| age |
author |
description |
| 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 |
| 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 15:37:15 +0300 |
boris |
fix buges to repair usecases1.py |
| 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) |
| Mon, 31 Jan 2011 19:12:05 +0300 |
Daniil Alexeyevsky |
base.Alignment.process: added parameters to control what to copy |
| Mon, 31 Jan 2011 18:44:23 +0300 |
Daniil Alexeyevsky |
Fixed bugs & refactored base.Alignment.process & it's helpers |
| Wed, 26 Jan 2011 22:25:13 +0300 |
Daniil Alexeyevsky |
Implemented (uglyishly) Alignment.process. (see #25) |
| Wed, 26 Jan 2011 21:21:36 +0300 |
Daniil Alexeyevsky |
Implemented Alignment.remove_gap_columns() (see #25) |
| Wed, 26 Jan 2011 21:17:01 +0300 |
Daniil Alexeyevsky |
Block.flush_left() -> Alignment.flush("left"); implemented flushing left, right and center. (see #25) |
| Wed, 26 Jan 2011 21:03:23 +0300 |
Daniil Alexeyevsky |
Renamed Alignment.to_fasta -> Alignment.to_file. (see #25) |
| Wed, 26 Jan 2011 20:59:20 +0300 |
Daniil Alexeyevsky |
Renamed Alignment.column_at -> Alignment._column_at, since this is somewhat obscure method, not for external users. (see #25) |
| Wed, 26 Jan 2011 20:57:43 +0300 |
Daniil Alexeyevsky |
All base.Alignment.append_* methods now return self. (see #25) |
| Wed, 26 Jan 2011 20:56:33 +0300 |
Daniil Alexeyevsky |
Renamed Alignment.append_row -> Alignment.append_row_from_string. (see #25) |
| Wed, 26 Jan 2011 20:54:38 +0300 |
Daniil Alexeyevsky |
Removed all trailing spaces in base.py |
| Wed, 26 Jan 2011 20:45:34 +0300 |
Daniil Alexeyevsky |
Renamed Alignment.from_file -> Alignment.append_file |
| Mon, 24 Jan 2011 22:01:21 +0300 |
boris |
fix #22 |
| Fri, 21 Jan 2011 15:28:26 +0300 |
Daniil Alexeyevsky |
Fixed references to monomer code tables. (closes #17) |
| Thu, 20 Jan 2011 22:31:37 +0300 |
Daniil Alexeyevsky |
Renamed methods of Alignment as discussed (refs #12) |
| Thu, 20 Jan 2011 22:07:23 +0300 |
Daniil Alexeyevsky |
base: removed Sequence.from_fasta (rels #12) |
| Thu, 20 Jan 2011 22:06:57 +0300 |
Daniil Alexeyevsky |
base: introduced Sequence.from_monomers instead of Sequence() (rels #12) |
| Thu, 20 Jan 2011 22:01:41 +0300 |
Daniil Alexeyevsky |
Removed all irrelevant super() invocations. (rels #13) |
| Fri, 17 Dec 2010 16:36:00 +0300 |
Daniil Alexeyevsky |
Added somewhat reasonable str and repr for Monomer and Sequence |
| Fri, 17 Dec 2010 16:28:58 +0300 |
Daniil Alexeyevsky |
Got rid of all MonomerType classes |
| Fri, 17 Dec 2010 00:57:06 +0300 |
Daniil Alexeyevsky |
Column object must be hashable, by identity. |
| Fri, 17 Dec 2010 00:35:31 +0300 |
Daniil Alexeyevsky |
Added to base.Monomer missing properties: code1, code3, name, is_modified |
| Fri, 17 Dec 2010 00:32:13 +0300 |
Daniil Alexeyevsky |
Trivial bugfixes in base. Fixed Alignment.from_fasta and Sequence interface |
| Fri, 17 Dec 2010 00:25:46 +0300 |
Daniil Alexeyevsky |
Trivial fixes in allpy.base.Block |
| Fri, 17 Dec 2010 00:22:16 +0300 |
Daniil Alexeyevsky |
Trivial fixes in base.Block |
| Fri, 17 Dec 2010 00:18:19 +0300 |
Daniil Alexeyevsky |
Block is actually a mixing for Alignment |
| Thu, 16 Dec 2010 23:45:57 +0300 |
Daniil Alexeyevsky |
Added allpy.base.Sequence.__hash__: sequences are hashed by identity |
| Thu, 16 Dec 2010 23:43:18 +0300 |
Daniil Alexeyevsky |
Fixed module imports of allpy.base |
| Thu, 16 Dec 2010 23:42:42 +0300 |
Daniil Alexeyevsky |
Moved leftover junk from allpy.base to allpy.pdb |
| Thu, 16 Dec 2010 23:42:14 +0300 |
Daniil Alexeyevsky |
Changed interfaces of allpy.fasta, updated allpy.base accordingly |
| Thu, 16 Dec 2010 22:30:32 +0300 |
Daniil Alexeyevsky |
Added base.Block.flush_left |
| Thu, 16 Dec 2010 22:20:22 +0300 |
Daniil Alexeyevsky |
Removed obsolete methods from base Block: save_fasta, save_xstring, xstring, monomers |
| Thu, 16 Dec 2010 21:08:03 +0300 |
Daniil Alexeyevsky |
Added calls to super to all classes in allpy.base |
| Thu, 16 Dec 2010 20:47:09 +0300 |
Daniil Alexeyevsky |
Moved base.Blog.geometrical_cores to pdb.Block |
| Thu, 16 Dec 2010 20:45:57 +0300 |
Daniil Alexeyevsky |
Moved PDB-related stuff from base Block to allpy.pdb.Block |
| Thu, 16 Dec 2010 20:42:42 +0300 |
Daniil Alexeyevsky |
Converted docstrings and init of base.Block to match our plan |
| Thu, 16 Dec 2010 19:24:22 +0300 |
Daniil Alexeyevsky |
Allow user to specify gap characters when parsing alignment |
| Thu, 16 Dec 2010 19:08:16 +0300 |
Daniil Alexeyevsky |
Added explanation for algorithm to add gapped line to base Alignment |
| Thu, 16 Dec 2010 19:05:11 +0300 |
Daniil Alexeyevsky |
Added method column_at() to base Alignment to aid creation of new columns. |
| Thu, 16 Dec 2010 18:56:21 +0300 |
Daniil Alexeyevsky |
Removed controversial methods of allpy.base.Alignment: length, height, identity |
| Thu, 16 Dec 2010 18:55:01 +0300 |
Daniil Alexeyevsky |
Added (stub of) the class allpy.base.Column |
| Thu, 16 Dec 2010 18:51:05 +0300 |
Daniil Alexeyevsky |
Implemented allpy.base.Alignment row/column model: methods rows(), *_as_lists() |
| Thu, 16 Dec 2010 18:35:56 +0300 |
Daniil Alexeyevsky |
Removed obsolete allpy.base.Alignment.column() method |
| Thu, 16 Dec 2010 18:35:25 +0300 |
Daniil Alexeyevsky |
Moved allpy.base.Alignment.muscle_align to allpy.protein |
