| 6d68832 | Ronny Lorenz | 01 September 2016, 17:45:17 UTC | Minor changes in Changelog file | 01 September 2016, 17:45:17 UTC |
| 43107b8 | Ronny Lorenz | 01 September 2016, 17:44:37 UTC | Change the way we determine if the compiler can deal with C11 features we use | 01 September 2016, 17:44:37 UTC |
| 6e9b858 | Ronny Lorenz | 01 September 2016, 09:48:19 UTC | Update packaging/debian/changelog | 01 September 2016, 09:48:19 UTC |
| 30b992b | Ronny Lorenz | 31 August 2016, 17:00:19 UTC | Remove -std=c++11 since C++ doesn't support unnamed structs in any known standard - However, g++ and clang support them | 31 August 2016, 17:00:19 UTC |
| 7efe4e2 | Ronny Lorenz | 31 August 2016, 16:16:55 UTC | Silence some compiler warnings | 31 August 2016, 16:16:55 UTC |
| dd24a51 | Ronny Lorenz | 31 August 2016, 16:00:11 UTC | Bump version to 2.2.9 | 31 August 2016, 16:00:11 UTC |
| a09c69b | Ronny Lorenz | 31 August 2016, 14:33:58 UTC | Really force no TTY colors when build for Windows, and cleanup of gengetopt files | 31 August 2016, 14:33:58 UTC |
| 4c232d9 | Ronny Lorenz | 30 August 2016, 22:07:41 UTC | Disable TTY color for MS Windows - cmd.exe doesn't support ANSI codes | 30 August 2016, 22:07:41 UTC |
| 639be5e | Ronny Lorenz | 30 August 2016, 20:30:33 UTC | Make RNAsubopt colorful and add option to print free energy for Boltzmann samples | 30 August 2016, 20:30:33 UTC |
| 1e34ea8 | Ronny Lorenz | 30 August 2016, 20:28:40 UTC | Add function subopt function that calls a callback for each generated structure instead of printing to some filepointer | 30 August 2016, 20:28:40 UTC |
| ab520d2 | Ronny Lorenz | 30 August 2016, 16:42:27 UTC | Fix SHAPE reactivity incorporation in RNAalifold and colorize its subopt output | 30 August 2016, 16:42:27 UTC |
| 0f27767 | Ronny Lorenz | 30 August 2016, 11:14:53 UTC | Add commandline parameters and colored output to RNAcofold - provide commandline parameters to manipulate input IDs - Use colored output whenever possible | 30 August 2016, 11:14:53 UTC |
| 9b2bbd5 | Ronny Lorenz | 30 August 2016, 11:14:25 UTC | Remove bogus comment in RNAfold.c | 30 August 2016, 11:14:25 UTC |
| b40661c | Ronny Lorenz | 30 August 2016, 11:13:25 UTC | Raise error on empty input in RNAalifold | 30 August 2016, 11:13:25 UTC |
| a61ffdf | Ronny Lorenz | 30 August 2016, 11:12:19 UTC | Differentiate between empty alignments (no sequences) and no records in file_formats_msa.c | 30 August 2016, 11:12:19 UTC |
| f803e44 | Ronny Lorenz | 30 August 2016, 10:43:27 UTC | Add colored output for table data | 30 August 2016, 10:43:27 UTC |
| 2d0f1a1 | Ronny Lorenz | 29 August 2016, 19:25:21 UTC | Do not attempt to free string constants in RNAfold.c | 29 August 2016, 19:25:21 UTC |
| c7427df | Ronny Lorenz | 29 August 2016, 17:40:24 UTC | Add commandline parameters to RNAfold to enable modification of sequence IDs | 29 August 2016, 17:42:10 UTC |
| 2d4ef03 | Ronny Lorenz | 29 August 2016, 06:05:12 UTC | Make RNAfold colorful | 29 August 2016, 17:42:08 UTC |
| 5480039 | Ronny Lorenz | 29 August 2016, 12:25:45 UTC | Make RNAalifold colorful | 29 August 2016, 17:42:05 UTC |
| 492d1c7 | Ronny Lorenz | 28 August 2016, 12:06:52 UTC | Add tons of new command line parameters to RNAalifold - parameters to manipulate alignment ID generation - parameter to enable usage of SS_cons entry as constraint | 29 August 2016, 17:41:54 UTC |
