Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-08-13

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All times shown according to UTC.

Time Nick Message
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17:40 balin hi guys, do you remember that problem I had yesterday with slicing a domain from an alignment? I used column_from_residue_number() in LocatableSeq to solve it. Here is the code if you are interested http://gist.github.com/167330
17:48 pyrimidine balin: very succinct
17:49 pyrimidine mjensen isn't around; he should add that to the scrapbook
17:54 balin by the way, it looks like column_from_residue_number() does not use globally defined gap symbols: '-' and '.' are hardcoded there.
18:03 pyrimidine balin: Yes, unfortunately that's found all over the place in SimpleAlign.  It's cruft from the original implementations.
18:04 pyrimidine Only thing we can do is store that internally; will add it to the refactoring page we have on the wiki.
21:29 biomoose joined #bioperl
21:29 biomoose biome: Christopher Fields master SHA1-154a567
21:29 biomoose updates
21:29 biomoose http://bit.ly/iLHOB
21:29 biomoose biome: Christopher Fields master SHA1-8fa5151
21:29 biomoose initial TagTree implementation; not passing all tests (something wrong with coercion of same class for duplication)
21:29 biomoose http://bit.ly/4lCs0I
21:29 biomoose biome: Christopher Fields master SHA1-50e65f6
21:29 biomoose * add test files for Error and Annotation::Collection
21:29 biomoose http://bit.ly/Osjdi
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21:40 biomoose biome: Christopher Fields master SHA1-512f519
21:40 biomoose Bio::Moose->Biome
21:40 biomoose http://bit.ly/kyBhe
21:40 biomoose biome: Christopher Fields master SHA1-1eddb50
21:40 biomoose cleanup
21:40 biomoose http://bit.ly/4CGSSj
21:40 biomoose biome: Christopher Fields master SHA1-466ad26
21:40 biomoose cleanup
21:40 biomoose http://bit.ly/PpsDJ
21:40 biomoose biome: Christopher Fields master SHA1-a9a88dc
21:40 biomoose cleanup
21:40 biomoose http://bit.ly/i1Ibl
21:40 biomoose biome: Christopher Fields master SHA1-eeaf332
21:40 biomoose Merge branch 'master' of git@github.com:cjfields/biome
21:40 biomoose http://bit.ly/qWI3r
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21:48 biomoose biome: Christopher Fields master SHA1-f8e98e1
21:48 biomoose add collection and typemanager
21:48 biomoose http://bit.ly/2vVxKO
21:48 biomoose biome: Christopher Fields master SHA1-39e748a
21:48 biomoose Merge branch 'master' of git@github.com:cjfields/biome
21:48 biomoose http://bit.ly/efzil
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21:51 biomoose biome: Christopher Fields master SHA1-d19e3f6
21:51 biomoose * this should finish the clean up; some things got lost in last few merges
21:51 biomoose http://bit.ly/4BpSLo
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21:53 biomoose biome: Christopher Fields master SHA1-4efdfa5
21:53 biomoose add simple Tree/Node abstract roles (nothing defined yet)
21:53 biomoose http://bit.ly/tDzWY
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