| age |
author |
description |
| Fri, 21 Jan 2011 17:01:21 +0300 |
Daniil Alexeyevsky |
Added virtual monomer types for undefined letters N and X, changed all previous such monomers to be considered modified |
| Fri, 21 Jan 2011 15:28:26 +0300 |
Daniil Alexeyevsky |
Fixed references to monomer code tables. (closes #17) |
| Fri, 21 Jan 2011 15:28:00 +0300 |
Daniil Alexeyevsky |
Fixed docs for monomer code tables; changed names to better ones |
| Fri, 21 Jan 2011 15:22:22 +0300 |
Daniil Alexeyevsky |
Split data/codes into three separate lists (for rna, dna and proteins), (refs #17) |
| Fri, 21 Jan 2011 15:00:23 +0300 |
Daniil Alexeyevsky |
Fixed references to base interface according to previous changes (closes #12) |
| 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) |
| Thu, 20 Jan 2011 21:51:24 +0300 |
Daniil Alexeyevsky |
Changed names & docstrings of classes in allpy.pdb to identify their mixinity. (closes #13) |
| Wed, 19 Jan 2011 20:33:51 +0300 |
Daniil Alexeyevsky |
Added script to automatically set paths |
| Wed, 19 Jan 2011 17:22:02 +0300 |
Daniil Alexeyevsky |
Fixed syntax errors in usecase2 |
| Wed, 19 Jan 2011 16:57:38 +0300 |
Daniil Alexeyevsky |
Fixed: rna & dna sequences did not know their monomer types. |
| Wed, 19 Jan 2011 16:26:27 +0300 |
Daniil Alexeyevsky |
Implemented dummy Alignment and Block for dna and rna |
| Wed, 19 Jan 2011 16:11:04 +0300 |
Daniil Alexeyevsky |
Merge |
| Wed, 19 Jan 2011 16:10:27 +0300 |
Daniil Alexeyevsky |
Backed out changeset 2e9cbe32a554 |
| Fri, 14 Jan 2011 19:48:53 +0300 |
Daniil Alexeyevsky |
Added README.devel with a few words about PYTHONPATH |
| Wed, 12 Jan 2011 22:27:08 +0300 |
Andrei |
flush_left renamed to flush_left_vblock. flush_left_vblocks created for multiple blocks flush left |
| Wed, 12 Jan 2011 20:23:22 +0300 |
Andrei |
MSF output format by request implemented |
| Wed, 12 Jan 2011 19:55:00 +0300 |
Andrei |
Helps refined |
| Wed, 12 Jan 2011 19:36:16 +0300 |
Andrei |
Automated merge with ssh://kodomo.fbb.msu.ru/allpy |
| Wed, 12 Jan 2011 19:36:09 +0300 |
Andrei |
Command line parameters added |
| Sat, 18 Dec 2010 00:17:48 +0300 |
Daniil Alexeyevsky |
Added util flush_left.py |
| Sat, 18 Dec 2010 00:16:20 +0300 |
Daniil Alexeyevsky |
Syntax error in allpy.fasta |
| Fri, 17 Dec 2010 20:54:35 +0300 |
Daniil Alexeyevsky |
Fixed bug: fasta reader broke on files with Windows EOLs broke |
| 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 00:58:54 +0300 |
Daniil Alexeyevsky |
Bugfixes in test/usecase1. |
| Fri, 17 Dec 2010 00:57:35 +0300 |
Daniil Alexeyevsky |
save_fasta: always prepend space before description, even if no name is given |
| Fri, 17 Dec 2010 00:57:06 +0300 |
Daniil Alexeyevsky |
Column object must be hashable, by identity. |
| Fri, 17 Dec 2010 00:45:20 +0300 |
Daniil Alexeyevsky |
Added usecases from wiki to test/ directory |
| Fri, 17 Dec 2010 00:38:40 +0300 |
Daniil Alexeyevsky |
Fixed allpy.fasta.parse_file to not produce bogus empty sequence |
| 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 00:22:50 +0300 |
Daniil Alexeyevsky |
Added proper subclasses instantiation in allpy.protein |
| 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 19:17:08 +0300 |
Daniil Alexeyevsky |
Added allpy.util.remove_each helper |
| Thu, 16 Dec 2010 19:15:34 +0300 |
Daniil Alexeyevsky |
Added docstrings to allpy.util |
| 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 |
| Thu, 16 Dec 2010 18:30:43 +0300 |
Daniil Alexeyevsky |
Moved allpy.base.Alignment.secstr_has to allpy.pdb |
| Thu, 16 Dec 2010 03:26:57 +0300 |
Daniil Alexeyevsky |
allpy.base.Alignment is not a list of columns, but an object with attributes: sequences, columns |