| e7142b0 | Ronny Lorenz | 28 August 2016, 19:09:14 UTC | Various changes in warning messages coming from library functions - corrected warnings, errors, and info messages in file_formats_msa.c - more human friendly warnings in constraints_hard.c | 29 August 2016, 14:04:09 UTC |
| b9057b3 | Ronny Lorenz | 28 August 2016, 19:08:46 UTC | Enable colored output to terminal in utils.c - We have 3 messaging functions, vrna_message_error(), vrna_message_warning(), and vrna_message_info() that from now on use the colors red, magenta, and blue if the output is printed to a TTY - The function that prints the 'input sequence data' is also colored now - An include src/bin/color_output.inc allows to easily use colored output for our executable programs - Colored TTY output can be deactivated at configure time | 29 August 2016, 14:04:00 UTC |
| 6568ec5 | Ronny Lorenz | 28 August 2016, 12:05:32 UTC | Fix potential memory leak in file_formats_msa.c - Some Stockholm files have multiple SS_cons entries. This patch fixes a memory leak where previously found secondary structures would have been lost | 29 August 2016, 12:52:01 UTC |
| 81b5fee | Ronny Lorenz | 27 August 2016, 17:44:32 UTC | Enable PS_color_dot_plot() to deal with sequence names longer than 30 characters | 29 August 2016, 12:51:43 UTC |
| d354e3d | Ronny Lorenz | 27 August 2016, 17:42:19 UTC | Update scale and expMLbase in pf matrices upon call of vrna_exp_params_rescale() only if matrices are present - This also makes vrna_exp_params_rescale() polymorphic | 29 August 2016, 12:34:39 UTC |
| 2c4ef2b | Ronny Lorenz | 26 August 2016, 14:22:41 UTC | Fix multiloop free energy issue for comparative MFE - base pairs within a multiloop had wrong orientation since moving ML MFE code into multibranch_loops.c - index ij was wrong | 29 August 2016, 12:33:57 UTC |
| 117d121 | Ronny Lorenz | 26 August 2016, 09:41:09 UTC | Add parser for MAF formatted MSA files and include them in RNAalifold | 26 August 2016, 10:10:08 UTC |
| c355401 | Ronny Lorenz | 26 August 2016, 05:45:29 UTC | Fix behavior of vrna_file_msa_read_record() when supplied multiple formats - Make Stockholm parser static - Cleanup some MSA parser code - Add documentation for vrna_msa_read_record() | 26 August 2016, 05:45:29 UTC |
| ade7bc5 | Ronny Lorenz | 25 August 2016, 17:07:25 UTC | Finalized initial implementation of MSA parsers for different file formats - The parser implementations are located in file_formats_msa.c - RNAalifold now defaults to ClustalW formatted input (again) in interactive mode and when data is read directly from TTY. The expected input format can be specified via commandline parameter --input-format. If the alignment is read from file, the default is to guess the MSA input format and select the parser automagically. - From now on, RNAalifold is totally unrestricted in terms of number of sequences in the alignment. Available memory is the only limit here. TODO: - Stockholm format allows for multiple alignments within a single file. The parser implementations already allow for record extraction, so RNAalifold only requires a simple change to loop over input records to process all alignments in a file instead of exiting after the first entry. - Parsing of MAF formatted files should be easy to implement as well - Stockholm formatted input must not be wrapped! I don't know yet, if this is already in the specification of this format. If not, the parser should be adapted to deal with wrapped Stockholm format as well. | 25 August 2016, 17:07:25 UTC |
