Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-27

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All times shown according to UTC.

Time Nick Message
00:20 Adrian[] joined #bioclipse
00:36 Adrian[] left #bioclipse
05:23 masak joined #bioclipse
05:28 egonw joined #bioclipse
06:34 Gpox joined #bioclipse
06:58 egonw Gpox: is the periodic table online yet?
06:59 egonw the plugin is not yet part of the cheminf feature
06:59 egonw and I was not sure how to use it...
06:59 Gpox There is no use yet, it only shows the table and properties if you click on a element
06:59 egonw ok, good
07:00 egonw can I make it part of the cheminfo feature anyway?
07:00 Gpox sure
07:00 egonw even as just a periodic table it is useful
07:00 egonw actually...
07:00 egonw we should have a periodic perspective...
07:00 egonw post-2.0
07:31 edrin joined #bioclipse
07:37 olass joined #bioclipse
08:09 shk3 joined #bioclipse
08:18 jonalv joined #bioclipse
08:54 CIA-40 bioclipse: miguelrojasch * r10760 /bioclipse2/trunk/plugins/net.bioclipse.reacti​on/src/net/bioclipse/reaction/editparts/tree/ (ReactionTreeEditPart.java TreeEditPartFactory.java): Synchronization between ReactionEditor and OutLinePage
09:10 CIA-40 bioclipse: jonalv * r10761 /bioclipse2/trunk/plugins/net.bi​oclipse.core/src/net/bioclipse/ (3 files in 2 dirs): fix bug 1113. Had a look at changes olass++ and I made in a rush yesterday.
09:10 zarah bug #1113 | http://tinyurl.com/oz6acu
09:45 CIA-40 bioclipse: miguelrojasch * r10762 /bioclipse2/trunk/plugins/net.bioclipse​.reaction/src/net/bioclipse/reaction/ed​itparts/tree/ReactionTreeEditPart.java: Synchronization between source connection and OutLinePage
10:49 egonw joined #bioclipse
11:06 CIA-40 bioclipse: shk3 * r10763 /bioclipse2/trunk/_playgroun​d_/net.bioclipse.medea.case/ (2 files in 2 dirs): correct class name, commented out outdated logging
11:09 CIA-40 bioclipse: shk3 * r10764 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (9 files in 5 dirs): added output of problems when check fails at startup
11:17 CIA-40 bioclipse: miguelrojasch * r10765 /bioclipse2/trunk/plugins/net.bioclipse.reacti​on/src/net/bioclipse/reaction/editparts/tree/ (8 files): Change the name of the reaction OutLinePage
11:22 ilbot2 joined #bioclipse
11:22 Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/ || Our Wonderful Nature http://www.spiegel.de/video/video-30120.html
11:34 masak now you can enjoy the iupac-alkanes project on github: http://github.com/masak/iupac-alkanes/
11:34 zarah masak's link is also http://tinyurl.com/oogpay
11:34 CIA-40 bioclipse: goglepox * r10766 /bioclipse2/trunk/plugins/net.bioclips​e.reaction/src/net/bioclipse/reaction/ (2 files in 2 dirs): No @Override annotation for interfaces in java 1.5
11:35 CIA-40 bioclipse: goglepox * r10767 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (9 files in 4 dirs): Added MoleculeTableManager
11:36 CIA-40 bioclipse: goglepox * r10768 /bioclipse2/trunk/plugins/ (14 files in 7 dirs):
11:36 CIA-40 bioclipse: Moved SDFIndex and method createSDFIndex form
11:36 CIA-40 bioclipse: net.bc.cdk.business to net.bc.cdk.ui.sdfeditor.business
11:47 CIA-40 bioclipse: jonalv * r10769 /bioclipse2/trunk/plugins/net.bioclipse.co​re.tests/src/net/bioclipse/managers/tests/​AbstractManagerMethodDispatcherTest.java: Corrected broken test. Now tests for condition in bug: 1114
