| age |
author |
description |
| Wed, 28 Nov 2012 14:42:15 +0400 |
Boris Nagaev |
pair-cores/web: copy pair-cores.cpp to compare-aln-3d.cpp |
| Wed, 28 Nov 2012 00:35:35 +0400 |
Boris Nagaev |
pair_cores/web: add note about support by Ministry of Education and Science |
| Thu, 04 Oct 2012 02:46:09 +0400 |
Boris Nagaev |
fix a typo in description of columns_as_lists() |
| Mon, 16 Jul 2012 20:06:26 +0400 |
Daniil Alexeyevsky |
util.Silence: remove temporary file in all cases, not just if an exception occured |
| Fri, 29 Jun 2012 19:37:28 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Fri, 29 Jun 2012 19:34:21 +0400 |
Daniil Alexeyevsky |
utils/markup_to_file: added ability to specify multiple markup file names for batch tranformation as positional arguments |
| Tue, 19 Jun 2012 16:55:44 +0400 |
Mmmasha! |
Automated merge with ssh://kodomo/allpy |
| Tue, 19 Jun 2012 16:55:37 +0400 |
Mmmasha! |
markup_to_html. Html template files and path to imported module can be passed on the command line. In the imported module can be function "init" which takes an alignment for adding some attributes after alignment is loaded. |
| Tue, 19 Jun 2012 15:51:12 +0400 |
Mmmasha! |
Messages about wrong descripitons while reading markup. |
| Thu, 14 Jun 2012 20:24:26 +0400 |
Daniil Alexeyevsky |
Reverted draft changes to allpy/util.py accidentally added to commit [bc1a7595d9d1] |
| Thu, 14 Jun 2012 19:05:28 +0400 |
Daniil Alexeyevsky |
Clean rewrite or markup_to_file.py util; --markup is now optional and allows specifying multiple markups as a comma-separated list |
| Sun, 10 Jun 2012 16:08:47 +0400 |
Daniil Alexeyevsky |
Partially reversed [afed1f] (see #49) |
| Sun, 10 Jun 2012 15:20:37 +0400 |
Daniil Alexeyevsky |
Collected Debian changelog entries from released revisions |
| Sun, 10 Jun 2012 15:11:54 +0400 |
Daniil Alexeyevsky |
Re-packaged for Debian (previous packaging erroneously excluded codes.py)1.4.3 |
| Sat, 09 Jun 2012 21:23:11 +0400 |
Daniil Alexeyevsky |
markup_to_file did not actually work until now, rather it removed all gaps from alignment |
| Sat, 09 Jun 2012 21:14:55 +0400 |
Daniil Alexeyevsky |
Fixed indentation in markup_to_file.py |
| Sat, 09 Jun 2012 21:03:13 +0400 |
Daniil Alexeyevsky |
Fixed a serious bug with saving sequence markups when alignment does not have all of the sequence monomers |
| Sat, 09 Jun 2012 19:15:44 +0400 |
Daniil Alexeyevsky |
Added to dna.Sequence method `translate` to translate into protein sequence using given genetic code |
| Tue, 05 Jun 2012 15:22:43 +0400 |
Boris Burkov |
Check, whether alignment_index_markup was already created in blocks_finder.1.4.2 |
| Sun, 03 Jun 2012 23:55:00 +0400 |
Daniil Alexeyevsky |
allpy logo: better font sizes |
| Sun, 03 Jun 2012 23:45:21 +0400 |
Daniil Alexeyevsky |
Re-painted allpy logo (the idea is exactly the same) |
| Sun, 03 Jun 2012 12:09:41 +0400 |
Daniil Alexeyevsky |
Added meta-processor `FixNamesAndOrder`; called from `Needle` and `Muscle` (closes #134) |
| Sat, 02 Jun 2012 22:33:50 +0400 |
Daniil Alexeyevsky |
processors.Needle: also check that sequence name is not empty (needle fails on those too) |
| Sat, 02 Jun 2012 22:15:27 +0400 |
Daniil Alexeyevsky |
Reorganized tests to make them more readable |
| Sat, 02 Jun 2012 21:56:13 +0400 |
Daniil Alexeyevsky |
Removed tests for long-removed "ss" markup |
| Sat, 02 Jun 2012 19:52:06 +0400 |
Daniil Alexeyevsky |
Renamed test_fastq -> test_io_fastq for uniformity |
| Sat, 02 Jun 2012 19:33:42 +0400 |
Daniil Alexeyevsky |
Added backreferences to `Seqeunce`s from `Monomer`s (closes #49) |
| Sat, 02 Jun 2012 19:29:40 +0400 |
Daniil Alexeyevsky |
Added test for `dna.Sequence.reverse_complemented()` |
| Fri, 01 Jun 2012 14:32:07 +0400 |
