Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-06-29

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All times shown according to UTC.

Time Nick Message
04:43 egonw joined #bioclipse
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07:12 olass moin
07:12 zarah ni hao olass
07:57 CIA-54 bioclipse: goglepox * r11519 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/MoleculeTableViewer.java:
07:57 CIA-54 bioclipse: Added a eventBinding for SWT.COMMAND to nattable
07:57 CIA-54 bioclipse: So that selected multiple structures work on OS X
07:57 CIA-54 bioclipse: Solves bug #1368
07:57 zarah bug #1368 | http://tinyurl.com/matsl8
08:06 rojasm left #bioclipse
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08:24 olass joined #bioclipse
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08:57 egonw moin
08:57 zarah hello egonw, you fantastic person you
09:18 maclean joined #bioclipse
09:18 maclean hi
09:18 zarah saluton maclean
09:18 maclean morning, bot.
09:20 masak joined #bioclipse
09:30 maclean olass : ping
09:30 olass maclean: pong
09:31 * olass is preparing the RC4 release
09:32 olass hopefully my laptop will not die again :(
09:32 * olass has hardware problems
09:32 maclean :)
09:32 maclean er :(
09:32 * stain is preparing as well - Taverna 2.1b2
09:32 maclean (mispelling)
09:32 masak maclean: sadist! :)
09:32 olass ;)
09:32 maclean I typed the wrong bracket!
09:32 olass lol
09:33 maclean oh, to my question : it's about signatures again
09:33 olass fire off
09:33 masak maclean: Freduian slip...
09:33 maclean I downloaded the binary for osx that is in bioclipse svn
09:33 maclean but it was compiled against a different version of openbabel
09:33 maclean is the source available?
09:34 olass I don't think so
09:34 maclean (I have the source from faulon, but it won't compile)
09:34 olass but
09:34 maclean should I ask this other guy?
09:34 olass I'll ask him
09:34 maclean I can't remember his name
09:34 olass Lars
09:34 olass Carlsson
09:34 maclean ah, yes.
09:34 olass I hope it will be available
09:35 masak "Carlsson. Lars Carlsson."
09:35 maclean I am getting there with a signature-based structure enumerator,
09:36 maclean that comma isn't going anywhere. except that I should get back to it...
09:37 olass maclean: are you implementing the signatures in Java?
09:37 maclean yes
09:38 maclean but canonization is tricky
09:38 olass great
09:38 olass I know that Lars said it is tricky at some parts
09:38 maclean it's all colors that are numbers, and other maths.
09:38 olass I know he also said there were problems with the Furol scheme
09:38 olass thay changed stuff at some parts
09:38 maclean Faulon?
09:38 olass I suggest: Email Lars
09:39 olass I'm sure he'll be happy to help
09:39 maclean And yes, there were some minor errors in at least one paper.
09:39 maclean Ok, will do. Tack.
09:39 olass I'm about to call him this efternoon so will ask him too
09:39 olass but do email
09:39 maclean Ok.
09:48 edrin joined #bioclipse
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10:16 CIA-54 bioclipse: ospjuth * r11520 /bioclipse2/trunk/ (44 files in 44 dirs): Set version to 2.0.0.RC4 for release candidate 4.
10:16 CIA-54 bioclipse: ospjuth * r11521 /bioclipse2/trunk/plugins/ (10 files in 10 dirs): Set version to 2.0.0.RC4 for release candidate 4.
10:17 CIA-54 bioclipse: ospjuth * r11522 /bioclipse2/trunk/ (17 files in 17 dirs): Set version to 2.0.0.RC4 for release candidate 4.
10:18 CIA-54 bioclipse: ospjuth * r11523 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Set version to 2.0.0.RC4 for release candidate 4.
10:19 CIA-54 bioclipse: ospjuth * r11524 /bioclipse2/trunk/features/ne​t.bioclipse.platform_feature/ (bioclipse.product feature.xml): Set version to 2.0.0.RC4 for release candidate 4.
10:20 CIA-54 bioclipse: ospjuth * r11525 /bioclipse2/trunk/ (12 files in 12 dirs): Set version to 2.0.0.RC4 for release candidate 4.
10:49 egonw joined #bioclipse
10:50 olass wb egonw
10:51 egonw hej :)
10:51 egonw free wireless at the mässe
10:54 egonw bbl
10:56 CIA-54 bioclipse: ospjuth * r11526 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business/src/net/bioclipse/cdk/d​omain/CDKMoleculePropertySource.java: Catch the case when CDKMolPropSrc tries to update properties view and page is a TabbedPropertySheetPage.
11:27 edrin test
11:27 edrin hi
11:27 zarah saluton edrin
11:29 masak saluton edrin
11:29 edrin hi masak
11:55 olass joined #bioclipse
11:58 CIA-54 bioclipse: goglepox * r11527 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (3 files in 2 dirs):
11:58 CIA-54 bioclipse: Consolidated CalculatePropertyHanlers into one class
11:58 CIA-54 bioclipse: Merged CalculatePropertyForFileHandler with
11:58 CIA-54 bioclipse: CaluclatePropertyHandler to minimize duplication of
11:58 CIA-54 bioclipse: code and enable reuse of behavior.
11:58 CIA-54 bioclipse: Solves bug #1370 by executing on open editor if such
11:58 CIA-54 bioclipse: is open for a given file.
11:58 zarah bug #1370 | http://tinyurl.com/nbsvfa
12:18 CIA-54 bioclipse: ospjuth * r11528 /bioclipse2/trunk/plugins/net​.bioclipse.ui/html/workbench/ (images/bioclipse-banner_300w.png wb_help.html): Added a bioclipse logo on the first help page to show this is really Bioclipse and not Eclipse.
