| 140d3db | Ronny Lorenz | 06 March 2018, 11:59:40 UTC | Prepare for release v2.4.4 | 06 March 2018, 14:39:08 UTC |
| 8d5b665 | Ronny Lorenz | 06 March 2018, 14:02:52 UTC | Fix wrong direction of enclosed base pair in eval_int_loop_comparative() - This resolves a regression introduced in 2bcfbfca1ff85c8beb74836794f9f69d202cd9f8 | 06 March 2018, 14:30:26 UTC |
| d93b98d | Ronny Lorenz | 06 March 2018, 07:33:29 UTC | Do not convert structure part of ligand motif to uppercase in RNAfold.c | 06 March 2018, 07:33:29 UTC |
| 39f7209 | Ronny Lorenz | 05 March 2018, 16:43:37 UTC | Fix annotation for sc-based ligand motifs in RNAfold - This patch fixes bogus annotation for soft-constraint based ligand motif binding predictions in RNAfold. It also removes the function vrna_sc_get_hi_motif() in favor of the new function vrna_sc_ligand_get_all_motifs() from the RNAlib API. | 05 March 2018, 16:48:34 UTC |
| f2c464d | Ronny Lorenz | 27 February 2018, 15:53:00 UTC | Prevent potentially undefined return value in computeFreedInterval() in neighbor.c | 27 February 2018, 15:53:00 UTC |
| dbca377 | Ronny Lorenz | 27 February 2018, 15:49:59 UTC | SWIG: Ignore CPP warnings about unused variables/labels in Python/Python3 interface | 27 February 2018, 15:50:58 UTC |
| db90721 | Ronny Lorenz | 21 February 2018, 15:27:24 UTC | Allow for lowercase letters in ct2db input and add some fall-through comments to make gcc happy | 23 February 2018, 17:00:04 UTC |
| 89c3e3d | Ronny Lorenz | 07 February 2018, 15:39:40 UTC | CLEANUP: Reduce compiler warnings in utils.c | 23 February 2018, 17:00:04 UTC |
| 847b2c2 | Ronny Lorenz | 07 February 2018, 15:39:19 UTC | CLEANUP: Reduce compiler warnings in unstructured_domains.c | 23 February 2018, 17:00:04 UTC |
| 8178be8 | Ronny Lorenz | 07 February 2018, 15:38:50 UTC | CLEANUP: Reduce compiler warnings in svm_utils.c | 23 February 2018, 17:00:04 UTC |
| c6ad816 | Ronny Lorenz | 07 February 2018, 15:38:39 UTC | CLEANUP: Reduce compiler warnings in structure_utils.c | 23 February 2018, 17:00:04 UTC |
| 1f2e899 | Ronny Lorenz | 07 February 2018, 15:38:21 UTC | CLEANUP: Reduce compiler warnings in sequence.c | 23 February 2018, 17:00:03 UTC |
| d0185f7 | Ronny Lorenz | 07 February 2018, 15:38:11 UTC | CLEANUP: Reduce compiler warnings in pertubation_fold.c | 23 February 2018, 17:00:03 UTC |
| 6b244e6 | Ronny Lorenz | 07 February 2018, 15:37:54 UTC | CLEANUP: Reduce compiler warnings in part_func_co.c | 23 February 2018, 17:00:03 UTC |
| 7b80844 | Ronny Lorenz | 07 February 2018, 15:37:38 UTC | CLEANUP: Reduce compiler warnings in part_func.c | 23 February 2018, 17:00:03 UTC |
| 64af16a | Ronny Lorenz | 07 February 2018, 15:37:20 UTC | CLEANUP: Reduce compiler warnings in neighbor.c | 23 February 2018, 17:00:03 UTC |
| 80adca5 | Ronny Lorenz | 07 February 2018, 15:37:08 UTC | CLEANUP: Reduce compiler warnings in move_set.c | 23 February 2018, 17:00:03 UTC |
| 8a56c4e | Ronny Lorenz | 07 February 2018, 15:36:40 UTC | CLEANUP: Reduce compiler warnings in model.c | 23 February 2018, 17:00:03 UTC |
| 56325e0 | Ronny Lorenz | 07 February 2018, 15:36:26 UTC | CLEANUP: Reduce compiler warnings in mfe.c | 23 February 2018, 17:00:03 UTC |
