Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-09-01

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All times shown according to UTC.

Time Nick Message
02:36 mgerlich joined #bioclipse
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07:17 jonalv joined #bioclipse
07:24 jonalv oh hai
07:24 zarah hello jonalv, you fantastic person you
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08:28 Gpox joined #bioclipse
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08:59 edrin f
09:02 jonalv k
09:04 edrin I got scooped!
09:04 edrin shiozdfkl
09:05 jonalv edrin: sry what? scooped?
09:06 edrin jonalv: this means when another group published/s exactly the same ideas and results you just did/have yourself...
09:06 jonalv edrin: aha, hate when that happends
09:06 edrin i even started wrting thew damnit manuscript
09:07 jonalv yea..
09:07 jonalv at least it means that you where onto something good
09:13 CIA-63 bioclipse.structuredb: jonalv FileStore * r0aa77e9 / plugins/net.bioclipse.structuredb.tes​ts/tests/net/bioclipse/structuredb/pe​rsistence/dao/DBMoleculeDaoTest.java : Use DBMolecule with file for testing. - http://bit.ly/vdbZS
09:13 CIA-63 bioclipse.structuredb: jonalv FileStore * r7a6eec0 / (2 files in 2 dirs):
09:13 CIA-63 bioclipse.structuredb: INCHI for molecule comparisons, impl. getInchi
09:13 CIA-63 bioclipse.structuredb: Now the hasValuesEqualsTo method for DBMolecule uses INCHI for comparing the
09:13 CIA-63 bioclipse.structuredb: actual molecules. Also implemented the INCHI generation for DBMolecule. I can
09:13 CIA-63 bioclipse.structuredb: not use the INCHIManager because it has to work when running the non-plugin
09:13 CIA-63 bioclipse.structuredb: tests used for StructureDB. - http://bit.ly/2EKV5f
09:17 masak joined #bioclipse
09:32 edrin jonalv: I know I was into something good
09:32 jonalv edrin: yea...
09:33 edrin I kill them
09:33 jonalv "Silence, I kill you"
09:33 jonalv :)
09:42 CIA-63 bioclipse.structuredb: jonalv FileStore * rd7102d4 / (3 files):
09:42 CIA-63 bioclipse.structuredb: Fixed borken tests.
09:42 CIA-63 bioclipse.structuredb: Updated outdated tests cases. - http://bit.ly/4kSacu
09:50 jonalv zarah: seen egonw
09:50 zarah egonw was last seen 4 d 20 h 2 m 53 s ago in #bioclipse saying 'hi stain'
10:02 CIA-63 bioclipse.structuredb: jonalv FileStore * rb668ae1 / plugins/net.bioclipse.structuredb/src/net/b​ioclipse/structuredb/domain/DBMolecule.java :
10:02 CIA-63 bioclipse.structuredb: SMILES gen. moved from constructor to toSMILES()
10:02 CIA-63 bioclipse.structuredb: Lazy variant where we only calculates it if we need it. It should be persisted though once it's been calculated. - http://bit.ly/E1lSC
10:02 CIA-63 bioclipse.structuredb: jonalv FileStore * r76d589c / plugins/net.bioclipse.structuredb.tes​ts/tests/net/bioclipse/structuredb/pe​rsistence/dao/DBMoleculeDaoTest.java : layout - http://bit.ly/e0vvP
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13:37 egonw moin
13:37 zarah hello egonw, you fantastic person you
13:37 masak egonw: o/
13:42 jonalv hi egonw
13:42 jonalv egonw: all good?
13:44 egonw tired
13:44 egonw woke up at 4:30 to catch my bus to the airport
13:48 egonw just got home 20 minutes ago or so
13:53 jonalv egonw: ah so you are back home now? :)
13:53 egonw yes
13:53 jonalv how has your trip been?
13:55 egonw exhausting as always...
13:55 egonw but good
13:55 egonw short talk
13:55 egonw went overtime
13:55 egonw but all speakers did :)
13:55 jonalv ah
13:55 jonalv yea that sounds familiar...
13:56 egonw and I repeated it later that day at Merck, a pharma company in Darmstadt just south of Frankfurt, for which I was invited on Saturday :)
13:56 egonw at the chem- and bioinformatics group there
13:56 egonw masak: ping
13:56 jonalv okey nice
13:56 egonw masak: that reminds me...
13:56 jonalv egonw: masak is afk for the moment...
13:57 egonw @tell masak one of the workers there had a student work on Jmol and sequences in the past...
13:57 zarah Consider it noted.
13:57 egonw @tell masak and we talked about contributing that code to Bioclipse...
13:57 zarah Consider it noted.
13:57 egonw jonalv: you might have met him... he did the MolWind talk at the CDK workshop
13:58 jonalv egonw: maybe you can explain to me why CDK uses so many factoreis which I ahve to instantiate my self...
13:58 egonw explain... mmm... because you need those to creating things...
13:58 jonalv egonw: yea probably but I can't even remember what MolWind is right now. That workshop was full of new things for me...
13:59 jonalv egonw: well yes but why do I instantiate them_
13:59 jonalv egonw: I mean there are no difference betweeen the instances right_
13:59 jonalv egonw: meaning that I don't really want to create multiple FooFactories
14:00 jonalv In fact I want to get the same FooFactory that I was using the last time I was out Fooing...
14:01 jonalv egonw: but now I ahve to chache it myself. And in a complex program like Bioclispe this is sort of impossible. So we are bound to end up with multiple FooFactories in Bioclipse...
14:01 jonalv egonw: One real example is the InchiFactgory that I had to instantiate for DBMolecule. I at least placed it as a static field for the class but I know that the CDKManager has one other instance of that class...
14:02 jonalv egonw: do you follow?
14:04 egonw no
14:04 egonw was afk
14:04 egonw still am
14:04 egonw brb
14:13 egonw back
14:16 egonw jonalv: most CDK factories are by now singleton classes
14:17 jonalv egonw: sounds good
14:17 egonw and if not, please write a 'fix'
14:17 jonalv egonw: so I can look forward to a InchiFactorySingleton?
14:17 egonw that one is a bad example
14:17 egonw since C++ integration stuff...
14:17 jonalv egonw: explain
14:18 egonw not entirely sure how that works...
14:18 jonalv egonw: shouldn't matter..
14:18 egonw however, if you write a patch, I'm sure it will be reviewed soon
14:18 jonalv I might do that some day now :)
14:19 jonalv egonw: but such a thing would change api..
14:19 jonalv egonw: so I guess it must be for some later version or how does it work?
14:19 egonw 2.3.x
14:19 egonw which we use in BC2.2
14:20 jonalv egonw: to be honest with you I don't quite know how to send such a patch...
14:20 jonalv egonw: can I use github for that? And against what if so?
14:21 egonw CDK master
14:21 egonw yeah, surely you can use GitHub for that...
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