| age |
author |
description |
| Thu, 07 Jul 2011 22:32:21 +0400 |
Daniil Alexeyevsky |
Implemented markup fileIO (closes #56) |
| Thu, 07 Jul 2011 22:27:14 +0400 |
Daniil Alexeyevsky |
Renamed Markup.as_list() to Markup.sorted_values() and added Markup.sorted_keys() |
| Thu, 07 Jul 2011 21:22:53 +0400 |
Andrei |
Automated merge with ssh://kodomo.fbb.msu.ru/allpy |
| Thu, 07 Jul 2011 21:22:45 +0400 |
Andrei |
Static method .case_homology added |
| Thu, 07 Jul 2011 21:21:29 +0400 |
Andrei |
Makes (case sensitive by request) homology classes for a number of input fasta alignments |
| Thu, 07 Jul 2011 21:19:30 +0400 |
Andrei |
Function case_homology moved to allpy.homology |
| Thu, 07 Jul 2011 19:32:44 +0400 |
Daniil Alexeyevsky |
API cleanup: alignment.to_file() now returns self |
| Thu, 07 Jul 2011 19:21:12 +0400 |
Daniil Alexeyevsky |
Added fileio.File.read_alignment and fileio.File.write_alignment [closes #57] |
| Thu, 07 Jul 2011 12:53:53 +0400 |
Andrei |
Automated merge with ssh://kodomo.fbb.msu.ru/allpy |
| Thu, 07 Jul 2011 12:53:42 +0400 |
Andrei |
alignment_blocks method added to homology and tested. Blocks found in monomer homology file can be now returned to alignment blocks |
| Wed, 06 Jul 2011 20:49:31 +0200 |
boris |
structure/SequenceMixin: add resi_begin and resi_end parameters to PDB loader |
| Wed, 06 Jul 2011 18:05:51 +0400 |
Andrei |
In homology 'residue' changed to 'monomer' everywhere |
| Wed, 06 Jul 2011 18:04:58 +0400 |
Andrei |
In homology 'residue' changed to 'monomer' everywhere |
| Wed, 06 Jul 2011 14:08:46 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Tue, 05 Jul 2011 19:33:22 +0400 |
Daniil Alexeyevsky |
Added NEWS entry about Markups |
| Wed, 06 Jul 2011 11:42:41 +0400 |
Andrei |
The util makes residue holomogy file from fasta alignment. May take in account case of letters |
| Tue, 05 Jul 2011 21:54:21 +0400 |
Andrei |
Automated merge with ssh://kodomo.fbb.msu.ru/allpy |
| Tue, 05 Jul 2011 21:54:10 +0400 |
Andrei |
homology endowed with column_number in all methods and passed through tests |
| Tue, 05 Jul 2011 19:19:10 +0400 |
Daniil Alexeyevsky |
Added test for SequenceCaseMarkup and SequenceMarkup.as_list() |
| Tue, 05 Jul 2011 19:18:35 +0400 |
Daniil Alexeyevsky |
Added *Markup.as_list method (represent markup as a list). |
| Tue, 05 Jul 2011 19:10:47 +0400 |
Daniil Alexeyevsky |
base: Extracted common part of different base classes of markups to a common ancestor class |
| Tue, 05 Jul 2011 18:30:42 +0400 |
Daniil Alexeyevsky |
Implemented SequenceCaseMarkup along with the required changes to Monomer. |
| Tue, 05 Jul 2011 16:55:34 +0400 |
Daniil Alexeyevsky |
Minor code cleanup |
| Mon, 04 Jul 2011 22:38:59 +0400 |
Andrei |
Method homology.highest_blocks is implemented. Blocks are constructed from residue homology file. Test version. |
| Mon, 04 Jul 2011 15:28:21 +0400 |
Andrei |
homology.write_block passed through test |
| Mon, 04 Jul 2011 13:42:28 +0400 |
Andrei |
homology.write_block added |
| Sat, 02 Jul 2011 19:40:11 +0400 |
Andrei |
homology.py passes through tests of methods: .write_monomer,.write_class,.read,.compare_with,.two_vs_one |
| Sat, 02 Jul 2011 16:43:41 +0400 |
Andrei |
Automated merge with ssh://kodomo.fbb.msu.ru/allpy |
| Sat, 02 Jul 2011 16:43:35 +0400 |
Andrei |
Minor changes of homology.py |
| Sat, 02 Jul 2011 15:43:48 +0400 |
