| feb0567 | Ronny Lorenz | 01 August 2017, 19:53:13 UTC | Add more missing latex packages to .travis.yml | 01 August 2017, 19:54:51 UTC |
| ed227fe | Ronny Lorenz | 01 August 2017, 19:23:08 UTC | Updte .travis.yml | 01 August 2017, 19:23:08 UTC |
| 46a8f68 | Ronny Lorenz | 01 August 2017, 18:49:09 UTC | Merge commit '47395c8271086e67668639f8d16a53f451285233' into release_v2.4.0 | 01 August 2017, 18:49:09 UTC |
| 47395c8 | Ronny Lorenz | 01 August 2017, 18:49:09 UTC | Squashed 'src/RNAlocmin/' changes from 06f6b75e..bccf5eff bccf5eff Use automatic detection of C++11 standard in RNAlocmin git-subtree-dir: src/RNAlocmin git-subtree-split: bccf5effb8bae64941bc41da159a518d57859d78 | 01 August 2017, 18:49:09 UTC |
| 59bf84f | Ronny Lorenz | 01 August 2017, 14:19:50 UTC | Update packaging rules for binary distributions | 01 August 2017, 18:45:05 UTC |
| 78d3512 | Ronny Lorenz | 31 July 2017, 16:14:51 UTC | Prepare for release 2.4.0 | 01 August 2017, 18:45:05 UTC |
| b9c590c | Ronny Lorenz | 01 August 2017, 18:42:44 UTC | Add missing <ctime> in RNAlocmin/pknots.cpp | 01 August 2017, 18:45:05 UTC |
| 16bcd47 | Ronny Lorenz | 01 August 2017, 11:13:38 UTC | Use LC_ALL=C in python3 unit tests - This should be safe to use on any platform using any locale settings | 01 August 2017, 11:15:46 UTC |
| dd108c7 | Ronny Lorenz | 01 August 2017, 10:13:50 UTC | Fix out-of-memory access in neighbor.c | 01 August 2017, 11:15:42 UTC |
| f50604a | Ronny Lorenz | 01 August 2017, 08:11:22 UTC | Fix buffer overflow in hairpin loop sequence motif extraction for circular RNAs | 01 August 2017, 11:15:38 UTC |
| fa1cd57 | Ronny Lorenz | 31 July 2017, 20:14:33 UTC | Adjust viennarna.spec to disable RNAlocmin when required - Some older distributions do not ship with a compiler capable to deal with C++11 specific code. Therefore, we simply turn off building RNAlocmin for Fedora < 22, and RedHat/Scientific Linux/CentOS < 7 | 01 August 2017, 11:15:34 UTC |
| 1062b71 | Ronny Lorenz | 31 July 2017, 20:08:35 UTC | Use automatic detection of C++11 standard in RNAlocmin | 01 August 2017, 11:15:30 UTC |
| 728d44f | Ronny Lorenz | 31 July 2017, 16:10:18 UTC | Add SHAPE support to RNALfold | 31 July 2017, 16:10:18 UTC |
| 3224f90 | Ronny Lorenz | 31 July 2017, 13:01:02 UTC | Change behavior of RNAfold --outfile option - From now on, the -o option simply switches output-to-file on. If an optional filename is following immediately after the -o option, any output is written to this file. Existing files will not be overwritten but the output is appended to them. If no filename is specified, the default filename is "RNAfold_output.fold" as long as the --auto-id option is unset and the input does not contain FASTA headers. Otherwise, the sequence id is used as filename with suffix ".fold", e.g. "sequence_0001.fold". This patch finally matches the behavior of the -o option as used in RNAsubopt and RNALfold. | 31 July 2017, 14:14:47 UTC |
| 7956a78 | Ronny Lorenz | 08 May 2017, 12:17:37 UTC | Replace input_id_helper macros with C functions | 31 July 2017, 14:14:38 UTC |
| 7605e6a | Ronny Lorenz | 28 July 2017, 17:31:31 UTC | Include Tutorial into autoconf/automake toolchain | 31 July 2017, 12:04:17 UTC |
| 752168e | Ronny Lorenz | 31 July 2017, 10:51:50 UTC | Merge commit '59c1821d7eac09dab7c2e3350c2ee248701692bb' as 'doc/tutorial' | 31 July 2017, 10:51:50 UTC |
