Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-01-18

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All times shown according to UTC.

Time Nick Message
00:08 CIA-20 bioclipse: ospjuth * r4713 /branches/bioclipse2/bioinformatics​/plugins/net.bioclipse.biojava.ui/: Initial import.
00:09 CIA-20 bioclipse: ospjuth * r4714 /branches/bioclipse2/bioinformatics​/plugins/net.bioclipse.biojava.ui/ (22 files in 9 dirs): Started the biojava.ui plugin to hook in content in Navigator for sequences.
07:20 CIA-20 bioclipse: carl_masak * r4715 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java:
07:20 CIA-20 bioclipse: [JsConsoleView.java]
07:20 CIA-20 bioclipse: * renamed methods
07:20 CIA-20 bioclipse: ** startR -> switchToR
07:20 CIA-20 bioclipse: ** stopR -> switchToJs
07:30 rojasm joined #bioclipse
07:38 CIA-20 bioclipse: updatebjarni * r4716 /branches/bioclipse2/core/plugins/net.biocli​pse.r/src/net/bioclipse/r/TextRFactory.java: Corrected IOException -> NoRException.
07:39 CIA-20 bioclipse: updatebjarni * r4717 /branches/bioclipse2/core/plugins/net.biocli​pse.r/src/net/bioclipse/r/NoRException.java: R throws this when it fails.
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07:40 CIA-20 bioclipse: carl_masak * r4718 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java:
07:40 CIA-20 bioclipse: [JsConsoleView.java]
07:40 CIA-20 bioclipse: * R now doesn't start until requested
07:42 CIA-20 bioclipse: carl_masak * r4719 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java:
07:42 CIA-20 bioclipse: [JsConsoleView.java]
07:42 CIA-20 bioclipse: * R now doesn't start until requested
07:42 CIA-20 bioclipse: * "improvement" to last commit
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08:15 CIA-20 bioclipse: carl_masak * r4720 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
08:15 CIA-20 bioclipse: [ScriptingConsoleView.java]
08:15 CIA-20 bioclipse: * printMessage now breaks lines
08:25 olas joined #bioclipse
08:33 egonw olas: just saw the pointers I gave for use cases on the BC2 wiki page...
08:33 egonw I also saw the link for the BioJava Cookbook...
08:34 egonw what about a Bioclipse Cookbook, with cleaned up documentation which we already have, like the tutorials?
08:34 egonw and put that on lulu.com?
08:35 egonw but I guess no one has time to coordinate something like that
08:38 CIA-20 bioclipse: updatebjarni * r4721 /branches/bioclipse2/core/plugins/net.bio​clipse.r/src/net/bioclipse/r/TextR.java: Arrrr!
08:47 CIA-20 bioclipse: carl_masak * r4722 /branches/bioclipse2/core/plugins/net.b​ioclipse.ui/src/net/bioclipse/ui/views/ (3 files):
08:47 CIA-20 bioclipse: [net.bioclipse.ui.views]
08:47 CIA-20 bioclipse: * tab completion functionality merged into ScriptingConsoleView
08:47 CIA-20 bioclipse: * script-specific key binding hooks removed
08:52 Annzi joined #bioclipse
09:08 steinbeck joined #bioclipse
09:08 steinbeck moin
09:18 CIA-20 bioclipse: ospjuth * r4723 /branches/bioclipse2/chemoinformatics/n​et.bioclipse.cdk.ui/src/net/bioclipse/c​dk/ui/views/MoleculeLabelProvider.java: getText should return null if element is not handled.
09:19 CIA-20 bioclipse: ospjuth * r4724 /branches/bioclipse2/bioinformatics/plugins/​net.bioclipse.biojava.ui/src/net/bioclipse/b​iojava/ui/views/SequenceLabelProvider.java: getText should return null if element is not handled.
09:19 CIA-20 bioclipse: ospjuth * r4725 /branches/bioclipse2/bioinformatics​/plugins/net.bioclipse.biojava.ui/ (4 files in 3 dirs): It is now possible to expand Sequences in GUI
09:20 CIA-20 bioclipse: ospjuth * r4726 /branches/bioclipse2/bioinformatics/plugins/net.b​ioclipse.biojava.ui/src/net/bioclipse/biojava/ui/ (6 files in 2 dirs): Added SequenceEditor stub and actions to translate sequences.
09:25 CIA-20 bioclipse: ospjuth * r4727 /branches/bioclipse2/core/plugins/net.bioclipse.c​ore/src/net/bioclipse/core/domain/ISequence.java: Added getName for ISequence
09:26 CIA-20 bioclipse: ospjuth * r4728 /branches/bioclipse2/bioinformatics/plugins/net​.bioclipse.biojava.business/src/net/bioclipse/b​iojava/domain/BiojavaSequenceCollection.java: Return sequences when asked for!
09:26 egonw yeah, you bloody thing
09:27 olas :-)
09:27 olas hi egonw
09:27 egonw hi olas
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12:07 masak joined #bioclipse
12:28 edrin joined #bioclipse
12:29 edrin hi
13:06 edrin http://xkcd.com/154/
13:07 viklund yea, that's a good one
13:08 viklund todays' was pretty ok too
13:08 viklund http://xkcd.com/372/
13:09 egonw yeah, US is a marvelous country...