| 4dd3851 | Ronny Lorenz | 25 August 2016, 11:55:33 UTC | Add parsing of ClustalW and FASTA formatted multiple sequence alignments in vrna_file_alignment_read() - This patch also adds some documentation on MSA file formats and the corresponding functions in file_formats_aln.c | 25 August 2016, 11:55:33 UTC |
| 7cab8c8 | Ronny Lorenz | 24 August 2016, 16:26:19 UTC | Moved parsing of alignment files into separate file and implemented new STOCKHOLM parser | 24 August 2016, 16:32:14 UTC |
| e811d03 | Ronny Lorenz | 24 August 2016, 16:31:20 UTC | Minor changes for polymorphic features in interior loop and multiloop evaluation | 24 August 2016, 16:32:12 UTC |
| ae6dcad | Ronny Lorenz | 22 August 2016, 16:07:46 UTC | Small update in 'install' section of reference manual | 22 August 2016, 16:07:46 UTC |
| a286ab3 | Ronny Lorenz | 19 August 2016, 19:57:40 UTC | Relocate MFE for multibranch loops in comparative mode - was in mfe.c, is now in multibranch_loops.c - renamed E_mb_loop_fast() to vrna_E_mb_loop_fast() - renamed E_mb_stems_fast() to vrna_E_mb_stems_fast(), also note change in argument order The above changes finally make most of the multibranch loop MFE predictions polymorphic with respect to the vrna_fold_compound_t type | 20 August 2016, 08:08:09 UTC |
| 14e2987 | Ronny Lorenz | 19 August 2016, 17:01:25 UTC | Some cleanup in hairpin_loops.c | 19 August 2016, 17:01:25 UTC |
| f3e2469 | Ronny Lorenz | 19 August 2016, 17:00:13 UTC | Fix bug in hard constraints usage of exterior loop MFE prediction with odd dangles | 19 August 2016, 17:00:13 UTC |
| a2b505b | Ronny Lorenz | 19 August 2016, 15:30:41 UTC | Fix behavior of --without-swig configure script option | 19 August 2016, 16:09:47 UTC |
| 5a20a9b | Ronny Lorenz | 19 August 2016, 15:17:16 UTC | Relocate partition function for multibranch loops in consensus structure mode - was in part_func.c, is now in multibranch_loops.c - some cleanup in multibranch_loops.c | 19 August 2016, 16:09:39 UTC |
| db881ed | Ronny Lorenz | 19 August 2016, 13:30:09 UTC | Relocate partition function for interior loops in consensus structure mode - was in part_func.c, is now in interior_loops.c - some cleanup in interior_loops.c | 19 August 2016, 16:09:28 UTC |
| 40bcfc7 | Ronny Lorenz | 18 August 2016, 15:39:15 UTC | Some changes in internal documentation | 18 August 2016, 15:39:15 UTC |
| e5d5912 | Ronny Lorenz | 18 August 2016, 15:38:03 UTC | Allow for non-canonical base pairs in cofold and subopt if demanded by hard constraints | 18 August 2016, 15:38:03 UTC |
| d1c1ab6 | Ronny Lorenz | 18 August 2016, 15:35:57 UTC | Implemented 'A' command for hard constraints | 18 August 2016, 15:35:57 UTC |
| e48f1e4 | Ronny Lorenz | 18 August 2016, 12:40:35 UTC | Some Cleanup in ribo.c | 18 August 2016, 12:40:35 UTC |
| 7f357f5 | Ronny Lorenz | 18 August 2016, 12:39:41 UTC | Allow for non-canonical base pairs in MFE and partition function computations if demanded by hard constraints | 18 August 2016, 12:39:41 UTC |
| f803689 | Ronny Lorenz | 18 August 2016, 06:47:55 UTC | Free memory of SHAPE related commandline options in RNAfold | 18 August 2016, 06:47:55 UTC |
