| 11e29fc | Ronny Lorenz | 27 September 2018, 13:17:39 UTC | Fix .travis.yml to unpacka libsvm-3.23.tar.gz | 27 September 2018, 13:18:30 UTC |
| 42bc6ac | Ronny Lorenz | 27 September 2018, 12:44:39 UTC | Merge tag 'v2.4.10' This is version 2.4.10 | 27 September 2018, 12:44:39 UTC |
| b072585 | Ronny Lorenz | 26 September 2018, 12:45:53 UTC | Prepare for release of version 2.4.10 | 26 September 2018, 14:42:02 UTC |
| fcbecbf | Ronny Lorenz | 26 September 2018, 14:40:56 UTC | Resolve some remaining unused variable warnings in libRNA | 26 September 2018, 14:41:57 UTC |
| 851f6cf | Ronny Lorenz | 26 September 2018, 14:39:31 UTC | Fix signedness issue for comparative G-Quadruplex prediction functions in gquad.h | 26 September 2018, 14:41:57 UTC |
| 49487c1 | Ronny Lorenz | 26 September 2018, 14:38:52 UTC | Fix index error in subopt.c | 26 September 2018, 14:41:57 UTC |
| fd9f8e9 | Ronny Lorenz | 26 September 2018, 12:45:35 UTC | Update libsvm to version 3.23 | 26 September 2018, 12:45:35 UTC |
| e03ac4a | Ronny Lorenz | 26 September 2018, 11:26:55 UTC | Add hard constraints warning for base pairs that violate the min_loop_size of the model | 26 September 2018, 11:26:55 UTC |
| ca21e87 | Ronny Lorenz | 19 September 2018, 15:04:25 UTC | REFMAN: Some updates in scripting language interface overview page | 19 September 2018, 15:04:25 UTC |
| c09ec10 | Ronny Lorenz | 19 September 2018, 15:01:03 UTC | Remove VRNA_GQUAD_MISMATCH_PENALTY and VRNA_GQUAD_MISMATCH_NUM_ALI macros - They are replaced by global variables in params/default.c and new attributes gquadLayerMismatch, expgquadLayerMismatch, and gquadLayerMismatchMax in the parameter data structures `vrna_param_t` and `vrna_exp_param_t`. | 19 September 2018, 15:01:03 UTC |
| c529837 | Ronny Lorenz | 29 August 2018, 17:57:49 UTC | Add G-Quadruplex prediction support for comparative partition function - This also changes G-quad-enclosing loop length determination to new alifold scheme, i.e. elimination of gap characters whenever sequence lengths need to be determined. This also accounts for the linker lengths within the G-Quadruplex. | 10 September 2018, 15:39:56 UTC |
| 06ba21b | Ronny Lorenz | 30 August 2018, 16:27:41 UTC | Restore default function of '|' symbol in dot-bracket hard constraints - These constraints were ignored since version 2.2.0 unless the --enforceConstraint option was set. However, RNAfold < 2.2.0 used to add a bonus energy term for each base pair that complied with the constraint. We now always apply the '|' constraint as 'must not be unpaired', i.e. as if the --enforceConstraint option was set. | 30 August 2018, 16:27:41 UTC |
| 7f41238 | Ronny Lorenz | 29 August 2018, 15:28:05 UTC | Use full hard constraints matrix in equilibrium_probs.c and... ... merge single sequence and comparative base pair probability computations | 29 August 2018, 15:28:05 UTC |
| ff3b8ff | Ronny Lorenz | 23 August 2018, 09:39:21 UTC | Use full hard constraints matrix in subopt.c | 28 August 2018, 12:49:33 UTC |
| 12ab20c | Ronny Lorenz | 23 August 2018, 09:38:59 UTC | Use full hard constraints matrix in part_func.c | 28 August 2018, 12:49:33 UTC |
| c9ca626 | Ronny Lorenz | 23 August 2018, 09:38:23 UTC | Use full hard constraints matrix in mfe.c | 28 August 2018, 12:49:33 UTC |
| 34b2871 | Ronny Lorenz | 23 August 2018, 09:35:49 UTC | Use full hard constraints matrix in cofold.c | 28 August 2018, 12:49:33 UTC |
| 51f9b4c | Ronny Lorenz | 23 August 2018, 09:35:21 UTC | Use full hard constraints matrix in Boltzmann sampling | 28 August 2018, 12:49:33 UTC |
