Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-06-17

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All times shown according to UTC.

Time Nick Message
00:22 CIA-69 bioclipse.qsar: Ola Spjuth 2.4.x * ra67146e / plugins/net.bioclipse.qsar/src/net/bio​clipse/qsar/business/QsarManager.java : Made InChI optional. Solves #2003. - http://bit.ly/9HFGPd
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05:36 CIA-69 bioclipse.cheminformatics: Ola Spjuth 2.4.x * rfe92c5d / plugins/net.bioclipse.cdk.smartsmatc​hing/src/net/bioclipse/cdk/smartsmat​ching/views/SmartsMatchingView.java : handle cancel without NPE. Solves #1787. - http://bit.ly/buX4mj
05:36 CIA-69 bioclipse.cheminformatics: Ola Spjuth 2.4.x * r7cd1b3a / plugins/net.bioclipse.cdk.smartsma​tching/src/net/bioclipse/cdk/smart​smatching/model/SmartsWrapper.java : Implemented validate(). - http://bit.ly/b04ilE
05:36 CIA-69 bioclipse.cheminformatics: Ola Spjuth 2.4.x * r717efdb / (2 files in 2 dirs): Implemented validation on entry. Solves #1788. - http://bit.ly/9dSpZP
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07:01 egonw_ hi Gpox
07:01 egonw_ thanx for the bug report...
07:01 egonw_ I was looking at the problem this morning...
07:01 egonw_ your clues are very useful :)
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08:58 jonalv http://wiki.bioclipse.net/index.php?title​=How_to_make_a_manager_2#Running_manager_​methods_as_jobs_which_return_a_result_2
08:58 zarah jonalv's link is also http://tinyurl.com/ouun2r
08:58 jonalv zarah: thanks
08:58 zarah jonalv: ;)
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09:11 jonalv wb olass
09:15 egonw_ Gpox: ping
09:15 Gpox pong
09:15 egonw_ I think I found a bug in your AddBondDragModule
09:16 egonw_ Gpox: please have a look at line 107
09:16 egonw_ which assumes source != null
09:16 egonw_ but
09:16 egonw_ the third if clause at line 102 deals with the situation where the input is an IBond
09:16 egonw_ and source is not set
09:16 egonw_ causing a NPE
09:18 Gpox yes you are right
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09:29 ice9 hi! what is net.bioclipse.logback?
09:34 jonalv ice9: The logging toool to rule them all
09:34 jonalv ice9: (at least the current one)
09:34 jonalv (and hopefully the last)
09:35 jonalv egonw_: I would like to change behavior of cdk.fromString so that it correctly recognices SDF files and not only single molecules. Can that be done?
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09:36 ice9 jonalv: sounds great.
09:37 jonalv egonw_: or is there some other way to do that?
09:41 egonw_ jonalv: theoretically, yes
09:41 jonalv egonw_: why do I feel a "but" comming?
09:41 egonw_ but practically... perhaps
09:41 egonw_ not in 2.4 anyway
09:42 jonalv egonw_: could you have a wuick look at 1812 to see why I need it?
09:42 jonalv @pz 1812
09:42 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1812
09:42 jonalv egonw_: maybe you can suggest a better way?
09:42 jonalv egonw_: which can be done in 2.4...
09:44 egonw_ New File -> Text File -> Copy/Paste SDF file content -> Open in Editor ?
09:45 jonalv egonw_: no we don't want a zillion actions for each different data type
09:45 egonw_ that does not make sense....
09:45 jonalv oh hang on I am not sure I understood you
09:45 egonw_ yes, I think so
09:45 egonw_ this route already exists
09:46 egonw_ New Text File is an Eclipse thing
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09:46 jonalv egonw_: No normal human bing would think of it
09:46 jonalv only hackers
09:46 jonalv |being
09:46 * egonw_ had a quick look, and does not feel there is a quick hack
09:46 jonalv I know, I have studied them. It's very unintuitive
09:47 egonw_ the CDK file type recognizer should pick up if the file is a MDL SD file...
09:47 egonw_ if it doesn't there is no quick hack
09:47 jonalv egonw_: but we _must_ have code able to identify an sdf file somewhere, right?
09:47 egonw_ yes
09:48 egonw_ SDFFormat
09:48 jonalv egonw_:  ah so I only have to check for SDFFormat in the fromString implementation?
09:49 egonw_ yes, you could do that
09:49 jonalv sounds easy enough
09:49 egonw_ it's not particularly cheap operation, though
09:50 jonalv is that expected from a maniac method that takes any String and returns a CDK related BioObject?
09:50 jonalv right, I need to change from ICDKMolecule to IBIoObject on that method. (API changes might not be 2.4 stuff eh?)
09:50 jonalv (d\oh)
10:00 egonw_ jonalv: sorry... you lost me
10:05 CIA-69 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r721d258 / plugins/net.bioclipse.cdk.ui.sdfeditor/src/net/bio​clipse/cdk/ui/sdfeditor/editor/JCPCellPainter.java : Added the missing AtomNumberGenerator - http://bit.ly/dipDJs
10:05 CIA-69 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r8429adf / plugins/net.bioclipse.cdk.ui.sdfeditor/src/net/bio​clipse/cdk/ui/sdfeditor/editor/JCPCellPainter.java : Use the ExtendedAtomGenerator to fix the implicit hydrogen exception (fixes #2009) and show atoms in collapsed mode again - http://bit.ly/9tmjdq
10:05 zarah bug #2009 | http://tinyurl.com/39denf7
10:17 * egonw_ is glad that this Bioclipse workspace is one big git repository
10:18 * egonw_ just refered a file where I fixed a problem to be able to make a screenshot of the problem :)
10:39 CIA-69 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r856b94c / plugins/net.bioclipse.cml/src/net/biocli​pse/cml/managers/ValidateCMLManager.java : Fixed reporting non-valid CML is not in namespace (fixes #1456) - http://bit.ly/ba8bHo
10:39 zarah bug #1456 | http://tinyurl.com/369xg7b
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12:10 egonw_ http://chem-bla-ics.blogspot.com/2010/06/m​y-opentox-workshop-contribution-lost.html
12:10 zarah egonw_'s link is also http://tinyurl.com/396be72
12:10 egonw_ funny URL blogger made for that :)
12:15 CIA-69 bioclipse.cheminformatics: Arvid Berg 2.4.x * r2407eef / plugins/net.bioclipse.cdk.ui.sdfedit​or/src/net/bioclipse/cdk/ui/sdfedito​r/business/MoleculeTableManager.java :
12:15 CIA-69 bioclipse.cheminformatics: Hides the file before deleting it
12:15 CIA-69 bioclipse.cheminformatics: Solves bug 1989 - http://bit.ly/9iiFbq
12:15 zarah bug #1989 | http://tinyurl.com/37fjl6d
12:27 egonw_ jonalv: I love classics!
12:28 egonw_ thanx for the link
12:28 jonalv okeu, we are playing non stop "somewhere over the rainbow here"
12:28 jonalv :)
12:28 egonw_ hahahaha
12:28 jonalv that is a classic wouldn't you say?
12:30 egonw yes
13:28 egonw http://coderthoughts.blogspot.com/2010​/06/eek-java-reflection-can-cause.html
13:28 zarah egonw's link is also http://tinyurl.com/33fy2n5
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14:43 egonw http://area51.stackexchange.com/propos​als/6710/eclipse-rich-client-platform
14:43 zarah egonw's link is also http://tinyurl.com/24ey7z6
15:13 egonw jonalv: feel free to add questions yourself too
15:14 egonw I cannot vote OffT or OnT on my own questions
15:14 jonalv k
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