| 59c1821 | Ronny Lorenz | 31 July 2017, 10:51:50 UTC | Squashed 'doc/tutorial/' content from commit 9357ee9 git-subtree-dir: doc/tutorial git-subtree-split: 9357ee922ab0d228989c18f70403ee8cf7148a2d | 31 July 2017, 10:51:50 UTC |
| eaf6e8d | Ronny Lorenz | 30 July 2017, 18:46:47 UTC | Add RNAlocmin as a default target - We now officially ship RNAlocmin as a default program with the ViennaRNA Package. It is included as a git subtree project and compilation/installation can be turned-off through the main configure script | 30 July 2017, 18:46:47 UTC |
| 49b16e9 | Ronny Lorenz | 30 July 2017, 18:36:27 UTC | Squashed 'src/RNAlocmin/' content from commit 06f6b75e git-subtree-dir: src/RNAlocmin git-subtree-split: 06f6b75ea6bd9af7c7a58231630555ed8a2c1911 | 30 July 2017, 18:36:27 UTC |
| 6fe26ba | Ronny Lorenz | 30 July 2017, 18:36:27 UTC | Merge commit '49b16e9da2809b3d9d0fee546986edf41073d278' as 'src/RNAlocmin' | 30 July 2017, 18:36:27 UTC |
| 01dea52 | Ronny Lorenz | 28 July 2017, 15:33:27 UTC | Remove old RNAfold tutorial | 29 July 2017, 09:40:21 UTC |
| b57fd66 | Ronny Lorenz | 28 July 2017, 18:43:22 UTC | uncrustify boltzmann_sampling.[c.h] | 28 July 2017, 18:43:22 UTC |
| 6223a1f | Ronny Lorenz | 28 July 2017, 11:21:49 UTC | Print opening energies in RNAplfold as kcal/mol - This reverts the opening energy output back to kcal/mol instead of the faulty cal/mol that were introduced some commits back | 28 July 2017, 11:21:49 UTC |
| ada8fef | Ronny Lorenz | 18 July 2017, 15:21:50 UTC | Allow for passing commands file to RNAplfold - RNAplfold now uses the new API of RNAlib and can handle hard/soft constraints through comamnd file input | 18 July 2017, 15:21:50 UTC |
| b057a3e | Ronny Lorenz | 18 July 2017, 15:17:08 UTC | Allow for passing commands file to RNALfold - This enables constraints support (hard/soft) in sliding window MFE computations. | 18 July 2017, 15:17:08 UTC |
| 05c9e56 | Ronny Lorenz | 18 July 2017, 15:14:17 UTC | Add warnings for ignored commands in function vrna_commands_apply() | 18 July 2017, 15:14:17 UTC |
| 37e6617 | Ronny Lorenz | 17 July 2017, 11:25:44 UTC | Update libsvm to version 3.22 | 17 July 2017, 11:25:44 UTC |
| 7d63c48 | Ronny Lorenz | 15 July 2017, 09:18:55 UTC | Merge branch 'dev_pf_window_constraints' into 'development' Add constraints framework for sliding window partition function implementation See merge request !72 | 15 July 2017, 09:18:55 UTC |
| 7e9a751 | Ronny Lorenz | 15 July 2017, 08:50:10 UTC | Add SWIG wrapper unit tests for unpaired probability computations | 15 July 2017, 08:51:48 UTC |
| d8ed069 | Ronny Lorenz | 14 July 2017, 16:47:22 UTC | Some cleanup in SWIG unit test scripts | 15 July 2017, 08:51:48 UTC |
| 75ec54c | Ronny Lorenz | 13 July 2017, 16:56:42 UTC | Add SWIG unit tests for sliding window soft constraints feature | 15 July 2017, 08:51:48 UTC |
| f07ca6f | Ronny Lorenz | 15 July 2017, 08:35:17 UTC | Finalize soft constraints implementation for unpaired probabilities in LPfold.c | 15 July 2017, 08:51:48 UTC |
| aa16b41 | Ronny Lorenz | 13 July 2017, 16:56:14 UTC | Finalize soft constraints for pairing probabilities in sliding window pf implementations | 14 July 2017, 15:34:38 UTC |
| 5a55d07 | Ronny Lorenz | 13 July 2017, 10:22:10 UTC | Re-use code blocks in soft constraints preparation functions - ... and use 'unsigned int' types in constraints_soft.c whereever possible... | 13 July 2017, 10:54:27 UTC |