| 6a083be | Ronny Lorenz | 22 August 2018, 16:34:10 UTC | Use full hard constraints matrix in MFE/PF loop decompositions | 28 August 2018, 12:49:27 UTC |
| 2a003b6 | Ronny Lorenz | 22 August 2018, 13:29:16 UTC | Use full hard constraints matrix in Maximum Matching implementation | 28 August 2018, 12:26:24 UTC |
| e3dbe31 | Ronny Lorenz | 22 August 2018, 13:23:49 UTC | Add full hard constraints matrix - ...in contrast to the already existing upper-triangular. We do this in the hope to achieve better cache coherence upon access of individual elements in the corresponding recursion steps. | 28 August 2018, 12:26:24 UTC |
| f9b5082 | Ronny Lorenz | 28 August 2018, 12:25:30 UTC | Factor out pair decomposition in part_func.c | 28 August 2018, 12:25:30 UTC |
| 8598563 | Ronny Lorenz | 24 August 2018, 16:47:34 UTC | Further refactorization in equilibrium_probs.c | 27 August 2018, 14:41:18 UTC |
| 96febcd | Ronny Lorenz | 24 August 2018, 13:42:03 UTC | CLEANUP: Uncrustify equilibrium_probs.c | 24 August 2018, 13:44:32 UTC |
| cc71de2 | Ronny Lorenz | 21 August 2018, 11:30:01 UTC | Refactor equilibrium_probs.c | 24 August 2018, 13:41:14 UTC |
| e890845 | Ronny Lorenz | 26 July 2018, 14:55:53 UTC | Add functions to set auxiliary grammar extension rules | 24 August 2018, 11:39:00 UTC |
| ff6c431 | Ronny Lorenz | 24 August 2018, 11:36:36 UTC | Update README.md, INSTALL and remove INSTALL.configure | 24 August 2018, 11:36:57 UTC |
| 817079a | Ronny Lorenz | 22 August 2018, 10:10:57 UTC | AUTOTOOLS: Add configure-time check for -ftree-vectorize compile flag - ... and clean-up some remnants in m4 code base | 22 August 2018, 10:10:57 UTC |
| d7bc7d8 | Ronny Lorenz | 22 August 2018, 10:10:23 UTC | SWIG: Add wrapper for maximum matching implementation | 22 August 2018, 10:10:23 UTC |
| e404a29 | Ronny Lorenz | 22 August 2018, 10:08:53 UTC | Add faster (cache-optimized) version of Nussinov Maximum Matching algorithm | 22 August 2018, 10:08:53 UTC |
| ca096fa | Ronny Lorenz | 20 August 2018, 11:57:54 UTC | Fix subopt backtracking with unusually high delta energies (>=INF) | 20 August 2018, 11:57:54 UTC |
| f30eeec | Ronny Lorenz | 06 August 2018, 09:14:31 UTC | Fix output-filename issue with binary opening energies in RNAplfold | 06 August 2018, 09:14:31 UTC |
| 22844a7 | Ronny Lorenz | 30 July 2018, 15:37:43 UTC | Fix broken SSE4.1 support for multibranch loop MFE computation | 30 July 2018, 15:37:43 UTC |
| d190583 | Ronny Lorenz | 13 July 2018, 19:29:39 UTC | SWIG: Fix behavior of fold_compound's subopt() method when writing to file | 13 July 2018, 19:29:39 UTC |
| 5880600 | Ronny Lorenz | 12 July 2018, 09:19:42 UTC | Merge tag 'v2.4.9' into development This is version 2.4.9 | 12 July 2018, 09:19:42 UTC |
| 34d23a0 | Ronny Lorenz | 12 July 2018, 09:19:29 UTC | Merge tag 'v2.4.9' This is version 2.4.9 | 12 July 2018, 09:19:29 UTC |
| 97ffeb4 | Ronny Lorenz | 11 July 2018, 09:28:23 UTC | Prepare for release v2.4.9 | 12 July 2018, 08:56:55 UTC |
| a493ae4 | Ronny Lorenz | 11 July 2018, 06:49:21 UTC | Fix publication date in README.md | 11 July 2018, 06:49:54 UTC |
| b399194 | Ronny Lorenz | 10 July 2018, 20:49:10 UTC | Slight adaptations to .gitignore files | 11 July 2018, 06:49:54 UTC |
| dd93afc | Ronny Lorenz | 10 July 2018, 20:48:24 UTC | Remove Readseq related lines as it has been removed from the package some time ago | 11 July 2018, 06:49:54 UTC |
