Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-06-18

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All times shown according to UTC.

Time Nick Message
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08:17 CIA-47 bioclipse: jonalv * r5869 /bioclipse/trunk/playground/plugins/ (3 files in 2 dirs): To the expression parser used in Brunn: renamed valueOf to safeValueOf to reflect the exception catching taking place in it and added valueOf that doesn't catch those exception. (they contain info of what went wrong)
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12:51 CIA-47 bioclipse: goglepox * r5870 /bioclipse2/trunk/plugins/net.bioclipse.core/ (26 files in 8 dirs): Added two new file system types 'memory:' and 'zip:'
12:51 CIA-47 bioclipse: goglepox * r5871 /bioclipse2/trunk/plugins/net.bioclipse.co​re/src/net/bioclipse/core/Activator.java: A new project named Virtual is now created every time Bioclipse is opened. This project exist only in memory and will be deleted when the aplication is closed.
12:53 egonw oh no...
12:53 egonw boulahrouz left the training under policy guidance...
12:54 egonw not rasmussen all over again, /me hopes...
12:55 * jonalv has honestly no idea about what egonw is talking about. Should he feel uneducated?
12:56 egonw :)
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13:35 olas joined #bioclipse
13:35 olas hi
13:37 edrin hi olas
13:38 edrin jonalv_: maybe it's football?
13:38 jonalv_ edrin: you know it might be :)
13:38 jonalv_ I wouldn't know. olas, I guess you would?
13:39 jonalv_ hm olas isn't even here :)
13:39 jonalv_ hm or yea he is
13:41 CIA-47 bioclipse: jonalv * r5872 /bioclipse/trunk/playground/plugins/net.b​ioclipse.keyring/src/net/bioclipse/keyrin​g/preferences/KeyRingPreferencePage.java: moved a button which was way off placed. (wondering how it will look in linux / OSX now...)
13:47 olas what is?
13:47 * olas is confused
13:48 jonalv_ member:egonw: boulahrouz left the training under policy guidance...
13:48 jonalv_ member:egonw: not rasmussen all over again, /me hopes...
13:48 CIA-47 bioclipse: ospjuth * r5873 /bioclipse2/trunk/plugins/net.biocl​ipse.pcore/src/net/bioclipse/pcore/ (12 files in 3 dirs): Now uses a separate UI model wrapping files, molecules and conformers.
13:49 olas yup, football
13:49 jonalv so, what happened to rasmussen then?
13:50 egonw rasmussen was in the yellow jersey in the Tour de France
13:50 egonw for a Dutch team
13:50 egonw but then accused of using forbiden incentives
13:50 egonw and then they found some reason to expel him
13:51 egonw goodbye 'Dutch' TdF victory
13:51 egonw fortunately, Boulahrouz just left because of family business
13:51 jonalv hm
13:51 egonw (as it seems now)
13:51 egonw and not steroids or whatever...
13:52 egonw ... reason to disqualify the dutch team
13:52 egonw not now that we can actually win the EC
13:52 olas sure
14:24 olas egonw: you removed old.Renderer2D
14:24 olas what is the new equivalent?
14:24 egonw yes
14:24 egonw umm... the SWT widget
14:24 olas that did break cdk.ui
14:24 egonw oh, interesting...
14:24 egonw cdk10
14:24 egonw or cdk?
14:24 olas JChemPaintWidget holds Renderer2D
14:25 egonw should not
14:25 egonw that was a bug :)
14:25 olas could you look at it now?
14:25 egonw hang on
14:25 egonw yes, think so
14:25 olas really need that urgently
14:25 olas thanks
14:26 egonw sorry, did not know Bioclipse was using that..
14:26 olas net.bc.cdk.ui.widgets.JChemPaintWidget
14:26 egonw this is why we have cdk10
14:26 olas I thought that was the new renderer!
14:26 egonw no, cdk10 is the old renderer
14:26 egonw cdk should use the new one
14:26 olas this is not cdk10
14:26 olas this is cdk.ui
14:26 olas oh, are we not using the new widget?
14:26 olas I thought we were...
14:27 egonw well, apparently not
14:27 egonw I was thinking too that the new widget was being used
14:27 olas could you please please add that now?
14:27 egonw add what?
14:27 olas the new structure widget!
14:28 olas replace JchemPaintWidget with the new SWTWidget
14:28 olas I will move it to cdk10
14:28 olas ok?
14:29 egonw no, copy please
14:29 egonw will commit a fix, to make it use the new widget
14:29 egonw but need to test it in action
14:29 olas ok, I'll copy it
14:30 olas will stand by here and test when you are done
14:30 egonw commit pending...