| 48451e7 | Ronny Lorenz | 07 February 2018, 15:36:09 UTC | CLEANUP: Reduce compiler warnings in gquad.h | 23 February 2018, 17:00:03 UTC |
| 9901f18 | Ronny Lorenz | 07 February 2018, 15:35:47 UTC | CLEANUP: Reduce compiler warnings in fold_compound.c | 23 February 2018, 17:00:03 UTC |
| 270eb5a | Ronny Lorenz | 07 February 2018, 15:35:16 UTC | CLEANUP: Reduce compiler warnings in file_utils.c | 23 February 2018, 16:58:31 UTC |
| f3d4206 | Ronny Lorenz | 07 February 2018, 15:34:51 UTC | CLEANUP: Reduce compiler warnings in file_formats_msa.c | 23 February 2018, 16:58:31 UTC |
| cd259ca | Ronny Lorenz | 07 February 2018, 15:34:21 UTC | CLEANUP: Reduce compiler warnings in equilibrium_probs.c | 23 February 2018, 16:58:31 UTC |
| 10b4d58 | Ronny Lorenz | 07 February 2018, 15:34:00 UTC | CLEANUP: Reduce compiler warnings in dp_matrices.c | 23 February 2018, 16:58:31 UTC |
| 27334eb | Ronny Lorenz | 07 February 2018, 15:33:42 UTC | CLEANUP: Reduce compiler warnings in constraints_soft.c | 23 February 2018, 16:58:31 UTC |
| f99be6e | Ronny Lorenz | 07 February 2018, 15:33:16 UTC | CLEANUP: Reduce compiler warnings in constraints_ligand.c | 23 February 2018, 16:58:31 UTC |
| c7d489a | Ronny Lorenz | 07 February 2018, 15:32:49 UTC | CLEANUP: Reduce compiler warnings in constraints_hard.c | 23 February 2018, 16:58:31 UTC |
| bd13d69 | Ronny Lorenz | 07 February 2018, 15:31:57 UTC | CLEANUP: Reduce compiler warnings in constraints_SHAPE.c | 23 February 2018, 16:58:31 UTC |
| dd5665f | Ronny Lorenz | 07 February 2018, 15:31:32 UTC | CLEANUP: Reduce compiler warnings in cofold.c | 23 February 2018, 16:58:31 UTC |
| f4f76c6 | Ronny Lorenz | 07 February 2018, 15:31:12 UTC | CLEANUP: Reduce compiler warnings in boltzmann_sampling.c | 23 February 2018, 16:58:31 UTC |
| 10445b1 | Ronny Lorenz | 07 February 2018, 15:30:52 UTC | CLEANUP: Reduce compiler warnings in alphabet.c | 23 February 2018, 16:58:30 UTC |
| 566ecc0 | Ronny Lorenz | 07 February 2018, 15:30:33 UTC | CLEANUP: Reduce compiler warnings in LPfold.c | 23 February 2018, 16:58:30 UTC |
| dbf9083 | Ronny Lorenz | 07 February 2018, 15:30:09 UTC | CLEANUP: Reduce compiler warnings in 2Dpfold.c | 23 February 2018, 16:58:30 UTC |
| 26e0d02 | Ronny Lorenz | 07 February 2018, 15:29:03 UTC | CLEANUP: Reduce compiler warnings in 2Dfold.c | 23 February 2018, 16:58:30 UTC |
| 54abc83 | Ronny Lorenz | 23 February 2018, 16:45:25 UTC | REFMAN: Add documentation to SWIG wrapper for functions in neighbor.h and walk.h | 23 February 2018, 16:46:44 UTC |
| 23fefcc | Ronny Lorenz | 22 February 2018, 09:02:00 UTC | SWIG: Add neighbor.i | 23 February 2018, 16:46:38 UTC |
| 659643d | Ronny Lorenz | 21 February 2018, 23:30:54 UTC | SWIG: Add walk.i | 23 February 2018, 16:30:08 UTC |
| 3e3b2d1 | Ronny Lorenz | 23 February 2018, 15:16:17 UTC | Add findpath functions that allow for specification of an upper bound for the saddle point | 23 February 2018, 15:16:17 UTC |
| 87ea9fc | Ronny Lorenz | 21 February 2018, 14:32:20 UTC | Fix constraint indices for MB loops in unpaired probability computations of LPfold.c | 21 February 2018, 14:32:20 UTC |
| c8983d7 | Ronny Lorenz | 21 February 2018, 14:30:57 UTC | Merge branch 'development' of krios.tbi.univie.ac.at:rna/viennarna into development | 21 February 2018, 14:30:57 UTC |