| 5d165b9 | Ronny Lorenz | 10 July 2018, 20:28:45 UTC | Use markdown syntax in CHANGELOG.md - And add changes to previous release up to this commit | 11 July 2018, 06:49:50 UTC |
| 5eeb2eb | Ronny Lorenz | 10 July 2018, 20:22:52 UTC | Rename ChangeLog to CHANGELOG.md | 10 July 2018, 20:22:52 UTC |
| 2ed711b | Ronny Lorenz | 10 July 2018, 20:12:02 UTC | Remove implicit exit() call for global MFE backtracking functions | 10 July 2018, 20:12:02 UTC |
| 50175d3 | Ronny Lorenz | 10 July 2018, 16:34:21 UTC | Warn on unsatisfiable hard constraints from dot-bracket string - The programs RNAfold and RNAcofold used to warn on unsatisfiable hard constraints, if they where read from constraints- or command files. Now, these programs and RNAalifold also raise the same warning if a provided dot-bracket string results in an empty solution space. | 10 July 2018, 16:34:21 UTC |
| b99f885 | Ronny Lorenz | 10 July 2018, 16:33:19 UTC | Fix potential errors with hard constraints in MFE stack energy evaluation | 10 July 2018, 16:33:19 UTC |
| 0432034 | Ronny Lorenz | 10 July 2018, 12:51:12 UTC | Print correct message to quit interactive mode in RNALalifold, RNAalifold, RNAeval, and RNAplot with MSA input | 10 July 2018, 12:52:50 UTC |
| fec433d | Ronny Lorenz | 10 July 2018, 12:50:25 UTC | Add short option -a as equivalent for --msa to RNAeval and RNAplot | 10 July 2018, 12:52:40 UTC |
| 7883bb5 | Ronny Lorenz | 10 July 2018, 12:37:03 UTC | Fix TTY batch input of multiple sequence alignments - The programs RNAalifold, RNALalifold, RNAeval, and RNAplot allow for multiple sequence alignment input (of various formats). Also, they allow for multiple alignments to run in batch mode, which works fine if input is read from file or is piped-in from stdin. In interactive mode, however, the programs stopped processing after the first alignment. As this was not the expected behavior, this is fixed now. | 10 July 2018, 12:52:24 UTC |
| 6d24045 | Ronny Lorenz | 10 July 2018, 12:13:43 UTC | Be more restrictive when parsing SS_cons line from Stockholm 1.0 input - Some Stockholm files seem to contain entries like #=GC SS_cons2 which also matched our checks for #=GC SS_cons. Consequently, these line where accidentally merged. We now explicitly parse only lines of the form #=GC SS_cons with at least one whitespace after the SS_cons. | 10 July 2018, 12:52:14 UTC |
| 427339a | Ronny Lorenz | 10 July 2018, 10:00:22 UTC | Merge branch 'user-contrib' into development | 10 July 2018, 10:00:22 UTC |
| f0d0c60 | Ronny Lorenz | 10 July 2018, 09:51:30 UTC | Allow for passing dot-bracket strings with '&' strand-end identifier to simple vrna_eval_* functions | 10 July 2018, 09:51:30 UTC |
| 89c0ab7 | Ronny Lorenz | 10 July 2018, 09:44:18 UTC | Merge pull request #36 from martin-mann/patch-4 docu update | 10 July 2018, 09:44:18 UTC |
| ab68c52 | Martin Raden | 10 July 2018, 08:34:09 UTC | docu update correcting bppm switch docu in V3 API function | 10 July 2018, 08:34:09 UTC |
| 62b98f8 | Ronny Lorenz | 09 July 2018, 16:14:20 UTC | Add missing soft constraints to Boltzmann sampling for single RNA sequences | 09 July 2018, 16:14:20 UTC |
| 1788e78 | Ronny Lorenz | 09 July 2018, 14:46:46 UTC | Enable -g option for G-Quadruplex support in RNAheat | 09 July 2018, 14:46:46 UTC |
| 178c8d2 | Ronny Lorenz | 09 July 2018, 14:34:00 UTC | Enable verbose output for G-Quadruplex correction in comparative vrna_eval_* functions | 09 July 2018, 14:34:00 UTC |