14:30 CIA-47 bioclipse: egonw * r5874 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui/src/net/bioclipse/cdk​/ui/widgets/JChemPaintWidget.java: Now uses the new renderer
14:30 egonw this is the widget used by the SD file editor?
14:31 egonw btw, I get errors on cdk10.jchempaint
14:31 olas will check that up
14:31 olas mom
14:31 olas fixing things now
14:32 egonw oh, never mind
14:32 egonw need to update the SVN bits of cdk10
14:32 egonw it's the bits by Miguel
14:33 egonw and my git does not auto update the svn bits
14:33 olas does it work with new renderer?
14:33 * olas will test
14:33 egonw the SDFEditor?
14:33 olas no
14:33 egonw ummm... get this error on .core:
14:33 egonw Manifest has no main section...
14:34 olas paintMolecule should be called first time with the bounds of the graphical object..
14:34 olas egon: this did break structure2Dview
14:35 egonw say again?
14:35 egonw [16:34] <olas> paintMolecule should be called first time with the bounds of the graphical object..
14:35 egonw what do you mean?
14:36 olas that was output when I expected to see 2D in structure2Dview
14:36 olas egonw: please open an SDFF
14:36 olas select a line in the table
14:36 olas you should see mol in structure2Dview
14:37 olas now it's blank
14:37 olas and that error msg is outputted
14:37 olas why?
14:38 egonw which plugin does that view come from?
14:38 olas it's in Java2DRenderer
14:38 olas line 117
14:38 egonw cdk.ui, right?
14:38 olas if (affine==null)
14:38 olas cdk trunk
14:38 egonw ack
14:39 olas what is affine?
14:39 olas and why is it null?
14:40 egonw I was using the wrong method, it seems...
14:40 egonw hang on...
14:41 CIA-47 bioclipse: ospjuth * r5875 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (3 files in 2 dirs): Added old Structure2DView to CDK10. Mostly for reference.
14:45 egonw grmph... I need a Rectangle2D...
14:49 olas where do they grow?
14:51 CIA-47 bioclipse: ospjuth * r5876 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (6 files in 4 dirs): CDK10 now has view Structure2D with old renderer that works.
14:53 egonw java.lang.InternalError
14:53 egonw nice
14:53 jonalv aouch
14:53 jonalv I never managed to get that :)
14:53 egonw olas: OK, the cdk10 based View works?
14:53 egonw then I give up on the cdk based one for now...
14:54 olas :-(
14:54 olas what is the problem?
14:54 egonw [16:53] <egonw> java.lang.InternalError
14:55 olas ??
14:55 egonw ok, never mind
14:55 egonw mixed up x,y,h,w
14:55 egonw it now works
14:56 CIA-47 bioclipse: egonw * r5877 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui/src/net/bioclipse/cdk​/ui/widgets/JChemPaintWidget.java: Fixed affine transformation null situation
14:56 egonw not sure why the atom symbols don't show up, though
14:57 olas a bug?
14:57 egonw maybe bad renderer option
15:05 egonw mmm... checked code... no idea
15:07 olas could you email niels?
15:08 egonw it is painting symbols...
15:08 * olas is afk for 30 mins
15:08 egonw but I guess at the wrong size
15:08 * egonw will go home soon
15:10 CIA-47 bioclipse: ospjuth * r5878 /bioclipse2/trunk/plugins/net.bioclipse.pcore/ (13 files in 4 dirs): It's now possible to execute Pcore queries, and results show up in molViewer. No highlighting yet, though.
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16:33 shk3 just reading bc2 documentation
16:33 shk3 http://wiki.bioclipse.net/index.php?title=Instruc​tion_for_how_to_check_out_and_compile_Bioclipse_2 says:
16:33 jonalv cool
16:33 shk3 Beware you will have compilation errors in some of your projects, even after running Project → Clean, until you have performed step 3.
16:34 shk3 step 3 is the repository location
16:34 shk3 this must be step 5, I think?
16:34 jonalv uhm hang on :)
16:34 jonalv yea
16:35 jonalv that's right
16:35 shk3 will change it
16:36 shk3 note this is a contribution ;-)
16:36 jonalv yea :)
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16:55 shk3 bc2 starts, but I get quite a few errors on the console.
16:55 shk3 Is this ok?
16:55 jonalv depends...
16:55 jonalv what error?
16:58 shk3 well, some classdefnotfound
16:58 jonalv shk3: sry, something came up I have to leave.
16:58 shk3 org/apache/log4j/Category
16:58 jonalv aouch
16:58 shk3 ok, see you tomorrow
16:58 shk3 Could not initialize class org.springframework.osgi.util.DebugUtils
16:58 jonalv then you probabaly didn't uncheck the the include optional dependecis when calculating which plugins to add
16:59 jonalv could be also be something else
16:59 jonalv but I have to leave
16:59 jonalv cya
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