| age |
author |
description |
| Tue, 15 Feb 2011 21:11:17 +0300 |
Daniil Alexeyevsky |
Fixed command line processing for mass_realine_blocks.py |
| Tue, 15 Feb 2011 21:03:19 +0300 |
Daniil Alexeyevsky |
Added mass_realign_blocks util to apply muscle to multiple blocks in multiple files |
| Tue, 15 Feb 2011 20:29:53 +0300 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Tue, 15 Feb 2011 20:29:48 +0300 |
Daniil Alexeyevsky |
Added util realign_block (almost exact copy of flush_left) |
| Tue, 15 Feb 2011 00:07:57 +0300 |
boris |
blocks3d/wt improvement |
| Mon, 14 Feb 2011 22:21:39 +0300 |
boris |
geometrical-core: export to fasta and msf |
| Mon, 14 Feb 2011 22:20:31 +0300 |
boris |
fix Markup |
| Mon, 14 Feb 2011 22:17:44 +0300 |
boris |
fix MsfIo |
| Mon, 14 Feb 2011 21:37:19 +0300 |
boris |
markup.py: add Markup.__setitem__ methor for convenience |
| Mon, 14 Feb 2011 21:04:47 +0300 |
boris |
improve markup module: |
| Mon, 14 Feb 2011 19:32:51 +0300 |
boris |
add class Markup (see #30) |
| Mon, 14 Feb 2011 16:21:29 +0300 |
boris |
geometrical-core: now can read from msf |
| Mon, 14 Feb 2011 16:19:42 +0300 |
boris |
msf io: fix bugs |
| Mon, 14 Feb 2011 12:33:39 +0300 |
boris |
graph.py: use "is not" instead of "!=" for columns |
| Mon, 14 Feb 2011 12:30:49 +0300 |
boris |
add Monomer.__ne__ (see #26) |
| Mon, 14 Feb 2011 12:07:08 +0300 |
boris |
merge |
| Mon, 14 Feb 2011 12:06:30 +0300 |
boris |
Backed out changeset 3a802644d798 (see #26) |
| Fri, 11 Feb 2011 19:15:58 +0300 |
boris (kodomo) |
In graph.py: costs renamed to weights |
| Fri, 11 Feb 2011 15:04:17 +0300 |
boris (netbook) |
add fileio module, remove fasta module, add msf support (see #31) |
| Fri, 11 Feb 2011 14:13:42 +0300 |
boris (netbook) |
pdb: fix a bug in save_pdb |
| Fri, 11 Feb 2011 01:02:34 +0300 |
boris |
geometrical_core: add surrounded columns to core (see #28) |
| Fri, 11 Feb 2011 00:30:43 +0300 |
Daniil Alexeyevsky |
Fixed docstring of base.Block to not make false imperssion that rows/columns are sets |
| Thu, 10 Feb 2011 23:35:57 +0300 |
boris |
graph: use "is" instead of "==" when compare vertices |
| Tue, 08 Feb 2011 21:54:20 +0300 |
Daniil Alexeyevsky |
Added tests for flush* operations |
| Tue, 08 Feb 2011 21:49:57 +0300 |
Daniil Alexeyevsky |
Fixed Alignment._wipe "dictionary changed size during iteration" error |
| Tue, 08 Feb 2011 21:09:35 +0300 |
Daniil Alexeyevsky |
Code cleanup in allpy.base.Alignment._wipe |
| Tue, 08 Feb 2011 21:03:10 +0300 |
Daniil Alexeyevsky |
test_base: test Alignment creation & output |
| Tue, 08 Feb 2011 20:59:56 +0300 |
Daniil Alexeyevsky |
Removed trailing spaces in FASTA files produced by allpy.fasta |
| Tue, 08 Feb 2011 20:40:38 +0300 |
Daniil Alexeyevsky |
Added a few tests on monomer construction |
| Tue, 08 Feb 2011 15:51:07 +0300 |
Daniil Alexeyevsky |
Code cleanup: removed no longer relevant comments in allpy.base |