| 6f23659 | Ronny Lorenz | 09 July 2018, 14:22:10 UTC | Pass-through G-Quadruplex annotation from WUSS format in vrna_db_from_WUSS() - This patch simply passes through the '++' stretches from the input WUSS format, if they are present and actually form a valid G-Quadruplex. | 09 July 2018, 14:22:10 UTC |
| 31aaf5a | Ronny Lorenz | 08 July 2018, 09:33:07 UTC | Update --help output for RNALalifold, RNAalifold, RNAcofold, RNAeval, RNAfold, and RNAplot | 08 July 2018, 09:33:07 UTC |
| 845a0ef | Ronny Lorenz | 07 July 2018, 21:35:56 UTC | Fix warning message when RNAplot is called with -j parameter but build without pthreads | 07 July 2018, 21:35:56 UTC |
| 31def9f | Ronny Lorenz | 07 July 2018, 16:52:39 UTC | Adapt RNAalifold, RNALalifold, and RNAplot --help output for non-wrapped aligment output | 07 July 2018, 18:01:49 UTC |
| 9920955 | Ronny Lorenz | 07 July 2018, 16:50:19 UTC | Allow for disabling alignment wrapping in vrna_file_PS_aln* functions | 07 July 2018, 16:53:41 UTC |
| 33712e2 | Ronny Lorenz | 07 July 2018, 16:33:45 UTC | Enable MSA input, multiple input files, and parallel batch processing for RNAplot - RNAplot now allows for MSA input (Stockholm 1.0 format). Besides secondary structure plots that may be color annotated by covariance of the base pairs in the consensus structure, RNAplot also allows for colored alignment EPS file output as available in RNAalifold and RNALalifold - Additionally, RNAplot now allows for multiple input files, and parallel processing of batch input | 07 July 2018, 16:53:36 UTC |
| df10000 | Ronny Lorenz | 07 July 2018, 16:33:04 UTC | Adapt usage string in --help output of RNAeval | 07 July 2018, 16:33:04 UTC |
| 50780a6 | Ronny Lorenz | 07 July 2018, 16:32:19 UTC | Fix (position) ruler string in EPS alignment plots | 07 July 2018, 16:32:19 UTC |
| 005d2b6 | Ronny Lorenz | 06 July 2018, 18:46:12 UTC | Merge branch 'dev_eval_comparative' into 'development' Add MSA processing capabilities to RNAeval See merge request rna/viennarna!77 | 06 July 2018, 18:46:12 UTC |
| f7a647d | Ronny Lorenz | 06 July 2018, 18:24:25 UTC | Add some sequence alignment specific parameters to RNAeval - This adds parameters to change the model settings for comparative structure energy evaluation, such as covariance score weighting, ribosum scoring, etc. - This commit also adds parallel processing to RNAeval, similar to that already available with RNAfold, RNAalifold, etc. | 06 July 2018, 18:38:56 UTC |
| 99ef54c | Ronny Lorenz | 06 July 2018, 17:11:19 UTC | Use vrna_eval_structure_cstr() in RNAeval - Now, all RNAeval output is collected on-the-fly and printed only to stdout or whatever file stream whenever it is time to do so. | 06 July 2018, 17:11:19 UTC |
| dd03b2b | Ronny Lorenz | 06 July 2018, 17:09:35 UTC | Use vrna_cstr_t for collecting output internally in eval.c - This also adds a function vrna_eval_structure_cstr() that allows for passing a vrna_cstr_t pointer that collects energy evaluation output from external programs. | 06 July 2018, 17:09:35 UTC |
| ee9132f | Ronny Lorenz | 06 July 2018, 17:08:31 UTC | Add vrna_cstr_print_eval_* functions | 06 July 2018, 17:08:31 UTC |
| a8055fe | Ronny Lorenz | 06 July 2018, 15:10:01 UTC | Add Stockholm input file processing capability to RNAeval - Still, MSA input for RNAeval can only be Stockholm 1.0 with SS_cons line and no SHAPE reactivity data. | 06 July 2018, 15:34:53 UTC |