| 34c3bba | Ronny Lorenz | 18 February 2018, 17:22:02 UTC | Add exterior_loops_sc_pf.inc to EXTRA_DIST files | 18 February 2018, 17:22:02 UTC |
| cd934a3 | Ronny Lorenz | 18 February 2018, 17:20:52 UTC | Fix CPPFLAGS for configure-time check of Perl interface build capabilities | 18 February 2018, 17:20:52 UTC |
| e8ddf10 | Ronny Lorenz | 08 February 2018, 22:13:50 UTC | SWIG: Ignore nested union warnings | 08 February 2018, 22:13:50 UTC |
| 7a1f145 | Ronny Lorenz | 06 February 2018, 16:27:37 UTC | Minor changes in README - Mostly beautification with Markdown | 06 February 2018, 16:27:37 UTC |
| 3e6f75a | Ronny Lorenz | 06 February 2018, 15:20:55 UTC | Use library functions for pair type retrieval in subopt.c | 06 February 2018, 15:20:55 UTC |
| dc1865b | Ronny Lorenz | 06 February 2018, 15:19:34 UTC | Use library functions for pair type retrieval in mfe_window.c | 06 February 2018, 15:19:34 UTC |
| de0910f | Ronny Lorenz | 06 February 2018, 15:19:07 UTC | Use library functions for pair type retrieval in mfe.c | 06 February 2018, 15:19:07 UTC |
| c3e8fb1 | Ronny Lorenz | 06 February 2018, 15:17:52 UTC | Use library functions for pair type retrieval in equilibrium_probs.c | 06 February 2018, 15:17:52 UTC |
| 57f0ab8 | Ronny Lorenz | 06 February 2018, 15:13:44 UTC | Use library functions for pair type retrieval in cofold.c | 06 February 2018, 15:13:44 UTC |
| 5bb25a3 | Ronny Lorenz | 06 February 2018, 15:12:43 UTC | Use library functions for pair type retrieval in boltzmann_sampling.c | 06 February 2018, 15:12:43 UTC |
| 240016b | Ronny Lorenz | 06 February 2018, 15:10:05 UTC | Use library functions for pair type retrieval in LPfold.c | 06 February 2018, 15:10:05 UTC |
| f9e32e5 | Ronny Lorenz | 06 February 2018, 13:13:04 UTC | Use library functions for pair type retrieval in haipin, interiorloop, and multiloop functions | 06 February 2018, 13:53:37 UTC |
| db5b380 | Ronny Lorenz | 06 February 2018, 13:08:50 UTC | TESTS: Update RNAfold unit tests according to changes in UD output | 06 February 2018, 13:08:50 UTC |
| 400eb16 | Ronny Lorenz | 01 February 2018, 14:18:10 UTC | Change verbose output for sc-motifs in RNAfold - Now, the verbose output prints the two intervals (5' and 3') for interior-loop like motifs, instead of some weird mix of coordinates. - Also, the example section of the RNAfold manpage was updated to reflect this output | 01 February 2018, 14:18:10 UTC |
| 229a9e6 | Ronny Lorenz | 29 January 2018, 17:01:19 UTC | Merge branch 'dev_restruct_eval' into 'development' Restructure Energy Evaluation Interface See merge request rna/viennarna!76 | 29 January 2018, 17:01:19 UTC |
| d204fb2 | Ronny Lorenz | 29 January 2018, 16:22:46 UTC | Add simplified interfaces for energy evaluation with Gquads and circular RNAs - This patch also adds more structure to the Energy evaluation section of the reference manual | 29 January 2018, 16:57:11 UTC |
| cb9c0d7 | Ronny Lorenz | 28 January 2018, 20:17:04 UTC | Add consensus structure counterparts for most energy evaluating functions | 28 January 2018, 20:50:22 UTC |
| 1157830 | Ronny Lorenz | 28 January 2018, 15:50:13 UTC | Separate energy evaluation functions from their wrappers | 28 January 2018, 16:16:12 UTC |
