Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-12-09

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All times shown according to UTC.

Time Nick Message
08:37 edrin joined #bioclipse
09:02 egonw joined #bioclipse
09:02 Gpox joined #bioclipse
09:04 jonalv joined #bioclipse
09:05 jonalv hi
09:05 zarah hi jonalv
09:17 shk3 joined #bioclipse
09:20 gilleain joined #bioclipse
09:27 CIA-32 bioclipse: jonalv * r8008 /bioclipse2/branches/jonalv-RunJSCommandsAsJob​s/plugins/net.bioclipse.core/META-INF/spring/ (context-osgi.xml context.xml): [jonalv-branch] two xml files. (Subversion is putting up a fight today...):
09:28 CIA-32 bioclipse: jonalv * r8009 /bioclipse2/branches/jonalv-RunJSComman​dsAsJobs/plugins/net.bioclipse.scriptin​g/src/net/bioclipse/scripting/business/ (. IJSJobCreatorAdvice.java JSJobCreatorAdvice.java): [jonalv-branch] a few files. (Subversion is putting up a fight today...):
09:35 edrin hi
09:35 zarah hi edrin
09:36 CIA-32 bioclipse: jonalv * r8010 /bioclipse2/branches/jonalv-RunJSCommandsAsJobs/​plugins/net.bioclipse.scripting/META-INF/spring/ (. context-osgi.xml context.xml): [jonalv-branch] a few xml files. (Subversion is really putting up a fight today...):
09:41 jonalv egonw, edrin: Would anyone of you have some cool Bioclipse2 js-script that I can test run?
09:41 edrin for bc1 yes
09:41 jonalv this was bc2...
09:58 egonw jonalv: can you come over?
09:58 jonalv egonw: yup
10:07 shk3 hi gpox
10:08 shk3 i am still trying the jcp swt stuff.
10:08 shk3 do you have a minute?
10:25 Gpox whats the problem?
10:28 egonw Gpox: did you write up bits we had in cdk10 but not yet in the new jcp yet in the wiki?
10:28 egonw Gpox: do we have subfragment coloring what Ola need? forgot to ask you on friday
10:30 Gpox i haven't tested it. the renderer uses the AtomColorer and there is a generator for external highlihgting
10:31 Gpox it is not active by default
10:33 gilleain by the way, I restored the highlight generator to use RenderModel's highlightModelRadius - sorry Gpox, I remember you saying that I had hardcoded it, but I forgot.
10:34 shk3 hi Gpox
10:34 gilleain it might be useful to have a similar variable for external highlight?
10:34 shk3 the problem is that no mouse events are detected.
10:34 Gpox you checked how the JCPEditorWidget dose it
10:36 shk3 gilleain is explaining it to me right now...
10:38 Gpox you basicly need a copy of jcpeditorwidget and change the modules used, wich should be refactored so what you are trying to achive would be easy
10:39 shk3 right now I am just using jcpeditorwidget
10:39 shk3 but there is no interaction
10:39 shk3 highlighting or whatever
10:39 shk3 gilleain is unsure, so I have to come back to you
10:40 Gpox gilleain: you are right, i use  a scale constant in the external highlighter now to make them larger that the normal one
10:40 Gpox shk3: dose the jcpeditor work for you?
10:41 Gpox the new one with colorfull icons
10:41 egonw Gpox: any pointers by email how I can activate it, would be much appreciated
10:42 shk3 yes
10:42 Gpox egonw: i am not sure what the we had in cdk10,
10:42 egonw Gpox: ok
10:42 shk3 i had a look at the code of jcpeditr
10:43 shk3 and I can'
10:43 shk3 t see a difference
10:43 shk3 I have no context menus
10:43 shk3 but these should not be needed?
10:43 shk3 Do I somehow need to pass mouse events to it
10:44 shk3 (the jcpeditorwidget isn't top level component for me)
10:54 edrin http://rogeralsing.com/2008/12/07/genet​ic-programming-evolution-of-mona-lisa/
10:54 zarah edrin's link is also http://tinyurl.com/5rm8af
11:02 gilleain i saw it : pretty cool.
11:11 shk3 Gpox: we found it is the particular cml which makes problems
11:11 shk3 if I open it in jchempaint, it also does not have highlighting etc.
11:11 shk3 might be a scale problem or so
11:11 shk3 I will file a bug report
11:51 shk3 I am trying to use a method from RendererModel
11:51 shk3 and eclipse complains about not accesible due to restrictions on
11:52 shk3 project org.os.cdk.render
11:52 shk3 the package is exported.
11:52 shk3 Is there anything else to do?
11:53 gilleain no idea. after all, the renderermodel is accessed elsewhere in bioclipse.
11:54 gilleain in the swt editor, for example.
11:56 shk3 the error is
11:56 shk3 the method setexternalselectedpart is not accesible
11:56 shk3 this sounds a bit like there is a sort of export on method level
11:57 shk3 I always thought it's per package only
11:58 gilleain me too
11:58 gilleain it's a public method
11:59 shk3 ah, i need org.os.cdk.render as dependency
11:59 gilleain ahhhh.
12:26 shk3 is rendering of the externalSelectedPart implemented in the new renderer?