| 5cfae3f | Ronny Lorenz | 06 July 2018, 14:08:34 UTC | Refactor RNAeval to allow for multiple input files - This is the first step towards a more flexible RNAeval that will be capable to process records from multiple files (in parallel). Also, the first steps are done to enable processing of multiple sequence alignment input. - To provide full backward compatibility, the vrna_eval_* functions need to be extended to allow for vrna_cstr_t input instead of FILE*. Otherwise, verbose output, i.e. individual loop energies per loop, are printed out-of-order with respect to the FASTA header, sequence, and dot-bracket structure string. | 06 July 2018, 14:08:34 UTC |
| ce70b55 | Ronny Lorenz | 03 July 2018, 16:20:25 UTC | Include base pair soft constraints in Boltzmann sampling for single sequences | 03 July 2018, 16:20:25 UTC |
| 6f2e991 | Ronny Lorenz | 03 July 2018, 16:16:50 UTC | Fix wrong applicaton of base pair soft constraints for partition function computations - We usually store constraints in container-like data structures and retrieve the actual contributions just before recursion start. The function responsible to prepare base pair soft constraints for global partition function unfortunately stored the total constraints per pair using iindx, while jindx was required! | 03 July 2018, 16:16:50 UTC |
| 73257d9 | Ronny Lorenz | 03 July 2018, 14:10:31 UTC | Speed-up backward compatibility layer for eval_wrappers.c | 03 July 2018, 14:10:31 UTC |
| 9b12f1a | Ronny Lorenz | 03 July 2018, 14:06:06 UTC | Fix wrong order of function arguments for vrna_path_findpath_saddle_ub() in vrna_path_findpath_ub() - ... and speed-up backward compatibility layer for find_path.c functions | 03 July 2018, 14:10:14 UTC |
| e1e314b | Ronny Lorenz | 23 June 2018, 12:54:37 UTC | Merge tag 'v2.4.8' into user-contrib This is version 2.4.8 | 23 June 2018, 12:54:37 UTC |
| 1f64e87 | Ronny Lorenz | 22 June 2018, 21:38:04 UTC | Prepare for release of v2.4.8 | 23 June 2018, 11:16:10 UTC |
| dc44af9 | Ronny Lorenz | 22 June 2018, 20:51:35 UTC | Revert "Limit unpaired probability/opening energie precision to 6 digits after decimal point" This reverts commit ef00c1eb4ed84b1cc9a3aefa4784ee7944cbd35f. | 22 June 2018, 20:51:35 UTC |
| ac45b44 | Ronny Lorenz | 22 June 2018, 20:48:59 UTC | Fix unpaired probability computation in LPfold.c - Internal loop contributions where not all taken into account. This mistake seems to have existed ever since version 1.8.x. Now, all internal loops up to MAXLOOP length are taken into account properly. | 22 June 2018, 20:48:59 UTC |
| ef00c1e | Ronny Lorenz | 22 June 2018, 14:36:12 UTC | Limit unpaired probability/opening energie precision to 6 digits after decimal point - A precision of 7 digits sometimes produced weird 'almost 1' output for cases where the output should have been exactly 1 (and was in the internal double precision arrays). This hopefully doesn't break any pipelines that rely on unpaired probability output... | 22 June 2018, 14:36:12 UTC |
| 2882d6a | Ronny Lorenz | 22 June 2018, 10:37:41 UTC | Move sliding-window MFE implementation into separate object file mfe_window_wrappers.o - Otherwise, linking against libRNA.a and requiring anything from mfe_wrappers.o would pull C++ dependencies as well. Though, Link Time Optimization would probably kick that dependency out again... | 22 June 2018, 11:15:32 UTC |
| 56e5cec | Ronny Lorenz | 21 June 2018, 15:52:10 UTC | Merge branch 'fixRNAforester' of github.com:s-will/ViennaRNA into development | 21 June 2018, 15:52:10 UTC |
| 95041ca | Ronny Lorenz | 21 June 2018, 14:51:18 UTC | TESTS: Add RNAalifold special feature tests | 21 June 2018, 14:51:18 UTC |