| 167b876 | Ronny Lorenz | 12 July 2017, 16:08:07 UTC | Some cleanup in data_structures.c | 12 July 2017, 16:08:07 UTC |
| cc4cde6 | Ronny Lorenz | 12 July 2017, 14:45:30 UTC | Add prepare() functions for ptypes-arrays and vrna_(exp_)param_t | 12 July 2017, 14:45:30 UTC |
| b89f9cf | Ronny Lorenz | 12 July 2017, 13:39:07 UTC | Introduce soft-constraint state flag - The vrna_sc_t structure now has a state flag that indicates whether the soft constraints container(s) have been altered since the last preparation step. This enables the vrna_sc_prepare() function to exit earlier and not re-fill the soft constraints arrays for energy evaluation in situations where nothing has changed since the last call. Consequently, this is a large performance improvement for subsequent vrna_eval*() calls which otherwise would re-fill the soft constraints arrays way too many times... | 12 July 2017, 13:39:07 UTC |
| ec8f2b0 | Ronny Lorenz | 12 July 2017, 11:17:36 UTC | Rename sliding-window hard constraints update function from vrna_hc_prepare() to vrna_hc_update() | 12 July 2017, 11:20:03 UTC |
| 1b38044 | Ronny Lorenz | 12 July 2017, 10:57:55 UTC | Change vrna_sc_prepare() function into something more reasonable - Now, vrna_sc_prepare() actually prepares soft constraints usage, while a new function vrna_sc_update() can be used to update the soft constraints during sliding-window computations | 12 July 2017, 10:57:55 UTC |
| 0a5ff59 | Ronny Lorenz | 11 July 2017, 19:31:58 UTC | Unify how soft constraints are handled in global and local structure prediction - By default, when soft constraints are added to a vrna_fold_compound_t they are now simply stored in a storage container. Algorithms that require them need to call vrna_sc_prepare() before actually accessing data fields such as sc->energy_up or sc->energy_bp. Usually, this task is handled by vrna_fold_compound_prepare() | 11 July 2017, 20:13:59 UTC |
| 81c4af4 | Ronny Lorenz | 05 July 2017, 14:08:17 UTC | Deal with SWIG wrappers for sliding-window partition function computations - Add separate wrapper file(s) for sliding-window partition function implementations - Add SWIG interfaces for the callback mechanism in sliding-window partition function implementations - Add a separate PERL5 wrapper for vrna_pfl_fold_up() since SWIG does not automatically wrap vector<vector<T> > for Perl5 - Add unit tests of the sliding-window partition function SWIG wrappers | 10 July 2017, 16:50:03 UTC |
| 3e8f132 | Ronny Lorenz | 05 July 2017, 14:03:56 UTC | Change function parameter order in vrna_probs_window() - Now, the callback and void *data are the last arguments, following the style of all other callback-aware functions in our library | 10 July 2017, 16:50:03 UTC |
| 3cbb382 | Ronny Lorenz | 05 July 2017, 14:01:45 UTC | Move SWIG wrappers for sliding-window MFE functions to separate file | 10 July 2017, 16:50:03 UTC |