| b68015e | Ronny Lorenz | 25 January 2018, 17:07:31 UTC | Add some missing references in man pages | 25 January 2018, 17:07:31 UTC |
| 88f731f | Ronny Lorenz | 23 January 2018, 18:29:43 UTC | Add some safety measures to sequence.c - Do not try adding sequences if fold_compound is not of type VRNA_FC_TYPE_SINGLE - Free memory for strand information data before allocating new | 23 January 2018, 18:36:17 UTC |
| 2bcfbfc | Ronny Lorenz | 23 January 2018, 18:26:59 UTC | Final fix for SHAPE derived constraints ala Deigan et al. in comparative PF | 23 January 2018, 18:29:12 UTC |
| c705cc3 | Ronny Lorenz | 22 January 2018, 20:39:24 UTC | Fix several SHAPE related things for comparative PF computation - SHAPE data is only stored as pseudo-energies, like we do it for single sequences. Boltzmann factors are pre-computed in the *prepare() step, right before the actual recursions. This finally allows for working stochastic backtracking in RNAalifold with SHAPE support - Fix sequence number in warning when sequence in SHAPE file doesn't exactly match sequence in alignment - Add more data in warning if something seems odd when assigning SHAPE data to sequences in alignment | 22 January 2018, 20:45:52 UTC |
| 06c9f61 | Ronny Lorenz | 17 January 2018, 20:52:59 UTC | Fix bug in eval_int_loop() that prevented propagation of energy evaluation for loops with nick in strands | 17 January 2018, 20:52:59 UTC |
| f78d57d | Ronny Lorenz | 16 January 2018, 10:03:36 UTC | SWIG: fix findpath wrapper - This changes the default behavior of get_path() and path_findpath() to always return native lists of structures along a refolding path. The 'old' C-array pointer hack is therefore removed from now on... | 16 January 2018, 10:03:36 UTC |
| ec785cf | Ronny Lorenz | 13 December 2017, 22:24:01 UTC | Start adding new API for implementation of exterior loop evaluations | 14 December 2017, 13:44:12 UTC |
| 1d8e616 | Ronny Lorenz | 12 December 2017, 18:56:54 UTC | Rip-apart exterior loop recursions for partition function | 14 December 2017, 13:42:18 UTC |
| 4f1181d | Ronny Lorenz | 07 December 2017, 14:09:58 UTC | Remove redundancies in exterior_loop.c and apply some performance tweaks | 14 December 2017, 13:42:18 UTC |
| e619bd9 | Ronny Lorenz | 06 December 2017, 14:02:19 UTC | Some cleanup in exterior_loops.c | 14 December 2017, 13:42:17 UTC |
| aea4ae8 | Ronny Lorenz | 05 December 2017, 21:14:11 UTC | Rip-apart f3 exterior loop (sliding window) recursions for comparative MFE - This also changes the difference in corner-case dangling end contributions between sliding window comparative MFE and global comparative MFE prediction in exterior loops | 14 December 2017, 13:42:17 UTC |
| 7aaf96d | Ronny Lorenz | 01 December 2017, 08:41:41 UTC | Rip-apart exterior loop f3 (sliding window) recursions for single sequence MFE | 14 December 2017, 13:42:17 UTC |
| c38da5a | Ronny Lorenz | 30 November 2017, 16:35:42 UTC | Cleanup exterior loop f5 MFE computations - This also moves the file exterior_loops.inc to exterior_loop_hc.inc since it only contains hard constraints wrapper code anymore. | 14 December 2017, 13:42:17 UTC |
