| age |
author |
description |
| Fri, 01 Jul 2011 16:05:51 +0400 |
Daniil Alexeyevsky |
Added trivial tests for basic markups |
| Fri, 01 Jul 2011 15:46:32 +0400 |
Daniil Alexeyevsky |
Added module markups with sample *Index and *Number markups |
| Fri, 01 Jul 2011 15:46:09 +0400 |
Daniil Alexeyevsky |
Added base classes for Sequence and Alignment markups |
| Fri, 01 Jul 2011 14:59:21 +0400 |
boris (kodomo) |
base: fix a bug (using UserList instead of util.UserList) |
| Fri, 01 Jul 2011 12:08:18 +0400 |
Boris Burkov |
Merge with Borya Nagaev |
| Fri, 01 Jul 2011 11:42:26 +0400 |
Boris Burkov |
Merge between me and central. |
| Fri, 01 Jul 2011 11:40:00 +0400 |
Boris Burkov |
This is a half-rollback commit with base.py from central repo and my blocks_finder.py |
| Fri, 01 Jul 2011 09:52:49 +0400 |
Boris Burkov |
Massive changes to my program |
| Fri, 01 Jul 2011 10:32:37 +0400 |
boris (kodomo) |
blocks3d/www: fix log-file caused bug of building |
| Fri, 01 Jul 2011 03:22:10 +0400 |
boris |
blocks3d/www: change test to represent conservative columns inside block |
| Fri, 01 Jul 2011 03:21:08 +0400 |
boris |
blocks3d/www: mark conservative columns inside blocks |
| Fri, 01 Jul 2011 03:01:17 +0400 |
boris |
blocks3d/www: fix disconnection of binders to mouseover after click |
| Fri, 01 Jul 2011 02:54:03 +0400 |
boris |
blocks3d/www: improve code, create function to test whether column is conservative |
| Thu, 30 Jun 2011 16:05:09 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Thu, 30 Jun 2011 16:04:38 +0400 |
Daniil Alexeyevsky |
Clarified NEWS record for bnagaev's changes |
| Wed, 29 Jun 2011 13:51:12 +0400 |
boris |
blocks3d/www: change color of block on mouse over |
| Wed, 29 Jun 2011 12:46:28 +0400 |
boris |
blocks3d/www: proportional brightness of conservative columns and the rest of block |
| Wed, 29 Jun 2011 11:55:16 +0400 |
boris |
add test for blocks3d/www |
| Mon, 27 Jun 2011 13:42:42 +0400 |
boris |
Improve javascript blocks viewer |
| Sat, 25 Jun 2011 00:46:13 +0400 |
Daniil Alexeyevsky |
Added attribute column to lists in result of columns_as_lists |
| Wed, 15 Jun 2011 17:12:05 +0400 |
Daniil Alexeyevsky |
Reverted 654:c32e728b98d7: Column knows its alignment now, Column.__repr__ is created to return <Column 112>. |
| Tue, 14 Jun 2011 22:22:04 +0400 |
boris |
blocks3d/www: chmod 644 source files |
| Tue, 14 Jun 2011 13:31:18 +0400 |
Boris Burkov |
Column knows its alignment now, Column.__repr__ is created to return <Column 112>. |
| Sun, 12 Jun 2011 15:36:07 +0400 |
Boris Burkov |
50% speed up for blocks_finder due to local application of remove_contained_preblocks. |
| Fri, 10 Jun 2011 16:15:35 +0400 |
Daniil Alexeyevsky |
Code cleanup: moved Alignment.row_as_list and Alignment.row_as_string to the proper position. |
| Fri, 10 Jun 2011 16:14:39 +0400 |
Daniil Alexeyevsky |
Cleaned up code & docstrings of Alignment.row_as_string and Alignment.row_as_list |
| Fri, 10 Jun 2011 16:07:13 +0400 |
Daniil Alexeyevsky |
NEWS entry for new methods of Alignment by BurkovBA |
| Fri, 10 Jun 2011 15:37:20 +0400 |
Boris Burkov |
Merge between pickled monomers and non-sequence-wise blocks_finder. |
| Fri, 10 Jun 2011 15:33:16 +0400 |
Boris Burkov |
Some testing done for blocks_finder:remove_contained_preblocks time-consumption optimisation. |
| Wed, 08 Jun 2011 15:15:57 +0400 |
Boris Burkov |
Changed the __repr__for sequence to <Sequence code1>. Renamed row() to row_as_list(). |
| Tue, 07 Jun 2011 17:37:06 +0400 |
Boris Burkov |
Changed __repr__ for sequence and monomer in allpy.base. Added row and |
| Wed, 08 Jun 2011 21:31:02 +0400 |