| 876bdb6 | Ronny Lorenz | 26 June 2017, 17:43:22 UTC | Unify max_bp_span usage among sliding window prediction algorithms - Previously, sliding window partition function and comparative MFE predictions used (j - i) <= max_bp_span (a.k.a. L) while sliding window single sequence MFE correctly used (j - i + 1) <= max_bp_span From now on, we define max_bp_span, a.k.a. L, as the interval a base pair (i,j) spans, i.e. (j - i + 1) <= max_bp_span! - This certainly results in different predictions of RNAplfold and RNALalifold when compared to 'older' versions, however, the behavior of these programs can be 'restored' by simply decreasing L by 1, i.e. RNAplfold -L 150 becomes RNAplfold -L 149 | 10 July 2017, 16:50:03 UTC |
| b5c29ea | Ronny Lorenz | 22 June 2017, 15:31:56 UTC | Introduce 'vrna_ep_t' struct as element for element pairing probability lists - This struct replaces 'vrna_plist_t' - Updated SWIG wrappers that deal with 'vrna_ep_t' structures/lists | 10 July 2017, 16:50:03 UTC |
| e3980bf | Ronny Lorenz | 21 June 2017, 18:56:04 UTC | Enable callback feature to retrieve ensemble free energy in LPfold.c | 10 July 2017, 16:50:03 UTC |
| 8d3affa | Ronny Lorenz | 21 June 2017, 18:53:59 UTC | Start SWIG interface for sliding-window partition function | 10 July 2017, 16:50:03 UTC |
| 5d702c8 | Ronny Lorenz | 21 June 2017, 18:50:50 UTC | Add base pair stack flag for plist entries | 10 July 2017, 16:50:03 UTC |
| 163ae8b | Ronny Lorenz | 26 April 2017, 17:10:51 UTC | Started to add constraints to unpaired probabilities in LPfold.c | 10 July 2017, 16:50:03 UTC |
| 9d81079 | Ronny Lorenz | 26 April 2017, 15:46:43 UTC | Add constraints to sliding window base pair probability computations | 10 July 2017, 16:50:03 UTC |
| b4f638d | Ronny Lorenz | 26 April 2017, 11:42:34 UTC | Re-use and extend library functions for forward recursions in LPfold.c - Here we introduce constraints (hard/soft) into the forward recursions of the sliding window partition function | 10 July 2017, 16:50:03 UTC |
| fba2958 | Ronny Lorenz | 25 April 2017, 17:18:59 UTC | More cleanup and changes in memory management in LPfold.c | 10 July 2017, 16:50:03 UTC |
| 5e62c81 | Ronny Lorenz | 25 April 2017, 17:18:16 UTC | Fix memory access in RNAplfold with unpaired probabilities and very short sequences | 10 July 2017, 16:50:03 UTC |
| 3fa7715 | Ronny Lorenz | 25 April 2017, 10:48:19 UTC | Some cleanup in LPfold.c - This makes vrna_probs_window working again on current development branch and splits apart the main recursions into smaller functions | 10 July 2017, 16:50:03 UTC |
| 9536aef | Ronny Lorenz | 05 July 2017, 13:56:56 UTC | Silence warnings SWIG warnings for global pointer variables and unknown struct bondT | 10 July 2017, 16:43:59 UTC |
| 0eea8eb | Ronny Lorenz | 10 July 2017, 16:35:07 UTC | Add SWIG interface for findpath implementation | 10 July 2017, 16:35:07 UTC |
| 47a9102 | Ronny Lorenz | 10 July 2017, 16:22:43 UTC | Cleanup Perl scripts in src/Utils - Removed ct2b.pl and colorrna.pl since they've been replaced by ct2db and relplot.pl for some time now. - Slight changes in POD of scripts in src/Utils | 10 July 2017, 16:22:43 UTC |
| 64ed191 | Ronny Lorenz | 10 July 2017, 13:22:14 UTC | Add note about SSE optimized code in reference manual | 10 July 2017, 13:23:39 UTC |
| 7e21bc9 | Ronny Lorenz | 07 May 2017, 18:12:33 UTC | Add documentation for callback features in reference manual | 10 July 2017, 13:23:06 UTC |
| 9e39614 | Ronny Lorenz | 10 July 2017, 12:34:19 UTC | Inline print functions in color_output.inc - This silences 'defined but not used' warnings whereever color_output.inc is included | 10 July 2017, 12:34:19 UTC |