| 6a76dd9 | Ronny Lorenz | 18 August 2016, 06:42:42 UTC | Fix order of hard constraints application when read from file - Previously we read all unpairedness hard constraints for single nucleotides, collected them and applied them as a batch job at the end of constraints parsing. This, however, breaks the intuitive behavior of constraint order as specified in the input file. This patch fixes this issue by only collecting successive hard constraints for unpairedness of single nucleotides. As soon as other constraints are encountered, previously collected ones are applied. | 18 August 2016, 06:42:42 UTC |
| 6a7f751 | Ronny Lorenz | 17 August 2016, 20:08:06 UTC | Fix cornercases in base pair probability computation where particular nucleotides must not be unpaired | 17 August 2016, 20:46:21 UTC |
| d4e0a3a | Ronny Lorenz | 17 August 2016, 20:06:50 UTC | Fix corner cases in MFE multiloop evaluation where particular nucleotides must not be unpaired | 17 August 2016, 20:21:50 UTC |
| 4a43860 | Ronny Lorenz | 17 August 2016, 20:04:03 UTC | Fix interpretation of 'P' hard constraint for single nucleotides | 17 August 2016, 20:20:06 UTC |
| 02a5e4c | Ronny Lorenz | 11 August 2016, 12:00:33 UTC | Savely add openmp flag(s) to automake variables - The AX_APPEND_FLAG macro can't handle appending of multiple flags at a time. Thus we better append the flag manually, just in case openmp flag consists of multiple flags for some compiler/linker combination | 11 August 2016, 12:00:33 UTC |
| 4daa383 | Ronny Lorenz | 11 August 2016, 11:59:37 UTC | Use -ffat-lto-objects if possible whenever LTO is activated and remove -flto from pkg-config file | 11 August 2016, 11:59:37 UTC |
| d28a543 | Ronny Lorenz | 11 August 2016, 10:20:43 UTC | Use a single function to update nonstandard base pairs in executable programs | 11 August 2016, 10:20:43 UTC |
| 22cb77e | Ronny Lorenz | 10 August 2016, 21:39:26 UTC | Merge branch 'development' of krios.tbi.univie.ac.at:/rna/viennarna into development | 10 August 2016, 21:39:26 UTC |
| 28e6637 | Ronny Lorenz | 10 August 2016, 21:35:38 UTC | Bugfix temperature setting in RNAplfold (and fix setting of less frequently options in other programs as well) | 10 August 2016, 21:35:38 UTC |
| 131aaca | Ronny Lorenz | 10 August 2016, 21:34:35 UTC | update in install section of reference manual | 10 August 2016, 21:34:35 UTC |
| 01c9dee | Ronny Lorenz | 09 August 2016, 16:39:45 UTC | Updated packaging/debian directory | 09 August 2016, 16:39:45 UTC |
| 7713b2c | Ronny Lorenz | 09 August 2016, 16:23:23 UTC | Fix RNAlib.pc | 09 August 2016, 16:23:23 UTC |
| d3324e6 | Ronny Lorenz | 09 August 2016, 13:07:51 UTC | Fix several spelling errors | 09 August 2016, 16:23:05 UTC |
| 9fbe27a | Ronny Lorenz | 05 August 2016, 15:14:19 UTC | Update installation page in reference manual | 05 August 2016, 15:14:19 UTC |
| 975c841 | Ronny Lorenz | 05 August 2016, 15:13:55 UTC | Add GSL linker flags to RNAlib2.pc if required | 05 August 2016, 15:13:55 UTC |
| a4ae89e | Ronny Lorenz | 04 August 2016, 13:50:28 UTC | Bump to slightly changed RNAforester sources | 04 August 2016, 13:50:28 UTC |