12:27 gilleain no
12:27 gilleain I don't think so
12:27 shk3 ok
12:27 gilleain that's what egon was asking about earlier
12:28 gilleain in principle, though, there is a generator for the elements, I think it just needs to be hooked up.
12:29 Gpox yeah the generator is there and it generates ovals and lines wich are supported elements in the renderer
12:29 Gpox just add it in createGenerator() method of the widget
12:30 gilleain that is, add a line like generatorList.add(new ExternalHighlightGenerator(renderer2DModel));
12:32 gilleain and note that the order of the generators is important, as each group of elements is rendered in sequence, with the last group on top of the others
13:04 shk3 could you try this?
13:04 shk3 I tried, but no success
13:04 shk3 perhaps something else is wrong
13:04 shk3 but I don't know much about the new renderer
13:16 edrin so,: what's going on?
13:24 gilleain oh, stuff.
13:24 gilleain stefan is making Specmol work with the new renderer
13:25 gilleain I am trying to get custom monitors work
13:25 gilleain and you?
13:42 edrin gilleain: I am doing an experiment using yeasts
13:43 gilleain oh right. mutating them and whatnot.
13:46 edrin well, using mutants, it's actually a incubation experiment
13:46 edrin wondering what gets out
13:46 edrin but i will earliest know tomorrow, if everything succeeds ...
13:47 gilleain ah that's the thing about real-life experiments, i suppose. slow turnaround :)
13:47 edrin that's the advantage of computer, you always know immediately if it works...
13:47 edrin yes
13:47 edrin :(
13:48 gilleain also computers won't die if you don't attend to them.
13:53 edrin yeah :)
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14:42 edrin where is egon? where is jonalv
14:42 edrin ?
14:43 gilleain no idea
14:43 gilleain @seen egonw
14:43 zarah egonw was last seen 4 h 1 m ago in #bioclipse saying 'Gpox: ok'
14:46 CIA-32 bioclipse: shk3 * r8011 /bioclipse2/trunk/plugins/net.bioclipse.specmol/ (8 files in 4 dirs): specmol editor works with new jcp
14:47 CIA-32 bioclipse: shk3 * r8012 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: added the external highlighting visitor
14:49 olass joined #bioclipse
14:49 olass hi
14:49 zarah hi olass
14:53 edrin hi olass
14:53 edrin welcome back
14:53 olass thx edrin
14:53 olass can really recommend Cuba
14:53 edrin how were your trips?
14:53 edrin ah
14:54 olass well
14:54 edrin nice :)
14:54 olass first some caribbean islands
14:54 olass barbados, St Vincent, Grenada, Jamaica Cuba
14:54 olass so quite a trip :-)
14:54 edrin cool
14:54 olass yeah
14:54 edrin did you need a visa for them?
14:54 olass things have moved fast here in the meantime
14:54 olass no
14:55 olass so getting up to speed
14:55 edrin ok
14:55 olass and you?
14:55 olass all is well?
14:55 edrin yes
14:56 olass been working on xmpp?
14:56 edrin i think its ok right now
14:57 edrin olass: http://xws4j.sourceforge.net/
14:57 olass so moved from bc SVN
14:57 edrin code is still in bioclipses sf svn
14:58 edrin so far no reason to move it
14:58 olass ok
14:59 edrin we thought about writing a plugin for taverna, too
15:00 gilleain olass : do you know much about ProgressMonitors, ProgressProviders, and Jobs?
15:01 gilleain also : hi, welcome back :)
15:01 olass hi and thx gilleain
15:01 olass well... I know some, but not ProgressProviders
15:01 olass not overly much though
15:02 gilleain hmm. Well it seems that the ProgressProvider is a class that makes ProgressMonitors.
15:02 gilleain and that you can maybe have a custom one - but it probably wouls have to be Bioclipse-wide
15:02 gilleain ^would
15:03 gilleain well, I'll try to update people on what I learn about them, anyway.
15:11 olass great
17:35 shk3 it looks like the net.bc.cdk.business.test plugin used cdk10 stuff.
17:35 shk3 can anybody confirm this?
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20:42 egonw moin
20:42 zarah hi egonw
20:42 edrin hi egonw
20:42 egonw hi edrin
20:42 edrin need some food, back in 10 minutes
20:44 edrin ah, egonw, btw. i copied the xmpp web services text in the google docs doc again
20:44 edrin left #bioclipse
21:00 edrin joined #bioclipse
21:00 edrin egonw: i moved/put the xws stuff to java docs again
21:00 edrin err google docs
21:00 egonw ok
21:00 egonw will try to read it asap
21:01 egonw things have been quite hectic here...
21:01 egonw sorry for that
21:01 edrin yes?
21:01 egonw have a departemental presentation to give tomorrow
21:01 egonw and we had a grant application last week
21:01 edrin ok ic
21:01 edrin ah
21:01 egonw and this bloody cold did the rest :(
21:01 edrin and got it?
21:02 edrin the grant application
21:02 edrin cold remains?
21:02 egonw well, we made the submit deadline...
21:02 egonw brb
21:02 edrin ok
21:15 CIA-32 bioclipse: egonw * r8013 /bioclipse2/trunk/net.bioc​lipse.cdk.business.test/: Removed duplicate folder (fixes #157)
21:15 zarah bug #157 | http://tinyurl.com/5e5w6h
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