13:09 egonw the country where everything is possible...
13:09 egonw even miracles, so it seems
13:11 masak joined #bioclipse
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13:12 edrin hehe
13:13 edrin yes
14:33 edrin left #bioclipse
14:33 edrin joined #bioclipse
14:34 edrin hi again
14:35 edrin left #bioclipse
14:35 edrin joined #bioclipse
15:28 jonalv joined #bioclipse
15:32 masak joined #bioclipse
15:57 edrin egon?
16:06 egonw_ joined #bioclipse
16:08 Annzi left #bioclipse
16:10 olas left #bioclipse
16:18 thomas_ku joined #bioclipse
16:23 edrin egonw?
16:23 jonalv joined #bioclipse
16:24 * jonalv grumbels about people breaking my Ubuntu installation and then going of to bed
16:25 edrin jonalv: how can ppl break *your* Ubuntu??
16:27 jonalv https://bugs.launchpad.net/ubuntu​/+source/xorg-server/+bug/183969
16:28 jonalv it might work now though
16:28 * jonalv brb (restatring X)
16:29 jonalv joined #bioclipse
16:29 jonalv nope :(
16:35 jonalv joined #bioclipse
16:37 jonalv oh well I can't seem to fix it but they say they are working on a new update so I am going home...
16:59 edrin egonw_: ?
17:07 egonw_ edrin: sorry... got your messages... but tied up in admin stuff for my thesis and defense in April...
17:07 egonw_ will comment later...
17:07 edrin ok
17:08 egonw_ quicky: NatPrec sounds like an excellent idea
17:08 egonw_ that was an easy one...
17:08 egonw_ bbl
18:59 egonw joined #bioclipse
22:25 RabidRabbit joined #bioclipse
22:25 RabidRabbit hey there I was wondering what was going on with the reactions plugin
22:26 RabidRabbit as in, how can I get it running
22:33 edr1n joined #bioclipse
22:34 RabidRabbit hey there
22:34 RabidRabbit I had a question about bioclipse development\
22:34 Topic for #bioclipseis now http://slashdot.org/articl​es/08/01/18/1748218.shtml
22:34 Topic for #bioclipseis now http://slashdot.org/articl​es/08/01/18/1748218.shtml
22:35 edr1n hi RabidRabbit
22:35 Topic for #bioclipseis now An open source workbench for chemo- and bioinformatics - http://www.bioclipse.net/ | BiclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.de/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse | Dieter wrote an article for Eclipse Magazine: http://eclipse-magazin.de/itr/ausg​aben/psecom,id,359,nodeid,228.html http://slash
22:35 Topic for #bioclipseis now An open source workbench for chemo- and bioinformatics - http://www.bioclipse.net/ | BiclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.de/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse | Dieter wrote an article for Eclipse Magazine: http://eclipse-magazin.de/itr/ausg​aben/psecom,id,359,nodeid,228.html http://slash
22:35 RabidRabbit hey
22:36 edr1n RabidRabbit: what is the question?
22:37 Topic for #bioclipseis now An open source workbench for chemo- and bioinformatics - http://www.bioclipse.net/ | BiclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.de/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse |  AOL Adopting Jabber (XMPP): http://slashdot.org/articl​es/08/01/18/1748218.shtml
22:37 Topic for #bioclipseis now An open source workbench for chemo- and bioinformatics - http://www.bioclipse.net/ | BiclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.de/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse |  AOL Adopting Jabber (XMPP): http://slashdot.org/articl​es/08/01/18/1748218.shtml
22:37 RabidRabbit I am starting to write a retrosynthesis program and I was hoping to use the bioclipse framework, as in a plugin, and I was hoping to use the reactions plugin but I couldn't find it on the svn
22:38 edr1n oh
22:38 edr1n hm
22:39 edr1n I would highly recommend to come here again on Mo-Fr at UTC daytime
22:40 edr1n or even another solutin: mail the mailing list ;)
22:40 RabidRabbit I'll give that a try, thanks
22:41 edr1n no prop
22:41 edr1n prob ;)
22:44 RabidRabbit left #bioclipse
22:53 CIA-20 bioclipse: ospjuth * r4729 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (2 files in 2 dirs): Implemented openEditor without file-based resource. Solves 1873550.
23:02 CIA-20 bioclipse: ospjuth * r4730 /branches/bioclipse2/bioinformatics​/plugins/net.bioclipse.biojava.ui/ (2 files in 2 dirs): Added fixme for jonalv (get biojavaManager from OSGI) and made translate actions visible (they don't work yet).
23:02 CIA-20 bioclipse: ospjuth * r4731 /branches/bioclipse2/ (6 files in 5 dirs): Added ScriptingException. Should probably have different name and different place but for now resides in scripting plugin.

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