| 1edbe7b | Ronny Lorenz | 04 August 2016, 13:40:49 UTC | Fix API change for cases where RNAlib is compiled with C11 features, but program linking against it is not (and vice versa) - This fix adds a new configure switch to disable C11/C++11 feature support. A corresponding macro definition is put into the RNAlib2.pc file, whenever RNAlib is compiled without C11/C++11 support - This also introduces a symbol vrna_C11_features() which is only present whenever RNAlib was build with C11/C++11 features. - We now also make sure that each source code file in the ViennaRNA Package includes config.h - Finally, we remove all rcsid variables, and 'Last changed' comments, since they are not required anymore. They rather introduces sources of merge conflicts | 04 August 2016, 13:40:49 UTC |
| d2d16ee | Ronny Lorenz | 04 August 2016, 13:39:29 UTC | Started page in reference manual to describe how to install, configure, and link RNAlib | 04 August 2016, 13:39:29 UTC |
| d7354c8 | Ronny Lorenz | 04 August 2016, 13:23:28 UTC | Fix autotools to display osx features only if activated | 04 August 2016, 13:23:28 UTC |
| 3729634 | Ronny Lorenz | 03 August 2016, 19:46:50 UTC | Reset internal pf_scale to global variable in backward compatibility interfaces for ali pf fold | 03 August 2016, 19:46:50 UTC |
| c907222 | Ronny Lorenz | 03 August 2016, 18:26:31 UTC | Use vrna_eval_structure for circular RNA sequence alignments | 03 August 2016, 18:26:31 UTC |
| 4cc3b2b | Ronny Lorenz | 03 August 2016, 18:25:35 UTC | Allow for circular sequences in consensus structure free energy evaluation | 03 August 2016, 18:25:35 UTC |
| 5da37a6 | Ronny Lorenz | 02 August 2016, 13:26:15 UTC | Update nsis windows installer scripts for ArchLinux | 02 August 2016, 13:26:15 UTC |
| f06beb2 | Ronny Lorenz | 01 August 2016, 14:07:49 UTC | Fix possible assertion failure in python/python3 tests - Some OS'es (at least debian 7 i386) did not properly evaluate the equality of energy_of_structure and mfe computation due to rounding errors. We therefore check for an absolute discrepancy in these cases | 01 August 2016, 14:07:49 UTC |
| 4334038 | Ronny Lorenz | 01 August 2016, 12:57:44 UTC | Fix debian build rules to prevent parallel 'make check' | 01 August 2016, 12:58:14 UTC |
| 898035a | Ronny Lorenz | 01 August 2016, 11:09:28 UTC | Updated viennarna.spec to include all files required for python2 interface in SUSE Linux | 01 August 2016, 12:04:55 UTC |
| 0074149 | Ronny Lorenz | 01 August 2016, 10:07:00 UTC | Updated packaging/debian/changelog | 01 August 2016, 11:06:55 UTC |
| a9dafef | Ronny Lorenz | 01 August 2016, 10:06:41 UTC | Updated Changelog file | 01 August 2016, 10:06:41 UTC |
| f56579c | Ronny Lorenz | 01 August 2016, 10:06:27 UTC | Bump to version 2.2.8 | 01 August 2016, 10:06:27 UTC |
| 5cbe3fa | Ronny Lorenz | 01 August 2016, 09:01:01 UTC | Fix linking of python2/python3 interfaces when libpython is in non-standard directory | 01 August 2016, 09:01:01 UTC |
| 36fb1f3 | Ronny Lorenz | 31 July 2016, 15:20:44 UTC | Fix --with-*/--without-* and --enable-*/--disable-* configure script behavior | 31 July 2016, 15:20:44 UTC |
| 2173fa1 | Ronny Lorenz | 31 July 2016, 12:25:15 UTC | Restructure viennarna.spec | 31 July 2016, 12:25:15 UTC |
| 543e861 | Ronny Lorenz | 29 July 2016, 14:28:57 UTC | Re-activate verbosity_level=0 in RNAeval - This re-enables default warnings whenever non-canonical pairs are encountered during free energy evaluation | 29 July 2016, 14:28:57 UTC |
| 3ebaee0 | Ronny Lorenz | 29 July 2016, 14:23:34 UTC | Add free energy evaluation functions that allow for specifying verbosity level | 29 July 2016, 14:23:34 UTC |
| cb84f4b | Ronny Lorenz | 29 July 2016, 12:45:50 UTC | Use latest Kinfold sources | 29 July 2016, 12:45:50 UTC |