| Tue, 08 Feb 2011 15:01:22 +0300 |
Daniil Alexeyevsky |
Removed obsolete protein.Alignment.muscle_realign, updated calls to it everywhere |
| Mon, 07 Feb 2011 22:02:20 +0300 |
boris |
merge |
| Mon, 07 Feb 2011 22:00:55 +0300 |
boris |
graph.py: remove useless copy of edges |
| Mon, 07 Feb 2011 21:46:43 +0300 |
Daniil Alexeyevsky |
Replaced all calls to obsolete Alignment.to_fasta() with Alignment.to_file() |
| Mon, 07 Feb 2011 21:44:38 +0300 |
Daniil Alexeyevsky |
Replaced all calls to obsolete Block.flush_left() with Block.flush("left") |
| Mon, 07 Feb 2011 21:40:14 +0300 |
Daniil Alexeyevsky |
Replaced calls to obsolete Alignment.from_file() with Alignment().append_file everywhere |
| Mon, 07 Feb 2011 21:08:23 +0300 |
boris |
blocks3d/wt: improved build file |
| Thu, 03 Feb 2011 21:09:15 +0300 |
boris |
graph.py: improvements |
| Thu, 03 Feb 2011 14:49:33 +0300 |
boris |
graph: reimplement bron_kerbosh with yields |
| Thu, 03 Feb 2011 13:56:57 +0300 |
boris |
align allpy_pdb.py with changes in graph.py |
| Thu, 03 Feb 2011 13:51:39 +0300 |
boris |
add __eq__ and __ne__ operators to Sequence and Column |
| Thu, 03 Feb 2011 13:18:05 +0300 |
boris |
merge |
| Thu, 03 Feb 2011 12:24:54 +0300 |
boris |
graph.py: refactoring |
| Wed, 02 Feb 2011 17:25:03 +0300 |
boris |
allpy_pdb: fixes |
| Wed, 02 Feb 2011 17:20:14 +0300 |
boris |
improve graph.py (tests, fixes) |
| Wed, 02 Feb 2011 22:09:41 +0300 |
Daniil Alexeyevsky |
Added test/freqs.py: a tool to print frequencies of letters by position in alignment |
| Wed, 02 Feb 2011 21:33:29 +0300 |
Daniil Alexeyevsky |
Fixed name error in base |
| Wed, 02 Feb 2011 21:28:55 +0300 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Wed, 02 Feb 2011 21:28:18 +0300 |
Daniil Alexeyevsky |
allpy.base: code cleanup |
| Wed, 02 Feb 2011 16:42:23 +0300 |
boris |
rename pdb.py to allpy_pdb.py |
| Wed, 02 Feb 2011 16:21:04 +0300 |
boris |
fix bug in allpy/pdb.py |
| Wed, 02 Feb 2011 15:50:20 +0300 |
boris |
refactoring of pdb-related code |
| Wed, 02 Feb 2011 15:37:15 +0300 |
boris |
fix buges to repair usecases1.py |
| Wed, 02 Feb 2011 15:31:10 +0300 |
boris |
fix usecase2.py (still not working) (see #1) |
| Tue, 01 Feb 2011 23:08:08 +0300 |
Daniil Alexeyevsky |
Changed the way related types are stored for Alignment, Block, Sequence, Monomer |
| Tue, 01 Feb 2011 18:46:23 +0300 |
Daniil Alexeyevsky |
Code cleanup in base.Alignment._merge helper for base.Alignment.process |
| Tue, 01 Feb 2011 18:42:03 +0300 |
Daniil Alexeyevsky |
base.Alignment.process allows `function` to override copy_descriptions and copy_contents |
| Tue, 01 Feb 2011 18:36:26 +0300 |
Daniil Alexeyevsky |
Added alignment_type & block_type to both Alignment & Block |
| Tue, 01 Feb 2011 17:11:33 +0300 |
boris |
fixed bugs; usecase1.py works (see #23) (see #1) |
| Tue, 01 Feb 2011 00:20:24 +0300 |
boris |
fix base processor (refs #23) |