11:47 zarah bug #1114 | http://tinyurl.com/qzeoxz
11:49 CIA-40 bioclipse: miguelrojasch * r10770 /bioclipse2/trunk/plugins/net.bioclipse.r​eaction/src/net/bioclipse/reaction/editpa​rts/tree/ReactionROutPageEditPart.java: Adapt synchronization between ReactionOutlinePage and PropertiesPage
12:14 maclean joined #bioclipse
12:43 egonw joined #bioclipse
13:10 jonalv hi egonw
13:10 egonw hej jonalv
13:11 CIA-40 bioclipse: jonalv * r10771 /bioclipse2/trunk/plugins/ (5 files in 2 dirs):
13:11 CIA-40 bioclipse: fixes bug: #1114
13:11 CIA-40 bioclipse: Now manager methods taking BioclipseUIJobs are run as jobs (as they should be)
13:11 zarah bug #1114 | http://tinyurl.com/qzeoxz
13:30 CIA-40 bioclipse: miguelrojasch * r10772 /bioclipse2/trunk/plugins/net.bioclips​e.reaction/src/net/bioclipse/reaction/ (34 files in 5 dirs): Modified class name fro Myblabla to Rblabla
13:47 CIA-40 bioclipse: jonalv * r10773 /bioclipse2/trunk/ (33 files in 22 dirs): renamed BioList into RecordableList. Fixes bug: #1075
13:47 zarah bug #1075 | http://tinyurl.com/qd6tz8
13:55 CIA-40 bioclipse: jonalv * r10774 /bioclipse2/trunk/plugins/ (9 files in 4 dirs): Renamed IPArtialReturner into IReturner. fixes bug: #1116
13:55 zarah bug #1116 | http://tinyurl.com/pm8qjx
13:56 egonw did not see #1116
13:56 egonw would something like IReturnListener not be more appriopriate?
14:05 maclean joined #bioclipse
14:08 masak @pz 625
14:08 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=625
14:14 maclean olass : thanks for the reply about signatures. I did download the c code that Faulon wrote, but it indeed does not compile on osx.
14:14 olass maclean: right
14:14 olass I think Lars did his own impl
14:15 maclean oh.
14:15 olass in C
14:15 maclean ja.
14:15 egonw olass: what's the license?
14:15 maclean I'm getting there in java, but.
14:16 egonw is it LGPL-compatible?
14:16 olass he wanted to write in Java for CDK
14:16 olass egonw: no
14:16 olass AZ internal
14:16 egonw ok
14:16 olass hmm, I think...
14:16 egonw clearly a CDK version would have to be
14:16 olass indeed
14:17 olass maclean: have you started working on it?
14:17 maclean I have "[C]([C]([C][C]([C][C]([C][​C])))[C]([C]([C][C])[C]))" as a signature for benzene
14:17 maclean I don't think that's quite right, though.
14:17 maclean What looks interesting to me is that the colours are atom types, and could be different
14:18 olass what you mean?
14:18 maclean so, in one paper, he has "cp" and "c_" for aromatic and aliphatic carbons
14:19 maclean but, more CDK-like atom types could be used.
14:20 maclean Or, in an example for glycine, "H_A" is used (like the PDB label HA, I suppose)
14:21 maclean Anyway, it looks promising (implementable, that is).
15:01 CIA-40 bioclipse: jonalv * r10775 /bioclipse2/trunk/ (40 files in 37 dirs): renamed IBioclipseManager.getNameSpace into IBioclipseManager.getManagerName. Fixes bug: #895
15:01 zarah bug #895 | http://tinyurl.com/q4uhtq
15:28 CIA-40 bioclipse: carl_masak * r10776 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): (log message trimmed)
15:28 CIA-40 bioclipse: [JsThread] now kills itself dead on cancel
15:28 CIA-40 bioclipse: Changes made in Activator and JsConsoleView to be able to boot up a new
15:28 CIA-40 bioclipse: JsThread when the old one has been killed dead.