Daniil Alexeyevsky |
Makefile: target tests implies using the current directory as PYTHONPATH |
| Sat, 02 Jul 2011 15:43:14 +0400 |
Daniil Alexeyevsky |
Fixed typos in markup tests |
| Sat, 02 Jul 2011 15:42:49 +0400 |
Daniil Alexeyevsky |
Fixed simple bugs in markups discovered by primitive tests |
| Sat, 02 Jul 2011 15:29:06 +0400 |
Daniil Alexeyevsky |
Added test for manual markups |
| Fri, 01 Jul 2011 19:50:08 +0400 |
Andrei |
Automated merge with ssh://kodomo.fbb.msu.ru/allpy |
| Fri, 01 Jul 2011 19:48:54 +0400 |
Andrei |
Residue homology classes added (module allpy/homology) |
| Fri, 01 Jul 2011 16:05:51 +0400 |
Daniil Alexeyevsky |
Added trivial tests for basic markups |
| Fri, 01 Jul 2011 15:46:32 +0400 |
Daniil Alexeyevsky |
Added module markups with sample *Index and *Number markups |
| Fri, 01 Jul 2011 15:46:09 +0400 |
Daniil Alexeyevsky |
Added base classes for Sequence and Alignment markups |
| Fri, 01 Jul 2011 14:59:21 +0400 |
boris (kodomo) |
base: fix a bug (using UserList instead of util.UserList) |
| Fri, 01 Jul 2011 12:08:18 +0400 |
Boris Burkov |
Merge with Borya Nagaev |
| Fri, 01 Jul 2011 11:42:26 +0400 |
Boris Burkov |
Merge between me and central. |
| Fri, 01 Jul 2011 11:40:00 +0400 |
Boris Burkov |
This is a half-rollback commit with base.py from central repo and my blocks_finder.py |
| Fri, 01 Jul 2011 09:52:49 +0400 |
Boris Burkov |
Massive changes to my program |
| Fri, 01 Jul 2011 10:32:37 +0400 |
boris (kodomo) |
blocks3d/www: fix log-file caused bug of building |
| Fri, 01 Jul 2011 03:22:10 +0400 |
boris |
blocks3d/www: change test to represent conservative columns inside block |
| Fri, 01 Jul 2011 03:21:08 +0400 |
boris |
blocks3d/www: mark conservative columns inside blocks |
| Fri, 01 Jul 2011 03:01:17 +0400 |
boris |
blocks3d/www: fix disconnection of binders to mouseover after click |
| Fri, 01 Jul 2011 02:54:03 +0400 |
boris |
blocks3d/www: improve code, create function to test whether column is conservative |
| Thu, 30 Jun 2011 16:05:09 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Thu, 30 Jun 2011 16:04:38 +0400 |
Daniil Alexeyevsky |
Clarified NEWS record for bnagaev's changes |
| Wed, 29 Jun 2011 13:51:12 +0400 |
boris |
blocks3d/www: change color of block on mouse over |
| Wed, 29 Jun 2011 12:46:28 +0400 |
boris |
blocks3d/www: proportional brightness of conservative columns and the rest of block |
| Wed, 29 Jun 2011 11:55:16 +0400 |
boris |
add test for blocks3d/www |
| Mon, 27 Jun 2011 13:42:42 +0400 |
boris |
Improve javascript blocks viewer |
| Sat, 25 Jun 2011 00:46:13 +0400 |
Daniil Alexeyevsky |
Added attribute column to lists in result of columns_as_lists |
| Wed, 15 Jun 2011 17:12:05 +0400 |
Daniil Alexeyevsky |
Reverted 654:c32e728b98d7: Column knows its alignment now, Column.__repr__ is created to return <Column 112>. |
| Tue, 14 Jun 2011 22:22:04 +0400 |
boris |
blocks3d/www: chmod 644 source files |
| Tue, 14 Jun 2011 13:31:18 +0400 |
Boris Burkov |
Column knows its alignment now, Column.__repr__ is created to return <Column 112>. |
| Sun, 12 Jun 2011 15:36:07 +0400 |
Boris Burkov |
50% speed up for blocks_finder due to local application of remove_contained_preblocks. |
| Fri, 10 Jun 2011 16:15:35 +0400 |
Daniil Alexeyevsky |
Code cleanup: moved Alignment.row_as_list and Alignment.row_as_string to the proper position. |