| 061264e | Ronny Lorenz | 30 November 2017, 14:35:27 UTC | Finalize soft constraint wrappers for f5 computations in exterior_loops.c - This now also enables dangles==1||3 for exterior loops in comparative structure prediction (global MFE) mode. | 14 December 2017, 13:42:17 UTC |
| 507341a | Ronny Lorenz | 14 December 2017, 13:35:05 UTC | Use pre-processor macro to disable instead enable backward compatibility | 14 December 2017, 13:35:05 UTC |
| d26c700 | Ronny Lorenz | 14 December 2017, 12:07:24 UTC | Add suggestions for alternatives when using the CPP to warn about deprecated functions | 14 December 2017, 12:07:24 UTC |
| f3421e1 | Ronny Lorenz | 13 December 2017, 23:15:39 UTC | Fix autoconf switch to enable deprecation warnings | 13 December 2017, 23:15:39 UTC |
| 559c820 | Ronny Lorenz | 11 December 2017, 13:03:35 UTC | Add configure-time linker check for python3 extension | 11 December 2017, 13:03:35 UTC |
| 57df6d4 | Ronny Lorenz | 06 December 2017, 15:37:08 UTC | Fix bug in interior-loop like G-quadruplex MFE (single sequence) - Enclosing pair (i,j) was reversed to (j,i) upon backtracing and therefore sometimes failed to find to correct decomposition path. | 06 December 2017, 15:37:08 UTC |
| 9a32c46 | Ronny Lorenz | 29 September 2017, 08:44:04 UTC | REFMAN: Use section tags instead of markdown headers in main.dox - Markdown annotated headings are not converted properly with the current doxyrest pipeline. Instead of <sect1><title> tags, the xml output consists of regular <para><heading> tags that do not enclose the entire following section... | 27 November 2017, 11:48:45 UTC |
| 19c88f4 | Ronny Lorenz | 26 September 2017, 08:23:13 UTC | DOXYGEN: Fix formula environments | 27 November 2017, 11:48:45 UTC |
| 71bc981 | Ronny Lorenz | 17 September 2017, 15:47:53 UTC | DOXYGEN: Heavy re-ordering of the reference manual - We now not only provide detailed modules description, but also add a 'Getting Started' section with some Hello World examples, and additional in-depth sections where we explain the most common concepts, data structures, I/O formats, and utitlities implemented in RNAlib. - We also add more example programs/scripts | 27 November 2017, 11:48:33 UTC |
| c183c3b | Ronny Lorenz | 24 November 2017, 15:28:54 UTC | Some simplifications/fixes for stochastic backtracking with single sequences | 24 November 2017, 15:28:54 UTC |
| a18437d | Ronny Lorenz | 24 November 2017, 15:28:34 UTC | CLEANUP: man/Makefile.am | 24 November 2017, 15:28:34 UTC |
| 3c61f8c | Ronny Lorenz | 10 November 2017, 00:29:07 UTC | Simplify comparative hairpin partition function for circular RNAs | 14 November 2017, 15:26:04 UTC |
| 916203e | Ronny Lorenz | 09 November 2017, 23:58:20 UTC | Re-add comparative MFE for circular RNAs | 14 November 2017, 15:26:03 UTC |
| bec287f | Ronny Lorenz | 11 September 2017, 17:48:18 UTC | Make MFE decomposition great again! - Turns out, removing the redundancy of a separate forward recursion for comparative structure prediction is not a good idea per-se. The single fill_arrays() function in mfe.c was slowed down by almost 50% compared to the previous implementation with two separate fill_array() functions for single sequences and sequence alignemnts, respectively. This patch adds a seemingly stupid switch conditional to allow for better compiler optimizations thereby making the code fast again. | 14 November 2017, 15:26:02 UTC |