12:19 * olass will now build RC4 if no commits on the way?
12:19 olass Gpox?
12:19 olass egonw?
12:19 olass anyone else?
12:19 olass maclean: Talked to Lars. He was very happy that you started working on Signatures
12:20 maclean ah, yes. he emailed me.
12:20 olass he was sort of on vacation but promised to look at your email soon
12:20 olass oh, nice
12:20 egonw no commits here
12:20 egonw moving inside for coffee
12:20 olass ack
12:20 egonw brb
12:26 egonw new EMBL/EBI REST-like webservice framework: http://friendfeed.com/ismbeccb2009/77aba8​32/tt07-mickael-goujon-new-bioinformatics
12:26 zarah egonw's link is also http://tinyurl.com/mbwjw2
12:53 steinbeck joined #bioclipse
12:56 masak looking at this piece of code: http://gist.github.com/137605
12:57 masak this is a trick I haven't encountered so far.
12:57 masak could someone explain why we want to do a lot of Class.forName calls this way?
12:59 maclean hmmm.
12:59 maclean you do that for java-sql bridges.
13:00 masak oh?
13:00 maclean whatdjamacallit, JDBC.
13:00 masak ok.
13:00 masak I doubt there's JDBC in BioJava. it's probably mostly files.
13:00 maclean "Calling the Class.forName automatically creates an instance of a driver and registers it with the DriverManager, so you don't need to create an instance of the class. If you were to create your own instance, you would be creating an unnecessary duplicate, but it would do no harm."
13:01 maclean so, perhaps there is a similar singleton pattern going on
13:01 masak I'll read on, and see what it might be used for. :)
13:02 masak thanks so far.
13:03 masak nope, nothing obvious.
13:03 masak time to try and run the tests with and without that part. :)
13:07 maclean heh. there's a very complex discussion on classloaders and class.forname:
13:07 maclean http://blog.bjhargrave.com/2007/09/cla​ssforname-caches-defined-class-in.html
13:07 zarah maclean's link is also http://tinyurl.com/d9m7a7
13:07 maclean (and about OSGi, too)
13:11 masak thanks.
13:14 masak that post was very informative. :)
13:15 masak but I still don't understand why those classes are loaded in this particular test file.
13:17 egonw steinbeck: just ran into Martin Koch, former CUBIC
13:17 egonw he wasn't doing something like LinkedIn, but maybe a Former-CUBIC-worker LinkedIn group would be nice
13:29 masak did you have cubicles at CUBIC?
13:30 egonw yes we did
13:30 masak what about Rubik's cubes?
13:30 steinbeck egonw: cool - greetings to him
13:31 steinbeck masak: only in the big office
13:31 masak :)
13:31 steinbeck but it should have been a must in all of them
13:31 egonw steinbeck: and you had a large one
13:32 steinbeck yes, I was sub-boss #1
13:32 steinbeck So I clearly deserved a large office
13:32 masak oh, I thought you meant a large Rubik's cube...
13:32 steinbeck did you ever see the size of the director's office. *That* was big
13:43 maclean I know a guy who owns a 4*4 Rubik's cube.
13:43 maclean He's a bit odd, though. He likes perl.
13:44 masak the horror! :P
13:44 masak I find the accusations against the line-noisiness of Perl to be largely unwarranted, by the way.
13:45 masak you can write APL in any language, even Java and Python.
13:45 masak experienced programmers with a bent on maintainability won't do that.
13:46 maclean Heh heh. I said nothing!
13:46 maclean Oh, he maintains Crypt::Blowfish_PP.
13:47 maclean why is that linked?
13:47 masak I'd like a 3*3*3*3 Rubik's cube. :)
13:47 maclean That would be difficult to handle.
13:48 masak well, each 'face' would be an ordinary R's cube in itself.
13:48 masak it'd basically be 8 magically connected Rubik's cubes.
13:49 masak (where the exact nature of the connection is left as an exercise to the reader...)
13:49 maclean connected by wireless
13:49 masak *lol*
13:49 maclean and they would robotically change
13:50 masak such a thing could actually be built.
13:50 edrin olass, egonw, available?
13:50 maclean it would be spooky
13:50 olass edrin: yes
13:50 egonw yes
13:50 egonw just ran into a collegue of last year
13:50 edrin can we meet in #xws
13:50 olass sure
14:04 masak wow. knowing the hotkeys of some common refactoring actions in Eclipse really helps!
14:11 egonw :)
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14:48 olass wohoo, RC4 is out
14:48 olass http://bioclipse.blogspot.com/2009/06/​bioclipse-20-release-candidate-4.html
14:48 zarah olass's link is also http://tinyurl.com/mrtxv9
14:53 masak olass++
14:53 olass :)
14:54 masak 'Latest news' on http://wiki.bioclipse.net/ needs updating.
14:57 egonw joined #bioclipse
15:13 * egonw is going offline and meeting up with dinner mates
15:14 egonw steinbeck: I'll upload the image for the CUBIC tomorrow
15:14 egonw bye
15:14 steinbeck egonw: cool
15:14 steinbeck bye
15:40 CIA-54 bioclipse: shk3 * r11529 /bioclipse2/trunk/plugins/net.bioclipse.seneca/ (11 files in 5 dirs): working on a ga job
15:46 CIA-54 bioclipse: shk3 * r11530 /bioclipse2/trunk/ (7 files in 7 dirs): building speclipse rc4
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