Daniil Alexeyevsky |
Fixed monomer pickling to avoid name clashes. This breaks pickle backwards-compatiblity! [see #35] |
| Fri, 03 Jun 2011 16:59:45 +0400 |
Daniil Alexeyevsky |
Added a test for pickling |
| Fri, 03 Jun 2011 16:51:56 +0400 |
Daniil Alexeyevsky |
Minor code cleanup: fixed order of imports for PEP8 compliance |
| Fri, 03 Jun 2011 16:49:44 +0400 |
Daniil Alexeyevsky |
Added necessary hooks for monomer pickling [closes #35] |
| Fri, 03 Jun 2011 15:30:48 +0400 |
Daniil Alexeyevsky |
Added some tests for allpy.fileio with format conversions and StringIO |
| Fri, 03 Jun 2011 15:29:47 +0400 |
Daniil Alexeyevsky |
allpy.fileio: use stdin/stdout when communicating with EMBOSS [closes #38] |
| Mon, 30 May 2011 20:38:58 +0400 |
Daniil Alexeyevsky |
allpy.fileio: wrapped some calls into try-finally; EmbossFile should now behave correctly if exceptions occur now |
| Wed, 25 May 2011 20:25:32 +0400 |
Daniil Alexeyevsky |
Added sectioning comments to allpy.processors |
| Wed, 25 May 2011 19:49:12 +0400 |
Daniil Alexeyevsky |
allpy.processors: cleaner reimplementation of remove_gaps option in Muscle |
| Wed, 25 May 2011 19:46:20 +0400 |
Daniil Alexeyevsky |
allpy.processors: code cleanup, added more docstrings |
| Tue, 24 May 2011 22:12:57 +0400 |
Daniil Alexeyevsky |
Implemented processor.FixOrder and processor.BypassEmpty as processors instead of hacky fix_order and fix_empty helper functions |
| Fri, 20 May 2011 13:35:09 +0400 |
Daniil Alexeyevsky |
Code cleanup allpy.processors: removed ExternalCommand.to_file; renamed no_gaps to remove_gaps in Muscle |
| Thu, 19 May 2011 22:32:38 +0400 |
Daniil Alexeyevsky |
NEWS entry about new Needle processor |
| Thu, 19 May 2011 22:29:38 +0400 |
Daniil Alexeyevsky |
Rewritten of test/usecase2 to make it work. It works, but is still hacky and ugly since it relies on markups, which are not sufficiently designed/implemented yet. |
| Thu, 19 May 2011 22:13:56 +0400 |
Daniil Alexeyevsky |
Implemented processors.Needle; hacky and dirty, just like the rest of the module |
| Wed, 18 May 2011 22:26:35 +0400 |
Daniil Alexeyevsky |
Fix fileio.EmbossFile: it was totally broken and serialized file objects to make arguments for seqret |
| Wed, 18 May 2011 22:25:40 +0400 |
Daniil Alexeyevsky |
Use more modern interfaces in test_base; document untested parts from code coverage test |
| Wed, 18 May 2011 21:38:17 +0400 |
Daniil Alexeyevsky |
Monomer.== now allows comparison with None |
| Mon, 16 May 2011 20:40:58 +0400 |
Daniil Alexeyevsky |
Added some docstrings to tests |
| Mon, 16 May 2011 20:32:39 +0400 |
Daniil Alexeyevsky |
Use python-coverage in nosetests |
| Mon, 16 May 2011 20:05:39 +0400 |
Daniil Alexeyevsky |
Ignore .coverage files from python-coverage |
| Wed, 04 May 2011 01:00:04 +0400 |
Daniil Alexeyevsky |
Added NEWS entry for the last change |
| Tue, 03 May 2011 21:06:36 +0400 |
Daniil Alexeyevsky |
Fixed import error for allpy.rna |
| Tue, 03 May 2011 21:04:29 +0400 |
Daniil Alexeyevsky |
Added base.Alignment.rows_as_strings |
| Tue, 03 May 2011 21:04:08 +0400 |
Daniil Alexeyevsky |
Added allpy.util.UserString, a clone of str with ability to add attributes |
| Fri, 29 Apr 2011 17:02:41 +0400 |
boris (kodomo) |
Merge with backout of 612:3a27920ff4ed and 613:71910cefe37a |
| Fri, 29 Apr 2011 17:01:29 +0400 |
boris (kodomo) |
Backout 612:3a27920ff4ed and 613:71910cefe37a |
| Fri, 29 Apr 2011 16:35:24 +0400 |
boris (kodomo) |
Automated merge with ssh://kodomo/allpy |
| Fri, 29 Apr 2011 16:21:23 +0400 |
boris (kodomo) |
pair_cores: add rasmol_output.py to generate rasmol script and superimposition |