| eb6a645 | Ronny Lorenz | 11 September 2017, 11:10:33 UTC | Some more simplifications in exterior_loops.c - Specifically, we introduce default soft constraints wrappers and rip-apart some recursions into smaller functions | 14 November 2017, 15:26:02 UTC |
| a5a0df5 | Ronny Lorenz | 14 November 2017, 12:13:39 UTC | Fix end-of-string null character | 14 November 2017, 15:26:01 UTC |
| 52fccfd | Ronny Lorenz | 08 September 2017, 14:26:28 UTC | UNCRUSTIFY: sequence.[c,h] | 14 November 2017, 13:31:29 UTC |
| df28d2a | Ronny Lorenz | 08 September 2017, 14:12:40 UTC | UNCRUSTIFY: fold.c | 14 November 2017, 13:31:28 UTC |
| bf9bc92 | Ronny Lorenz | 08 September 2017, 14:09:11 UTC | UNCRUSTIFY: part_func.c | 14 November 2017, 13:31:28 UTC |
| 6589a5f | Ronny Lorenz | 08 September 2017, 14:08:40 UTC | UNCRUSTIFY: pf_fold.c | 14 November 2017, 13:31:27 UTC |
| 60c573a | Ronny Lorenz | 08 September 2017, 14:03:04 UTC | SWIG: Include new header 'ViennaRNA/concentrations.h' | 14 November 2017, 13:31:27 UTC |
| 6d371cf | Ronny Lorenz | 08 September 2017, 13:56:57 UTC | Move implementations from part_func_co.c to proper compile units - This eliminates the redundant forward recursion, since it is already covered by the implementation(s) in part_func.c. The concentration computations were moved to a new compile unit 'concentrations.c' and the base pair and dimer probability computations are now located in equilibrium_probs.c where they actually belong. What left in part_func_co.c is a simplified interface wrapper and the backward compatibility wrapper... | 14 November 2017, 13:31:26 UTC |
| bfcb57e | Ronny Lorenz | 08 September 2017, 13:51:35 UTC | Move simplified wrappers and backward compatibility stuff from part_func.c into new file - part_func.c now only contains the basic implementation for global partition function forward recursions. All simplified wrappers and the backward compatibility wrappers can now be found in pf_fold.c | 14 November 2017, 13:31:26 UTC |
| 88df998 | Ronny Lorenz | 08 September 2017, 13:23:18 UTC | Remove redundant forward recursions for comparative global PF computation | 14 November 2017, 13:31:25 UTC |
| 8df13ef | Ronny Lorenz | 07 September 2017, 16:59:52 UTC | Add pf version for circularized interior loop computations to interior_loops_pf.c | 14 November 2017, 13:31:25 UTC |
| 81bd160 | Ronny Lorenz | 07 September 2017, 10:32:37 UTC | Remove redundant forward recursions for comparative global MFE prediction | 14 November 2017, 13:31:24 UTC |
| 9b44bf6 | Ronny Lorenz | 07 September 2017, 10:12:56 UTC | Always initialize strand information in vrna_fold_compound_t - We need to initialize at least the strand_number field even when processing a vrna_fold_compound_t of type VRNA_FC_TYPE_COMPARATIVE | 14 November 2017, 13:31:23 UTC |
| 84f56c5 | Ronny Lorenz | 01 September 2017, 17:21:39 UTC | Make init of default hard constraints in *_loops less error-prone - For that purpose, we introduce some helper functions that prepare the default hard constraint data structure and return the corresponding default hard constraint evaluation function | 14 November 2017, 13:31:23 UTC |