| 2a3fe36 | Ronny Lorenz | 29 July 2016, 12:44:09 UTC | Add correct OpenMP linker flag - We used to add -lgomp to the list of linker flags, but this only works for GNU compiler. Using the -fopenmp, -openmp, or whatever flag should instruct any linker to link against its preferred OpenMP library | 29 July 2016, 12:44:09 UTC |
| b5203b3 | Ronny Lorenz | 29 July 2016, 12:27:15 UTC | Fix several compiler warnings | 29 July 2016, 12:43:45 UTC |
| 675692b | Ronny Lorenz | 28 July 2016, 18:41:52 UTC | Minimize gcc warnings in SWIG interface(s) | 28 July 2016, 18:41:52 UTC |
| 60e4d16 | Ronny Lorenz | 25 July 2016, 14:23:53 UTC | Secure some functions in alphabet.c against NULL pointer arguments | 28 July 2016, 16:22:06 UTC |
| f681d1e | Ronny Lorenz | 28 July 2016, 14:19:47 UTC | Print MFE and delta energy in kcal/mol instead ugly dcal/mol in subopt.c to avoid post-sorting problems | 28 July 2016, 14:19:47 UTC |
| 119bb1d | Ronny Lorenz | 25 July 2016, 16:12:18 UTC | Fix leak in SWIG interface for user-provided target language callbacks | 25 July 2016, 16:54:27 UTC |
| efca978 | Ronny Lorenz | 18 July 2016, 13:30:10 UTC | Fix wrongly diregarded P i-j k-l command in constraints definition files | 18 July 2016, 13:30:10 UTC |
| f295c69 | Ronny Lorenz | 14 July 2016, 19:54:57 UTC | Make free energy evaluation functions polymorphic - This removes special functions in eval.c that computed free energies of consensus structures only and replaces them with their polymorphic counterparts | 15 July 2016, 17:22:51 UTC |
| 1d96083 | Ronny Lorenz | 08 July 2016, 18:11:44 UTC | Fix subopt for circular RNAs | 14 July 2016, 16:44:08 UTC |
| 9fdf25a | Ronny Lorenz | 14 July 2016, 16:43:38 UTC | Use only one API function to compute hairpin loop contributions for linear and circular cases | 14 July 2016, 16:43:38 UTC |
| bf4f384 | Ronny Lorenz | 14 July 2016, 15:35:27 UTC | Detach equilibrium probability computations from part_func.c - This creates a new source code file equilibrium_probs.c that implements base pair probability computations and alike | 14 July 2016, 16:31:46 UTC |
| b417d15 | Ronny Lorenz | 14 July 2016, 10:41:02 UTC | Fix free energy evaluation for circular RNAs in general and for RNAalifold | 14 July 2016, 15:02:18 UTC |
| 2f50403 | Ronny Lorenz | 11 July 2016, 15:02:21 UTC | Fix access to non-allocated memory in RNAalifold.c | 14 July 2016, 15:02:00 UTC |
| b0966d7 | Ronny Lorenz | 12 July 2016, 11:02:58 UTC | Add IUPAC sequence comparison in alphabet.c | 14 July 2016, 15:01:50 UTC |
| 8624083 | Ronny Lorenz | 12 July 2016, 11:40:26 UTC | Make pf_create_bppm() in part_func.c static as it was supposed to be | 14 July 2016, 15:01:34 UTC |
| ff1cdb1 | Ronny Lorenz | 13 July 2016, 20:49:46 UTC | Revert "Add documentation about post-condition of vrna_eval_move_pt()" This reverts commit b538c4df33cb78e597c5ef66726b83f05d84a5cd. | 13 July 2016, 20:49:46 UTC |
| 36eb209 | Ronny Lorenz | 13 July 2016, 20:48:38 UTC | Fix Makefiles for python bindings to be compatible with SWIG >= 3.0.9 | 13 July 2016, 20:48:38 UTC |
| b538c4d | Ronny Lorenz | 13 July 2016, 08:31:11 UTC | Add documentation about post-condition of vrna_eval_move_pt() | 13 July 2016, 08:31:11 UTC |
| 0050009 | Ronny Lorenz | 07 July 2016, 16:20:36 UTC | Fix potential syntax issues in the sources | 07 July 2016, 16:20:36 UTC |