| 1031357 | Ronny Lorenz | 10 July 2017, 12:16:43 UTC | Acknowledge signedness in SWIG typemap for simple nested STL vectors | 10 July 2017, 12:16:43 UTC |
| 436c309 | Ronny Lorenz | 10 July 2017, 11:37:49 UTC | Include builddir/tests in PERL5LIB path - When separating srcdir and builddir it can happen that the builddir/tests is not among the paths of PERL5LIB. However, our Perl5 unit tests require RNApath.pm which is created at configure-time and therefore resides in builddir/tests. We fix this problem by explicitly includin builddir/tests in the Perl5 include path. | 10 July 2017, 11:37:49 UTC |
| 4018e88 | Ronny Lorenz | 10 July 2017, 08:19:07 UTC | Fix sliding-window MFE backtracking (for real) - This is an addendum to 8b8535371d03a50d1ba8e688e4da6f161fba244d and should fix the backtracing errors for real. | 10 July 2017, 08:19:07 UTC |
| 975dfb0 | Ronny Lorenz | 06 July 2017, 19:09:53 UTC | Use automatic SWIG wrapper generation for vrna_enumerate_necklaces() | 06 July 2017, 19:11:20 UTC |
| 7e14821 | Ronny Lorenz | 06 July 2017, 19:06:48 UTC | Add SWIG typemap for simple nested STL vectors - This adds Perl5 support for automatic wrapping of functions returning std::vector<std::vector<int> > and std::vector<std::vector<double> > | 06 July 2017, 19:11:11 UTC |
| a21b13a | Ronny Lorenz | 06 July 2017, 12:34:58 UTC | Add explicit destructor for SWIG generated vrna_md_t objects - For some reason, the automatically generated one causes hick-ups in valgrind. | 06 July 2017, 12:34:58 UTC |
| 53269b4 | Ronny Lorenz | 04 July 2017, 16:08:44 UTC | Add SWIG wrapper for vrna_exp_params_rescale() | 04 July 2017, 16:08:44 UTC |
| 5d0ed46 | Ronny Lorenz | 04 July 2017, 15:58:45 UTC | Add proper SWIG interface for duplexfold, duplex_subopt, and its comparative variants | 04 July 2017, 15:58:45 UTC |
| 2bdaa25 | Ronny Lorenz | 04 July 2017, 14:44:18 UTC | Add proper SWIG interface for alignment and structure plotting functions | 04 July 2017, 14:44:18 UTC |
| 8b85353 | Ronny Lorenz | 04 July 2017, 13:08:19 UTC | Fix backtracking issues in sliding-window MFE implementation - This fixes issues that have been encountered when backtracking locally stable structures. In particular, backtracking always permitted the structure to be one nucleotide larger than actually allowed. Note again, that the output of RNALfold and RNALalifold will differ compared to implementations up to version 2.3.5! | 04 July 2017, 13:08:19 UTC |
| b5dcfb8 | Ronny Lorenz | 03 July 2017, 20:51:50 UTC | Prevent adding out-of-range base pair soft constraints | 03 July 2017, 20:53:46 UTC |
| 491b863 | Ronny Lorenz | 03 July 2017, 11:30:02 UTC | Fix wrong pre-processor flags when enabling single-precision PF computations | 03 July 2017, 18:44:53 UTC |
| 1227fcf | Ronny Lorenz | 03 July 2017, 11:28:32 UTC | Add dummy field in vrna_structured_domains_s - This solves compatibility issues between C and C++ code where empty structs are of different size | 03 July 2017, 11:28:32 UTC |
| d26e310 | Ronny Lorenz | 03 July 2017, 11:21:26 UTC | Make functions in pair_mat.h static inline - This ensures that including pair_mat.h in your sources but not using functions defined within it does not raise any defined-but-not-used warnings at compile time. | 03 July 2017, 11:21:26 UTC |
| ce9a725 | Ronny Lorenz | 27 June 2017, 17:06:15 UTC | Add first-level groups from modules section to mainpage in reference manual | 27 June 2017, 17:06:15 UTC |
