Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-09-09

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All times shown according to UTC.

Time Nick Message
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07:40 jonalv moin
07:40 zarah hi jonalv
08:16 olas joined #bioclipse
08:16 olas hi
08:16 zarah hi olas
08:23 egonw hi olas
08:24 olas hi egonw
08:50 thomas_ku joined #bioclipse
08:56 jonalv egonw: What't the word on the cml problem?
08:56 masak joined #bioclipse
09:02 egonw jim will rebuild jumbo + cmlxom jar this week
09:16 * jonalv hopes that will solve the problems...
09:20 olas egonw: jonalv is really stuck until we fix this
09:20 olas I tried to speed up Jim
09:20 olas maybe you could do the same, if you get the chance?
09:22 CIA-30 bioclipse: ospjuth * r6919 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (MoleculesPage.java QSARFormEditor.java QsarXMLEditor.java): Saving is now done via EMF. Added support for properties and outline. Still no undo/redo.
09:49 CIA-30 bioclipse: carl_masak * r6920 /bot/trunk/zarah.pl:
09:49 CIA-30 bioclipse: [zarah] now hangs on #november-wiki as well.
09:49 CIA-30 bioclipse: > svn:ignored the data files produced by a running instance of zarah
09:58 egonw olas: yes, did that too... he said this week...
09:58 egonw so make sure to ping him on wednesday or so
11:25 olas how hard can it be to compile jumbo for him?
11:25 olas it should take him a minute...
11:28 egonw no idea
11:39 rojasm joined #bioclipse
11:55 jonalv http://tinyurl.com/6csb74
12:12 CIA-30 bioclipse: jonalv * r6921 /bioclipse2/trunk/plugins/​net.bioclipse.structuredb/ (3 files in 2 dirs): [structuredb] Rewrote OpenAnnotationAction and RemoveAnnotationAction to work good with multiple selections
12:15 CIA-30 bioclipse: ospjuth * r6922 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (DescriptorLabelProvider.java DescriptorsPage.java): Updated to display descriptor parameters in label of Descriptor.
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14:30 olas egonw: around?
14:31 egonw sort of
14:31 egonw every now and then checking web
14:31 egonw like now
14:31 olas is serialization of results from a descriptor calculation to CML fully working?
14:31 olas is there a junit test for that?
14:31 egonw yes
14:31 olas good
14:31 egonw would need to look that up
14:31 egonw IIRC it is working
14:31 egonw but not entirely sure
14:31 egonw check qsarcml
14:31 olas ok
14:32 egonw or something like that
14:32 egonw that's the cdk module
14:32 olas sure
14:32 olas thx
14:32 egonw away again
14:32 olas like a magician
14:33 olas does it use the QSAR convention?
14:35 olas egonw: can't find it
14:35 olas can you help?
14:35 * olas swings his magic wand
14:35 olas @summon egonw
14:38 olas oh, found some
14:38 olas egonw: nvm
14:45 jonalv olas: The current help view in Bioclipse searches the help pages and gives links to hits when clicking around on different views. I think this takes us quite far. I think producing good help pages is what we should concentrate on first.
14:50 olas so dynamic is not necessary?
14:51 jonalv I am not sure....
14:52 jonalv I can't see what more we would use it for..
14:52 jonalv perhaps there is something I haven't thought about?
14:53 olas how do you control what is shown in teh help view when I click on something in Bioclipse?
14:53 jonalv Right now it searches the help files and shows links to relevant hits
14:54 jonalv That is actually very powerful
14:59 olas cool
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15:31 jonalv The jmol outline acts weird....
15:40 maclean it does? how
15:40 maclean + "?"
15:52 maclean ['?'] * 100
15:55 CIA-30 bioclipse: shk3 * r6925 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui/plugin.xml: changed the create 2d coordinates to actions
16:00 jonalv maclean: when opening a file with multiple models.
16:02 CIA-30 bioclipse: shk3 * r6926 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui/src/net/bioclipse/cdk​/ui/handlers/Create2dHandler.java: changed the create 2d coordinates to actions
16:02 jonalv (btw my irc client beeps when my name is mentioned so if you want my attention use my name :)
16:06 maclean ahhh.
16:08 maclean jonalv, jonalv, jonalv. I don't see any acting weird with 1ale.pdb (which has multiple models)
16:08 jonalv maclean: try selecint
16:08 maclean Oh, wait
16:08 maclean I just did - doesn't work, does it
16:08 jonalv selecting different models and atoms on different models
16:09 jonalv it sorta works a bit but it's very weird...
16:09 jonalv by selecting the different models you can show one mdel at a time
16:09 maclean yeaah. I see now.
16:10 maclean If you select 2 models in the outline, you show them both in the view
16:10 jonalv but selecting an atom in one model and shwo the other model higlights things in that model but doesn't show the atom actually selected
16:10 jonalv it's confuisng...
16:10 maclean hmmm.
16:11 jonalv more generally speaking I think we could do very much more cool stuff with jmol...
16:11 maclean true dat.
16:12 maclean Like have a 'current script' which could then be applied to every structure that you open.
16:13 jonalv hm yea perhaps
16:13 jonalv I also liked the console on the jmol view in bc1...
16:13 maclean that was nice,
16:14 jonalv it lacked a history though...
16:14 maclean hmm.
16:15 jonalv I guess some people would argue that we have the JavaScript console now but no reason not to have both...
16:15 jonalv I also think we should have a jmol script editor...
16:15 jonalv (there was something like that in bc1 right?)
16:15 maclean Yes to both. The jmol language is quite advanced nowadays.
16:15 maclean I don't know if there was a script editor in bc1
16:16 jonalv well there are many things with jmol that we could do... :)
16:18 jonalv I don't know how advanced it is. I haven't tried it. But there is supposed to be something
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16:37 jonalv I am out here! cya!
16:38 maclean see ya.
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