Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-12-02

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All times shown according to UTC.

Time Nick Message
06:23 Gpox joined #bioclipse
08:12 egonw joined #bioclipse
08:41 edrin joined #bioclipse
08:43 edrin hi egonw
08:45 egonw hi edrin
09:14 gilleain joined #bioclipse
10:03 CIA-32 bioclipse: egonw * r7914 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.control/src/org/opensc​ience/cdk/controller/ControllerHub.java: Added missing bit to make the new phenyl ring aromatic
10:17 jonalv joined #bioclipse
10:17 jonalv hi
10:17 zarah hi jonalv
10:17 gilleain hi
10:17 zarah hi gilleain
10:54 CIA-32 bioclipse: goglepox * r7915 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.jchempaint/src/net/bioclipse/cdk​/jchempaint/widgets/SWTRenderer.java: removed System.exit from old SWTRenderer
10:55 CIA-32 bioclipse: goglepox * r7916 /bioclipse2/trunk/cdk-externals/trunk/org​.openscience.cdk.extra/src/org/openscienc​e/cdk/io/random/RandomAccessReader.java:
10:55 CIA-32 bioclipse: Removed 'throws Exception' from method definition.
10:55 CIA-32 bioclipse: This method dose not need to throw an exception.
10:55 CIA-32 bioclipse: goglepox * r7917 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java):
10:55 CIA-32 bioclipse: Added method createSDFileIndex(IFile,IProgressMonitor)
10:55 CIA-32 bioclipse: This method creates an index file in the temp directory for the given SD-file.
10:55 CIA-32 bioclipse: goglepox * r7918 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (4 files in 2 dirs): Added nebula_comositetable.jar
10:56 CIA-32 bioclipse: goglepox * r7919 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (3 files): Molecules editor now uses CompositeTable from nebula package.
10:56 CIA-32 bioclipse: goglepox * r7920 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui.sdfeditor/.classpath: Removed local source and doc link
10:57 CIA-32 bioclipse: goglepox * r7921 /bioclipse2/trunk/plugins/net.bioc​lipse.seneca/src/net/bioclipse/sen​eca/views/BestStructureView.java:
10:57 CIA-32 bioclipse: Removed reference to removed method int Renderer2DModel,
10:57 CIA-32 bioclipse: setBackgroundDimension(...)
10:58 CIA-32 bioclipse: goglepox * r7922 /bioclipse2/trunk/plugins/ (4 files in 3 dirs):
10:58 CIA-32 bioclipse: Removed reference to removed method int Renderer2DModel,
10:58 CIA-32 bioclipse: setBackgroundDimension(...) and getBondLeangth()
11:09 shk3 joined #bioclipse
11:39 charlgren joined #bioclipse
13:43 CIA-32 bioclipse: jonalv * r7923 /bioclipse2/trunk/plugins/net.bioclipse​.structuredb/src/net/bioclipse/structur​edb/persistency/dao/DBMoleculeDao.java: [strucutredb] added (with the help of Gpox++) caching for browsing a label in the editor.
13:48 jonalv egonw: ping
13:53 egonw pong
13:55 jonalv ETA?
13:56 egonw can you come over?
13:56 jonalv yes
14:04 masak joined #bioclipse
14:25 Julio joined #bioclipse
14:25 Julio left #bioclipse
14:49 CIA-32 bioclipse: egonw * r7924 /bioclipse2/trunk/plugins/net.bioclipse​.structuredb/src/net/bioclipse/structur​edb/business/StructuredbManager.java: Jonalv: some debug statements for timing (should be removed upon release)
14:50 CIA-32 bioclipse: egonw * r7925 /bioclipse2/trunk/cdk-externals/tru​nk/org.openscience.cdk.standard/src​/org/openscience/cdk/fingerprint/ (Fingerprinter.java GraphOnlyFingerprinter.java): Cleaned up code: just use Set<String>. jonalv: ping, please run performance test before and after applying this commit
14:50 jonalv egonw: thanks
14:56 gilleain hmmm. interesting comment in the source for java.awt.Component:
14:56 gilleain /MACOSX
14:56 gilleain / every public entry point for drawing should
14:56 gilleain / disable/enable flushin to avoid screen flickering
14:57 gilleain :(
14:57 egonw yeah, OS/X is a brilliant OS
14:57 masak it's not the OS that handles drawing to the screen.
14:58 masak duh :P
15:00 gilleain well, clearly there's a need for this sun.java2d.SurfaceData class in all sorts of places in Component because of platform-specific issues.
15:00 gilleain It just makes this bug harder to track down...
15:00 egonw what source code are you looking at?
15:00 egonw IcedTea? OpenJDK?
15:03 gilleain ummm
15:03 gilleain Copyright 2004 Sun Microsystems, Inc.
15:03 gilleain ?
15:04 gilleain Whatever eclipse gives you on osx when you attach source.
15:05 egonw ah...
15:05 jonalv egonw: it changed from 234 to 229 on machine. I am not sure that's very significant...
15:06 egonw no, not really, is it...
15:06 jonalv but it was in the right direction at least :)
15:06 egonw hehehe
15:06 jonalv |on my machine
15:34 shk3 joined #bioclipse
15:55 shk3 joined #bioclipse
16:38 CIA-32 bioclipse: carl_masak * r7926 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java: [ScriptingConsoleView] fixed braino in javadoc comment
16:41 CIA-32 bioclipse: carl_masak * r7927 /bioclipse2/trunk/plugins/n​et.bioclipse.scripting.ui/ (3 files in 2 dirs):
16:41 CIA-32 bioclipse: [net.bioclipse.scripting.ui] created new scripting console
16:41 CIA-32 bioclipse: * does execute commands
16:41 CIA-32 bioclipse: * needs layout; that's my next thing on the list
16:42 gilleain oooh. a new scripting console, eh?
16:42 masak you have no idea how good it feels to steal one year's worth of good code and putting it in a new class, leaving all the bad code behind :)
16:43 gilleain I don't? :)
16:43 masak well, maybe a little, then.
16:43 masak I can guarantee that this new view will not have the problems of the old one -- it's physically impossible :)
16:44 gilleain Errr.
16:44 masak egonw++ # for the idea
16:44 gilleain just update n.b.scripting.ui?
16:45 masak aye
16:45 masak but don't try it yet! :)
16:45 shk3 "physically impossible" is a brave work if relating to software ...
16:45 masak let me finish the layout first...
16:45 masak shk3: well, it _is_, in this case
16:45 shk3 work=word
16:45 masak I'm not saying you won't have bugs, just not the same as before :)
16:46 gilleain "a brave work" would also be appropriate. A brave, noble work.
16:46 * masak blushes
16:50 gilleain heh. jcp.cleanup() works.
17:25 CIA-32 bioclipse: jonalv * r7928 /bioclipse2/trunk/cdk-externals/trunk/org​.openscience.cdk.standard/src/org/opensci​ence/cdk/fingerprint/Fingerprinter.java: A little speedup...
19:40 egonw joined #bioclipse
19:55 edrin hi again egon
19:55 egonw hi edrin
19:56 edrin what are you currently working on?
19:56 egonw writing mostly :(
19:56 edrin ah
19:56 edrin an article?
19:57 egonw grant proposal, book chapter, article
19:57 egonw IRC
19:57 edrin what kind of ?
19:58 edrin bioclipse or cheminformatics?
19:58 egonw bit of both, I guess
19:58 egonw actually, will try to release CDK 1.1.3 now
19:59 edrin ah
20:03 edrin olas is coming back soon?
20:03 egonw next week
20:03 edrin ok
21:57 edrin left #bioclipse

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