15:28 CIA-40 bioclipse: This solution involves Thread.stop(), a deprecated function. Doing things
15:28 CIA-40 bioclipse: like this is really not a good idea. See
15:28 CIA-40 bioclipse: http://java.sun.com/j2se/1.4.2/docs/gui​de/misc/threadPrimitiveDeprecation.html
15:36 CIA-40 bioclipse: jonalv * r10777 /bioclipse2/trunk/plugins/net.bioclipse.cor​e/src/net/bioclipse/jobs/BioclipseJob.java: Made error text more complete
15:46 CIA-40 bioclipse: ospjuth * r10778 /bioclipse2/trunk/plugins/ (36 files in 7 dirs): Updated icons and error reporting in DSView.
15:46 CIA-40 bioclipse: ospjuth * r10779 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/domain/ISubStructure.java: Made ISubStructure implement IAdaptable.
15:46 egonw I have a compile error in cdk.ui.sdfeditor
15:46 egonw am I the only one?
15:53 jonalv egonw: I don't seem to have any problems there no. What are the symptoms?
15:54 egonw compile error:
15:54 egonw Access restriction: The method getDefault from the type Activator is not accessible...
15:54 * jonalv updates.... :)
15:55 egonw the appropriate package is missing from the runtime export
15:55 egonw at least, for me...
15:55 jonalv egonw: not me, maybe you are runnign another Eclipse version that picks up on those things?
15:55 egonw who knows
15:55 egonw it's Eclipse after all
15:55 jonalv egonw: waht eclipse version are you running?
15:55 egonw Version: 3.4.2
15:55 egonw Build id: M20090211-1700
15:56 egonw 64 bit
15:56 jonalv so that's probably not it then...
15:57 egonw no, it's something in my branch
15:57 egonw it's rebased
15:57 egonw but not in sync
15:57 egonw weird
15:57 egonw maybe a misdid a merge conflict at some point
15:58 egonw ok, thanx for checking!
15:58 jonalv oki
16:11 CIA-40 bioclipse: miguelrojasch * r10780 /bioclipse2/trunk/plugins/net.bioclips​e.reaction/src/net/bioclipse/reaction/ (6 files in 3 dirs): At the moment the box position is store as properties in the cml molecule.
16:20 maclean joined #bioclipse
16:27 CIA-40 bioclipse: jonalv * r10781 /bioclipse2/trunk/plugins/net.bioclipse.scripting/ (2 files in 2 dirs): Added pop up warning about inconstent data after cancelling a JavaScript script
16:42 maclean joined #bioclipse
16:58 edrin left #bioclipse
17:00 CIA-40 bioclipse: shk3 * r10782 /bioclipse2/trunk/plugins/net.biocli​pse.scripting/META-INF/MANIFEST.MF: stupid bundle-version in here
17:08 egonw grmp
17:08 egonw the JSEditor does not show up in the editor registry...
17:08 egonw how can that be??
17:12 egonw argh...
17:13 egonw what's the difference between JSEditor and JsEditor ??
17:13 maclean dammit github.
17:13 maclean egonw : the capitalisation of the 's'.
17:13 egonw hahaha...
17:13 egonw and a big headache
17:13 maclean indeed.
17:14 maclean It also seems that github does not like the fact that my wireless connection is dynamic, or something.
17:17 egonw why would it care?
17:20 maclean it fails to push unless I change the ssh key
17:20 egonw oh, that's weird
17:21 egonw that should not matter at all
17:21 maclean well, it might be something else, I suppose.
17:21 maclean but this is the second time that it has failed...
17:23 egonw annoying indeed
17:25 maclean hmmm. maybe it was because I did not commit....
