| age |
author |
description |
| 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 |
| Wed, 15 Dec 2010 20:31:06 +0300 |
Daniil Alexeyevsky |
Added vim modeline to allpy.protein |
| Wed, 15 Dec 2010 20:26:56 +0300 |
Daniil Alexeyevsky |
Quick hack base.Alignment to resolve name errors in base |
| Wed, 15 Dec 2010 20:10:03 +0300 |
Daniil Alexeyevsky |
Removed base.Sequence.from_slice |
| Wed, 15 Dec 2010 20:06:27 +0300 |
Daniil Alexeyevsky |
base.Sequence major cleanup |
| Wed, 15 Dec 2010 19:19:11 +0300 |
Daniil Alexeyevsky |
Moved PDB parts of allpy.base.Sequence to allpy.pdb.Sequence |
| Wed, 15 Dec 2010 18:58:54 +0300 |
Daniil Alexeyevsky |
Converted base.Sequence.from_string to conform with new design |
| Wed, 15 Dec 2010 18:40:38 +0300 |
Daniil Alexeyevsky |
Removed line with trailing space to check mercurial hook |
| Wed, 15 Dec 2010 18:40:23 +0300 |
Daniil Alexeyevsky |
Added line with trailing space to check mercurial hook |
| Wed, 15 Dec 2010 18:30:19 +0300 |
Daniil Alexeyevsky |
Code cleanup: removed trailing spaces everywhere in the code |
| Wed, 15 Dec 2010 02:22:38 +0300 |
Daniil Alexeyevsky |
Fixed reference to module index in docs |
| Wed, 15 Dec 2010 02:13:30 +0300 |
Daniil Alexeyevsky |
Regenerated Sphinx autodocs cleaner. |
| Wed, 15 Dec 2010 01:51:52 +0300 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Wed, 15 Dec 2010 01:51:50 +0300 |
Daniil Alexeyevsky |
Trivial fixes to ReST in docstring markup |
| Wed, 15 Dec 2010 00:46:13 +0300 |
boris |
repeats: mistake in intersection determination fixed |