| 0d54079 | Ronny Lorenz | 19 June 2017, 17:49:28 UTC | Change data type of a2s array in comparative structure prediction - This is a major change that increases the storage size of the alignment-column to sequence position mapping array 'a2s'. In early implementations, it was only used in RNAalifold and related functions, i.e. global structure prediction where alignment columns never exceeded about 30,000. Thus an 'unsigned short' storage type seemed adequat. However, Now that it is used in local folding variants of our implementations which do not have this low limit of alignment columns it easily exceeds storage size, thereby producing integer overflows. Consequently, this array is now of type 'unsigned int' which allows us to process alignments up to some hundred millions of columns in length. | 19 June 2017, 17:49:28 UTC |
| 2bdfc72 | Ronny Lorenz | 19 June 2017, 16:14:13 UTC | Re-enable old-API random number functions in SWIG interface | 19 June 2017, 16:14:13 UTC |
| bd06826 | Ronny Lorenz | 17 June 2017, 08:33:28 UTC | Merge branch 'dev_eval_gquad' into 'development' Print G-Quadruplex corrections in verbose mode of RNAeval - This patch adds verbose free energy evaluation output for structured domains. For now we only consider G-Quadruplexes though. See merge request !71 | 17 June 2017, 08:33:28 UTC |
| a6d3f5c | Ronny Lorenz | 05 June 2017, 18:14:43 UTC | Print G-Quadruplex corrections in verbose mode of RNAeval - This patch adds verbose free energy evaluation output for structured domains. For now we only consider G-Quadruplexes though. | 17 June 2017, 08:32:13 UTC |
| 27d7b99 | Ronny Lorenz | 09 June 2017, 21:03:02 UTC | Fix G-Quadruplex backtracking corner case in RNALalifold - G-Quadruplexes that ended in the last column of the alignment were missing in the pre-backtracking function of BT_ext_loop_f3_pp_comparative() in exterior_loops.c | 09 June 2017, 21:03:02 UTC |
| d6e20fe | Ronny Lorenz | 09 June 2017, 18:56:40 UTC | Allow additional control characters in MAF MSA input that do not end a block | 09 June 2017, 19:10:34 UTC |
| 28a5de3 | Ronny Lorenz | 08 June 2017, 13:08:54 UTC | Fix Alidot link in RNAalifold manpage | 08 June 2017, 13:08:54 UTC |
| 1848b25 | Ronny Lorenz | 22 May 2017, 10:38:46 UTC | Restore capability to use non-standard alphabets for structure prediction - During the transition to constraints support with version 2.2 we lost the capability to use non-standard alphabets in structure prediction, e.g. sequences over the alphabet ABCD, etc. This patch restores this capability within the constraints framework | 22 May 2017, 10:38:46 UTC |
| 34dc5a1 | Ronny Lorenz | 19 May 2017, 11:29:03 UTC | Re-enable compilation of stand-alone findpath utility | 19 May 2017, 11:29:03 UTC |
| f5c9427 | Ronny Lorenz | 08 May 2017, 14:29:26 UTC | Fix parsing of STOCKHOLM 1.0 MSA files that contain MSA spanning multiple blocks - Also, sequences read from STOCKHOLM files are now always converted to uppercase letters | 08 May 2017, 14:52:29 UTC |
| b8246a9 | Ronny Lorenz | 07 May 2017, 18:11:11 UTC | Fix building mfe_window.c without SVM support | 07 May 2017, 18:11:11 UTC |
| 68f7a33 | Ronny Lorenz | 05 May 2017, 08:12:24 UTC | Fix regression for canonicalBPonly switch in RNAfold/RNAcofold/RNAsubopt | 05 May 2017, 08:41:56 UTC |
