| age |
author |
description |
| Thu, 21 Jul 2011 13:12:54 +0400 |
Daniil Alexeyevsky |
Allow markup to be tagged as saved / not saved (closes #83) |
| Tue, 19 Jul 2011 20:01:36 +0400 |
Daniil Alexeyevsky |
allpy.base.default_gaps is now list instead of set, with first item being the preferred output gap symbol |
| Tue, 19 Jul 2011 14:40:22 +0400 |
Daniil Alexeyevsky |
Added deprecation warnings to the deprecated functions. |
| Mon, 18 Jul 2011 18:12:03 +0400 |
Daniil Alexeyevsky |
allpy.base.MarkupContainerMixin: fix add_markup to always return the newly created markup |
| Fri, 15 Jul 2011 19:06:47 +0400 |
Daniil Alexeyevsky |
Enhanced allpy.base.Markup.sorted_values: it now accepts `map` and `default` arugments. Somewhat tested. (closes #67) |
| Fri, 15 Jul 2011 17:02:09 +0400 |
Daniil Alexeyevsky |
allpy.base: added parameter use_existing to *.add_markup() to allow same markup to be added multiple times explicitly [see #95] |
| Fri, 15 Jul 2011 16:43:03 +0400 |
Daniil Alexeyevsky |
Implemented & tested new markup API. See #95 |
| Fri, 15 Jul 2011 13:57:56 +0400 |
Daniil Alexeyevsky |
Added markups.by_name dictionary and markups.update() function to fill it. |
| Tue, 12 Jul 2011 23:52:54 +0400 |
Daniil Alexeyevsky |
allpy.base: when filling by_code3 tables, unmodified classes take precedence |
| Mon, 11 Jul 2011 17:24:30 +0400 |
Daniil Alexeyevsky |
allpy.base cleanup: removed excess empty lines. |
| Mon, 11 Jul 2011 14:29:54 +0400 |
Daniil Alexeyevsky |
Roll-back a bug introduces by dirty hand-merge in [723]. (closes #74) (see #76) |
| Fri, 08 Jul 2011 18:30:04 +0400 |
Boris Burkov |
create_monomer_homology once tested to return (not sure, whether the answer is perfect). allpy.base is essentially like dendik's one now (Column now doesn't know its alignment). |
| Fri, 08 Jul 2011 16:20:20 +0400 |
Boris Burkov |
Merge between Burkov and others. |
| Wed, 06 Jul 2011 22:28:11 +0400 |
Boris Burkov |
Merge between Burkov and others, I've saved self.alignment for Column. |
| Wed, 06 Jul 2011 21:16:41 +0400 |
Boris Burkov |
Mostly meaningless commit |
| Fri, 08 Jul 2011 12:03:43 +0400 |
Daniil Alexeyevsky |
Added docstrings to base markup classes |
| Thu, 07 Jul 2011 22:32:21 +0400 |
Daniil Alexeyevsky |
Implemented markup fileIO (closes #56) |
| Thu, 07 Jul 2011 22:27:14 +0400 |
Daniil Alexeyevsky |
Renamed Markup.as_list() to Markup.sorted_values() and added Markup.sorted_keys() |
| Thu, 07 Jul 2011 19:32:44 +0400 |
Daniil Alexeyevsky |
API cleanup: alignment.to_file() now returns self |
| Thu, 07 Jul 2011 19:21:12 +0400 |
Daniil Alexeyevsky |
Added fileio.File.read_alignment and fileio.File.write_alignment [closes #57] |
| Tue, 05 Jul 2011 19:18:35 +0400 |
Daniil Alexeyevsky |
Added *Markup.as_list method (represent markup as a list). |
| Tue, 05 Jul 2011 19:10:47 +0400 |
Daniil Alexeyevsky |
base: Extracted common part of different base classes of markups to a common ancestor class |
| Tue, 05 Jul 2011 18:30:42 +0400 |
Daniil Alexeyevsky |
Implemented SequenceCaseMarkup along with the required changes to Monomer. |
| Tue, 05 Jul 2011 16:55:34 +0400 |
Daniil Alexeyevsky |
Minor code cleanup |
| Sat, 02 Jul 2011 15:42:49 +0400 |
Daniil Alexeyevsky |
Fixed simple bugs in markups discovered by primitive tests |
| 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 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 |
| 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 13:31:18 +0400 |
Boris Burkov |
Column knows its alignment now, Column.__repr__ is created to return <Column 112>. |
| 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 15:37:20 +0400 |
Boris Burkov |
Merge between pickled monomers and non-sequence-wise blocks_finder. |
| 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 16:49:44 +0400 |
Daniil Alexeyevsky |
Added necessary hooks for monomer pickling [closes #35] |
| Wed, 18 May 2011 21:38:17 +0400 |
Daniil Alexeyevsky |
Monomer.== now allows comparison with None |
| Tue, 03 May 2011 21:04:29 +0400 |
Daniil Alexeyevsky |
Added base.Alignment.rows_as_strings |
| Sat, 26 Mar 2011 00:15:56 +0300 |
Daniil Alexeyevsky |
Fixed alignment output: don't use 'write_string', since in only works for fasta |
| Thu, 24 Mar 2011 21:10:12 +0300 |
Daniil Alexeyevsky |
Bug in base.Alignment.remove_gap_columns (reversed(enumerate(...)) is surprisingly illegal python construct) |
| Thu, 24 Mar 2011 20:46:06 +0300 |
Daniil Alexeyevsky |
Clean rewrite of fileio |
| Mon, 28 Feb 2011 21:17:41 +0300 |
Daniil Alexeyevsky |
Reimplemented flush(direction) as processor1.2.0 |
| Wed, 23 Feb 2011 19:52:04 +0300 |
boris (kodomo) |
export to msf: fix bugs |
| Thu, 17 Feb 2011 10:30:31 +0300 |
boris |
base: remove useless prints |
| Tue, 15 Feb 2011 22:45:34 +0300 |
Daniil Alexeyevsky |
Tested and fixed Block.process(*, False, False) |
| Tue, 15 Feb 2011 21:46:05 +0300 |
Daniil Alexeyevsky |
Fixed erroneous assertion in Alignment._replace_column_contents helper of Alignment.process |
| 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 15:04:17 +0300 |
boris (netbook) |
add fileio module, remove fasta module, add msf support (see #31) |
| 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 |
| 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 15:51:07 +0300 |
Daniil Alexeyevsky |
Code cleanup: removed no longer relevant comments in allpy.base |
| Thu, 03 Feb 2011 13:51:39 +0300 |
boris |
add __eq__ and __ne__ operators to Sequence and Column |
| Wed, 02 Feb 2011 21:33:29 +0300 |
Daniil Alexeyevsky |
Fixed name error in base |