| 64d6825 | Ronny Lorenz | 21 June 2018, 14:33:22 UTC | Fix several out-of-bounds access cases in eval.c | 21 June 2018, 14:34:20 UTC |
| f938fce | Sebastian Will | 21 June 2018, 13:28:18 UTC | Fix compilation of RNAforester - RNAforester used dynamic exception specification, which are depracted since C++11 and invalid since C++17. Such specs were simply removed. - fix catch of polymorphic exception by value (should be by ref), which caused a warning, but did not have other consequences | 21 June 2018, 13:31:41 UTC |
| afd45be | Ronny Lorenz | 21 June 2018, 13:19:46 UTC | Fix comparative external interior loop (circular) partition function computation - Here we actually fix two issues, one where the Boltzmann factor of the loop energy was erroneously multiplied to alignment column variable l, and a second, where loop lengths of the individual sequences in the alignment did overwrite the corresponding column-based loop length variables. | 21 June 2018, 13:23:29 UTC |
| faf79c5 | Ronny Lorenz | 21 June 2018, 13:17:27 UTC | Allocate n + 2 pair table items for structure of length n - It seems, there are some parts in the library that by default access outside sequence length range at position n + 1 (and usually expect to encounter a 0 at this position). | 21 June 2018, 13:17:27 UTC |
| b1d6019 | Ronny Lorenz | 21 June 2018, 13:16:17 UTC | Use memcpy() instead strcat() in io/file_formats.c io/file_formats_msa.c and io/io_utils.c | 21 June 2018, 13:16:17 UTC |
| 5c39d6c | Ronny Lorenz | 21 June 2018, 09:37:21 UTC | SWIG: Fix false-positive use of uninitialized value in Python3/file_py3.i | 21 June 2018, 09:37:21 UTC |
| 44d7083 | Ronny Lorenz | 21 June 2018, 09:37:10 UTC | CLEANUP: Removed unused variables/functions in Utils/ct2db.c | 21 June 2018, 09:37:10 UTC |
| 3b32ae5 | Ronny Lorenz | 21 June 2018, 09:36:21 UTC | CLEANUP: Removed unused variables/functions in RNAup.c | 21 June 2018, 09:36:21 UTC |
| 6863a8e | Ronny Lorenz | 21 June 2018, 09:36:21 UTC | CLEANUP: Removed unused variables/functions in RNAsubopt.c | 21 June 2018, 09:36:21 UTC |
| c3771e2 | Ronny Lorenz | 21 June 2018, 09:36:21 UTC | CLEANUP: Removed unused variables/functions in RNAplot.c | 21 June 2018, 09:36:21 UTC |
| bf49b3a | Ronny Lorenz | 21 June 2018, 09:36:21 UTC | CLEANUP: Removed unused variables/functions in RNAplfold.c | 21 June 2018, 09:36:21 UTC |
| 6eb1d62 | Ronny Lorenz | 21 June 2018, 09:36:20 UTC | CLEANUP: Removed unused variables/functions in RNApdist.c | 21 June 2018, 09:36:20 UTC |
| 830e2a9 | Ronny Lorenz | 21 June 2018, 09:36:20 UTC | CLEANUP: Removed unused variables/functions in RNAdistance.c | 21 June 2018, 09:36:20 UTC |
| 6f69c60 | Ronny Lorenz | 21 June 2018, 09:36:20 UTC | CLEANUP: Removed unused variables/functions in RNALfold.c | 21 June 2018, 09:36:20 UTC |
| 4fa4667 | Ronny Lorenz | 21 June 2018, 09:36:20 UTC | CLEANUP: Removed unused variables/functions in RNALalifold.c | 21 June 2018, 09:36:20 UTC |
| a9506d5 | Ronny Lorenz | 21 June 2018, 09:34:11 UTC | CLEANUP: Removed unused variables/functions in plotting/probabilities.c | 21 June 2018, 09:34:11 UTC |
| e8e20aa | Ronny Lorenz | 20 June 2018, 16:13:15 UTC | Fix tty input detection in RNAcofold - RNAcofold used to check whether `stdin` is an interactive terminal to decide whether or not additional output may be printed for the user. Now, we check the actual input which may be file streams as well. | 20 June 2018, 16:13:15 UTC |