| d71e597 | Ronny Lorenz | 24 April 2017, 11:04:48 UTC | Merge branch 'dev_mfe_window_constraints' into 'development' Add constraints support to sliding-window MFE algorithms See merge request !70 | 24 April 2017, 11:04:48 UTC |
| 58b5232 | Ronny Lorenz | 23 April 2017, 10:42:25 UTC | Make all constraint flags unsigned - To avoid unintended effects when converting char types that are used as bit-arrays to int or any other types, we make all of them unsigned. This should only amount to minimal effort to already existing generic (soft/hard) constraint callback implementations... | 24 April 2017, 10:21:12 UTC |
| 5042123 | Ronny Lorenz | 22 April 2017, 15:14:43 UTC | Adjust unit test framework for sliding-window MFE constraints | 24 April 2017, 10:21:12 UTC |
| 7ba4b20 | Ronny Lorenz | 18 April 2017, 08:27:23 UTC | Finish soft constraints for unpaired stretches in sliding window MFE - Unpaired stretches in the exterior loop still won't be returned through the callback. This is intended since we are usually interested only in structured regions. An implementation of the unstructured domains feature might change that behavior. - 'Fix' the backtracking for single sequence sliding window MFE backtracking. In previous versions, the conditions when to actually backtrace the next hit was slightly odd. - Add integer underflow detection to comparative sliding window MFE implementation | 24 April 2017, 10:21:12 UTC |
| 1b8a0d5 | Ronny Lorenz | 14 April 2017, 14:35:22 UTC | More on soft-constraints in sliding window MFE implementations | 24 April 2017, 10:21:12 UTC |
| bef0aa8 | Ronny Lorenz | 10 April 2017, 18:07:16 UTC | Add unit tests for sliding-window constraints framework | 24 April 2017, 10:21:12 UTC |
| 3cf0c68 | Ronny Lorenz | 10 April 2017, 15:31:38 UTC | Substitute pair type access with inline function calls in MB/Ext-loops - This is merely a fail-safe thingy to ensure that non-canonical base pairs always receive type == 7 | 24 April 2017, 10:21:12 UTC |
| 5c5e9c8 | Ronny Lorenz | 10 April 2017, 15:14:33 UTC | Fix base pair enforcing hard constraints for sliding window approach | 24 April 2017, 10:21:12 UTC |
| 1827cc0 | Ronny Lorenz | 10 April 2017, 14:39:16 UTC | Fix dangling end issues in mfe_window.c - The original implementation of the sliding window approach was designed for dangles == 2, but failed to correctly retrieve free energy contributions of the hits for dangles == 0, and possibly for the odd dangle models as well. This has been fixed now for single sequences and the comparative structure prediction... | 24 April 2017, 10:21:12 UTC |
| fb7290e | Ronny Lorenz | 07 April 2017, 14:53:18 UTC | Add (first draft for) soft constraints support to vrna_mfe_window() - Works for single sequence sliding window MFE predictions | 24 April 2017, 10:21:12 UTC |
| c491977 | Ronny Lorenz | 06 April 2017, 12:50:17 UTC | Fix redefinition of ON_SAME_STRAND() macro in subopt.c | 24 April 2017, 10:21:12 UTC |
| 35d2859 | Ronny Lorenz | 06 April 2017, 12:45:18 UTC | Add remaining (generic)hard constraints cases in *_loops.c - All loop evaluations in *_loops.c, i.e. global/local, single- sequence/sequence alignments, MFE/PF are fully hard constraints aware now. - Fake multibranch loops for co-folding are handled like exterior loops hard constraint-wise | 24 April 2017, 10:21:12 UTC |