Daniil Alexeyevsky |
Silenced all known noisy points in allpy |
| Fri, 01 Jun 2012 13:43:02 +0400 |
Daniil Alexeyevsky |
Added allpy.util.Silence to faciliate running most code with as little noise as possible |
| Thu, 31 May 2012 15:23:37 +0400 |
Daniil Alexeyevsky |
Removed the unuzed allpy.util.lazy_import |
| Wed, 30 May 2012 13:58:00 +0400 |
Daniil Alexeyevsky |
Updated the Debian changelog1.4.3 |
| Wed, 30 May 2012 13:38:27 +0400 |
Daniil Alexeyevsky |
Removed Alignment.process() and the code that it used (see #99) |
| Wed, 30 May 2012 13:38:41 +0400 |
Daniil Alexeyevsky |
Removed tag 1.4.3 |
| Wed, 30 May 2012 13:38:41 +0400 |
Daniil Alexeyevsky |
Removed tag 1.4.31.4.3 |
| Wed, 30 May 2012 13:38:27 +0400 |
Daniil Alexeyevsky |
Removed Alignment.process() and the code that it used (see #99)1.4.3 |
| Wed, 30 May 2012 13:35:04 +0400 |
Daniil Alexeyevsky |
Bugfixed the previous commit (decency verification), (see #98) |
| Wed, 30 May 2012 12:43:09 +0400 |
Daniil Alexeyevsky |
allpy.base: Added decency verification function to alignments (closes #98) |
| Wed, 30 May 2012 12:33:22 +0400 |
Daniil Alexeyevsky |
Changed FASTA-file parser to accept files with empty lines before the first record (fixes #144) |
| Fri, 25 May 2012 21:12:54 +0400 |
Daniil Alexeyevsky |
(closes #153) |
| Fri, 25 May 2012 21:03:57 +0400 |
Daniil Alexeyevsky |
Marked the new release date as today in debian/changelog & NEWS |
| Fri, 25 May 2012 20:59:16 +0400 |
Daniil Alexeyevsky |
Documented the changes since 1.4.0 in NEWS |
| Fri, 25 May 2012 20:53:18 +0400 |
Daniil Alexeyevsky |
Hidded the misbehaved not-to-be-released-publically SequenceSecondaryStructureMarkup class into allpy.structure to postpone the problem of introducing the proper secondary structure markup to after the release while not breaking the added functionality of blocks3d; please note, this is a very dirty hack |
| Fri, 25 May 2012 20:28:00 +0400 |
Daniil Alexeyevsky |
Replaced allpy.util.Binder with functools.partial everywhere (functools.partial is 2.5-compatible) |
| Fri, 25 May 2012 20:12:23 +0400 |
Daniil Alexeyevsky |
Automated merge |
| Fri, 25 May 2012 20:09:45 +0400 |
Daniil Alexeyevsky |
Removed obsolete allpy.markup module (see #99) |
| Thu, 17 May 2012 02:04:41 +0400 |
Boris Nagaev |
pair-cores/web: change font of State and Count-up to make them noticeable |
| Thu, 17 May 2012 02:02:33 +0400 |
Boris Nagaev |
pair-cores/web: Alignment is now required input field |
| Thu, 17 May 2012 01:49:47 +0400 |
Boris Nagaev |
pair-cores: exit with status 255 on fail |
| Thu, 17 May 2012 01:41:55 +0400 |
Boris Nagaev |
pair-cores/web: run the program with option '--no-read-local' |
| Thu, 17 May 2012 01:37:11 +0400 |
Boris Nagaev |
geometrical-core: add option '--no-read-local' |
| Thu, 17 May 2012 01:32:26 +0400 |
Boris Nagaev |
pair-cores: add option '--no-read-local' |
| Thu, 17 May 2012 01:31:26 +0400 |
Boris Nagaev |
structure: add parameter 'read_local' to auto_pdb() |
| Wed, 16 May 2012 23:33:24 +0400 |
Boris Nagaev |
pair-cores/web: change size of alignment textarea to 12x60 |
| Wed, 16 May 2012 23:27:22 +0400 |
Boris Nagaev |
pair-cores/web: remove "Markup" input |
| Wed, 16 May 2012 23:21:30 +0400 |
Boris Nagaev |
pair-cores/web: add field "Execution log" |
| Wed, 16 May 2012 23:20:28 +0400 |
Boris Nagaev |
pair-cores/web: upgrade wt-classes to 1.4.0 |
| Thu, 05 Apr 2012 19:29:24 +0400 |
Daniil Alexeyevsky |
Fixed a typo (NameError) introduced in [d3605c58a377] |
| Thu, 05 Apr 2012 19:27:32 +0400 |
Daniil Alexeyevsky |
Alignment._remove_gap_columns worked incorrectly on blocks (only removed columns that were globally empty in alignment) |
| Thu, 05 Apr 2012 19:25:16 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
