| age |
author |
description |
| 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 |
| Thu, 16 Dec 2010 03:16:52 +0300 |
Daniil Alexeyevsky |
Reimplemented allpy.base.Alignment.append_sequence |
| Thu, 16 Dec 2010 03:10:06 +0300 |
Daniil Alexeyevsky |
Added classes UserDict and UserList in allpy.util |
| Thu, 16 Dec 2010 03:09:02 +0300 |
Daniil Alexeyevsky |
Reimplemented allpy.base.Alignment.to_fasta |
| Thu, 16 Dec 2010 03:04:15 +0300 |
Daniil Alexeyevsky |
allpy.fasta.save_file: also do NOT produce extra spaces if either of name or description is not given |
| Thu, 16 Dec 2010 03:00:47 +0300 |
Daniil Alexeyevsky |
Do NOT produce ugly space at EOL in base.fasta.save_fasta |
| Thu, 16 Dec 2010 01:25:54 +0300 |
Daniil Alexeyevsky |
Experimenting with styles of docstrings in allpy.base.Alignment (to be recognized by Sphinx) |
| Thu, 16 Dec 2010 01:13:01 +0300 |
Daniil Alexeyevsky |
Removed trailing spaces |
| Thu, 16 Dec 2010 01:12:06 +0300 |
Daniil Alexeyevsky |
Clean reimplementation of allpy.base.Alignment.from_fasta |
| Wed, 15 Dec 2010 23:45:11 +0300 |
Daniil Alexeyevsky |
Fixed spaces |
| Wed, 15 Dec 2010 23:44:25 +0300 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Wed, 15 Dec 2010 23:44:20 +0300 |
Daniil Alexeyevsky |
Added base.Sequence.from_fasta |
| Wed, 15 Dec 2010 21:51:01 +0300 |
boris (kodomo) |
repeats: improve parsing |
| Wed, 15 Dec 2010 21:30:25 +0300 |
Daniil Alexeyevsky |
Fixed ReST warnings from docstrings in allpy.base |
| Wed, 15 Dec 2010 20:40:10 +0300 |
Daniil Alexeyevsky |
Proper rna.Monomer, rna.MonomerType, rna.Sequence |
| Wed, 15 Dec 2010 20:39:18 +0300 |
Daniil Alexeyevsky |
Proper dna.Monomer, dna.MonomerType, dna.Sequence |
| Wed, 15 Dec 2010 20:32:00 +0300 |
Daniil Alexeyevsky |
Made allpy.protein conform to PEP8 |
