| age |
author |
description |
| Tue, 08 Feb 2011 15:51:07 +0300 |
Daniil Alexeyevsky |
Code cleanup: removed no longer relevant comments in allpy.base |
| Tue, 08 Feb 2011 15:01:22 +0300 |
Daniil Alexeyevsky |
Removed obsolete protein.Alignment.muscle_realign, updated calls to it everywhere |
| Mon, 07 Feb 2011 22:02:20 +0300 |
boris |
merge |
| Mon, 07 Feb 2011 22:00:55 +0300 |
boris |
graph.py: remove useless copy of edges |
| Mon, 07 Feb 2011 21:46:43 +0300 |
Daniil Alexeyevsky |
Replaced all calls to obsolete Alignment.to_fasta() with Alignment.to_file() |
| Mon, 07 Feb 2011 21:44:38 +0300 |
Daniil Alexeyevsky |
Replaced all calls to obsolete Block.flush_left() with Block.flush("left") |
| Mon, 07 Feb 2011 21:40:14 +0300 |
Daniil Alexeyevsky |
Replaced calls to obsolete Alignment.from_file() with Alignment().append_file everywhere |
| Mon, 07 Feb 2011 21:08:23 +0300 |
boris |
blocks3d/wt: improved build file |
| Thu, 03 Feb 2011 21:09:15 +0300 |
boris |
graph.py: improvements |
| Thu, 03 Feb 2011 14:49:33 +0300 |
boris |
graph: reimplement bron_kerbosh with yields |
| Thu, 03 Feb 2011 13:56:57 +0300 |
boris |
align allpy_pdb.py with changes in graph.py |
| Thu, 03 Feb 2011 13:51:39 +0300 |
boris |
add __eq__ and __ne__ operators to Sequence and Column |
| Thu, 03 Feb 2011 13:18:05 +0300 |
boris |
merge |
| Thu, 03 Feb 2011 12:24:54 +0300 |
boris |
graph.py: refactoring |
| Wed, 02 Feb 2011 17:25:03 +0300 |
boris |
allpy_pdb: fixes |
| Wed, 02 Feb 2011 17:20:14 +0300 |
boris |
improve graph.py (tests, fixes) |
| Wed, 02 Feb 2011 22:09:41 +0300 |
Daniil Alexeyevsky |
Added test/freqs.py: a tool to print frequencies of letters by position in alignment |
| 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 16:42:23 +0300 |
boris |
rename pdb.py to allpy_pdb.py |
| Wed, 02 Feb 2011 16:21:04 +0300 |
boris |
fix bug in allpy/pdb.py |
| Wed, 02 Feb 2011 15:50:20 +0300 |
boris |
refactoring of pdb-related code |
| Wed, 02 Feb 2011 15:37:15 +0300 |
boris |
fix buges to repair usecases1.py |
| Wed, 02 Feb 2011 15:31:10 +0300 |
boris |
fix usecase2.py (still not working) (see #1) |
| 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) |
| Tue, 01 Feb 2011 00:20:24 +0300 |
boris |
fix base processor (refs #23) |
| Mon, 31 Jan 2011 23:39:26 +0300 |
boris |
Implemented base processor for realignments (see #23) |
| Mon, 31 Jan 2011 20:42:42 +0300 |
Daniil Alexeyevsky |
Removed sphinx docs for allpy.data, since it somehow confused sphinx |
| Mon, 31 Jan 2011 19:28:33 +0300 |
Daniil Alexeyevsky |
Rebuilt documentation indexes for Sphinx (re-run sphinx-autopackage) |
| 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 21:34:36 +0300 |
Daniil Alexeyevsky |
Implemented stub of allpy.processors module. (see #23) |
| 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 |
| Wed, 26 Jan 2011 16:01:50 +0300 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Tue, 25 Jan 2011 16:03:00 +0300 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Wed, 26 Jan 2011 15:38:36 +0300 |
boris (kodomo) |
improvements of mkcodes.py (see #16) |
| Tue, 25 Jan 2011 15:53:42 +0300 |
boris |
Add generator of codes.py file (rels #16) |
| Mon, 24 Jan 2011 22:01:21 +0300 |
boris |
fix #22 |
| Mon, 24 Jan 2011 21:40:10 +0300 |
boris |
fix lib/sequence.py. bug when pdb chain is empty string |
| Mon, 24 Jan 2011 21:36:08 +0300 |
boris |
(debug) ses_str.py |
| 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) |