17:44 CIA-40 bioclipse: shk3 * r10783 /bioclipse2/trunk/plugins/net.bioclipse.seneca/ (14 files in 6 dirs): some cleanup on the judges
17:44 CIA-40 bioclipse: shk3 * r10784 /bioclipse2/trunk/_playground_/net.bio​clipse.medea.case/src/net/bioclipse/pl​ugins/extensions/WCCMedeaJudge.java: the medea judge now starts (but still problems)
19:17 sneumann_ joined #bioclipse
20:21 sneumann_ Hi, is there a primer somewhere how to start a BC2 plugin ?
20:21 sneumann_ I am currently looking at the Eclipse new Plugin projet wizard page,
20:21 sneumann_ and there are many settings. For proper BC2 integration I probably need to get them right from the start.
20:22 egonw we unfortunately do not have a NewBC2PluginWizard
20:22 egonw there is template code in SVN
20:23 egonw also, starting from another plugin would work well...
20:23 sneumann_ thx
20:23 egonw what do you want to have the plugin do?
20:23 egonw then I can point you at a good example
20:23 sneumann_ shk3 asked for the mzML plugin
20:23 sneumann_ which is merely a generated editor for the mzML from XSD
20:24 sneumann_ So, new BC2 conforming project,
20:24 sneumann_ new EMF model from XSD
20:24 sneumann_ generate.
20:24 sneumann_ At least as a start.
20:24 egonw oh, best to ask Ola tomorrow then
20:24 sneumann_ Ack.
20:24 egonw he is experienced with EMF stuff
20:56 sneumann_ good night
20:58 CIA-40 bioclipse: egonw * r10785 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Use a single editor entry with multiple content type bindings, and better name (fixes #1071)
20:58 zarah bug #1071 | http://tinyurl.com/ohgn4x
20:59 CIA-40 bioclipse: egonw * r10786 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jche​mpaint/src/net/bioclipse/cdk/jchempaint/wizards/ (. NewMoleculeWizard.java): Attempt to make a new wizard without a file backend
20:59 CIA-40 bioclipse: egonw * r10787 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (3 files in 3 dirs): Implemented a NewMolecule wizard, which should open a CML file without a IFile backend
21:00 CIA-40 bioclipse: egonw * r10788 /bioclipse2/trunk/plugins/net.bioclipse.script​ing.ui/src/net/bioclipse/scripting/ui/wizards/ (. NewJavaScriptWizard.java): OK, editors now work, but open only in a text editor
21:01 CIA-40 bioclipse: egonw * r10789 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): OK, both new wizards open up in a text editor, and can finish early, and have no pages
21:01 CIA-40 bioclipse: egonw * r10790 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.jchempaint/META-INF/MANIFEST.MF: Fixed missing export
21:02 CIA-40 bioclipse: egonw * r10791 /bioclipse2/trunk/plugins/ (6 files in 5 dirs):
21:02 CIA-40 bioclipse: NewJavaScriptWizard now works (sort of):
21:02 CIA-40 bioclipse: * moved to jseditor plugin, that being used to open the script
21:02 CIA-40 bioclipse: * fixed the code and updated wiki.eclipse.org accordingly! :)
21:02 CIA-40 bioclipse: See http://wiki.eclipse.org/FAQ_How_do_I_open_a​n_editor_on_something_that_is_not_a_file%3F
21:02 zarah CIA-40's link is also http://tinyurl.com/pmffrs
21:02 CIA-40 bioclipse: egonw * r10792 /bioclipse2/trunk/plugins/net.bioclip​se.jseditor/src/net/bioclipse/jsedito​r/wizards/NewJavaScriptWizard.java: Allow editing. It also saves, and it might be confusing that this is possible without a persistable object... but it is the editor that does doSaveAs() etc... don't see a fix for that right now
21:03 CIA-40 bioclipse: egonw * r10793 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint/src/net/bioclipse/cdk/jch​empaint/wizards/NewMoleculeWizard.java: Updated to follow the code for the NewJavaScriptWizard

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