March 2019, 10:21:11 UTC | SWIG: Add pf_smooth global model details variable | 28 March 2019, 10:21:11 UTC |
| 3e4ff52 | Ronny Lorenz | 26 March 2019, 15:26:58 UTC | Update dependencies for Ubuntu/Debian binary packages | 26 March 2019, 15:26:58 UTC |
| 3ddc301 | Ronny Lorenz | 26 March 2019, 14:29:10 UTC | REFMAN: Minor updates for functions exposed through equilibrium_probs.h | 26 March 2019, 14:29:10 UTC |
| 64a24d4 | Ronny Lorenz | 26 March 2019, 14:25:23 UTC | Add function to compute positional entropies | 26 March 2019, 14:25:23 UTC |
| 60dac54 | Ronny Lorenz | 22 March 2019, 12:30:25 UTC | Add --noDP option to RNAfold and RNAalifold to suppress dot-plot output... ... while still computing base pair probability based features such as centroid- or MEA structure. | 22 March 2019, 12:30:25 UTC |
| a646852 | Ronny Lorenz | 14 March 2019, 14:29:13 UTC | SWIG: Add proper constructor for objects of type vrna_ep_t | 14 March 2019, 14:29:55 UTC |
| d676ad8 | Ronny Lorenz | 11 March 2019, 13:40:58 UTC | REFMAN: Fix typo in constraints/hard.h | 11 March 2019, 13:40:58 UTC |
