Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-11

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All times shown according to UTC.

Time Nick Message
00:26 edrin joined #bioclipse
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07:29 Gpox joined #bioclipse
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08:14 olass moin
08:20 egonw moin
09:08 masak joined #bioclipse
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09:37 edrin joined #bioclipse
09:39 edrin hi
09:39 CIA-55 bioclipse: egonw * r8742 /bioclipse2/trunk/features/ (5 files in 2 dirs): Set up a CDK Feature with the CDK Debug (cdx) manager (fixes #447)
09:39 zarah bug #447 | http://tinyurl.com/deolvd
09:50 egonw olass: ping
09:50 olass pong
09:50 edrin hi
09:50 olass hi
09:51 * olass is writing on the article
09:51 edrin fine :)
09:51 egonw olass: can you please list the managers that will end up in RC1 ?
09:51 egonw net.bioclipse.tests is not compiling for me...
09:51 egonw and needs updating reflecting which managers should be tested...
09:51 edrin yesterday it did not for me, too
09:53 egonw olass: I don't think the wiki is up to date
09:55 edrin it was missing a .Job import in my case
09:56 olass egonw: ok, will do
09:58 olass egonw: will cdkdebug feature be in release on update site?
09:58 egonw not?
09:58 olass egonw: that was a question...
09:58 egonw yes
09:58 egonw please do
09:59 egonw maybe should be renamed to 'CDK Power Tools' ?
09:59 egonw actually... does not really matter
09:59 olass yes, we discussed that earlier
09:59 olass you decide
10:00 egonw update site, current name
10:00 olass @tell shk3: please update info on wiki page: http://wiki.bioclipse.net/index.php?title​=List_of_stable_managers_in_bioclipse_2.0 Specmol and Spectrum managers are now stable AND unstable!
10:00 zarah olass's link is also http://tinyurl.com/68dyxn
10:00 zarah Consider it noted.
10:00 olass egonw: IMO only structuredb that was moved to unstable
10:01 olass ok?
10:01 egonw what's the question?
10:02 shk3 olass: will check later
10:03 zarah shk3: You have new messages. Write '/msg zarah @messages' to read them.
10:03 shk3 oops, wasn't that an easier command once upon times?
10:03 egonw @msg
10:03 zarah egonw: You have no new messages.
10:04 olass @msg
10:04 zarah olass: You have no new messages.
10:04 shk3 ah
10:08 masak shk3: there was, but all commands can now be sent privately, and that method is preferred on the theory that echoing a message to the channel a second time adds nothing useful.
10:08 masak the @tell, @ask and @ping commands can also be used privately.
10:13 egonw mmm... my Bioclipse does not boot
10:13 egonw Application not found in registry ...
10:19 masak egonw: this will probably not help at all, but: set target platform? launch from product? remove all features and re-add them?
10:19 olass egonw: remove all features, save, add desired features
10:19 olass yup
10:19 egonw masak: yeah, done that
10:19 egonw several times... just to make sure :)
10:19 * masak thought so
10:20 masak you did remember to save the product as well?
10:20 egonw stack trace is rather uninformative
10:20 egonw masak: yes
10:20 masak that's an important step.
10:20 masak :/
10:31 shk3 major problem in JCP, which seems to be new:
10:31 shk3 disconnected fragments can no longer be painted
10:32 shk3 if you have something and draw somwhere else, the new parts
10:32 shk3 are always appended.
10:32 shk3 did anybody observe this before?
10:32 egonw define: appended
10:32 shk3 does it work in jcp?
10:32 shk3 well, it becomes part of the existing molecule
10:32 egonw connected with bonds?
10:32 shk3 yes
10:33 egonw mmm...
10:33 shk3 or merged atoms, actually
10:33 shk3 paint one ring
10:33 shk3 paint a second one
10:33 shk3 somewhere outside
10:33 shk3 you get fused rings
10:33 egonw not good
10:33 egonw do you think you can reproduce that with a bit of javascript?
10:33 egonw and file that as bug report?
10:33 shk3 no idea about javascript
10:34 shk3 can you try in bioclipse
10:34 shk3 ?
10:34 shk3 by simply painting?
10:34 shk3 I don't have bc open
10:34 shk3 it looks a bit like a highlighting problem
10:34 egonw no, can't try right now
10:35 shk3 the attach point depends on where you are on the pane
10:35 egonw preparing a presentation for this afternoon
10:35 shk3 so it could be an atom is considered selected even if far away
10:35 shk3 not problem
10:35 shk3 I will try to dig into it
10:35 shk3 needs to be solved anyway
10:41 masak egonw: the difference between normal and mitochondrial translation is that the genetic code is slightly different, IIRC
10:41 masak @google genetic code mitochondrial
10:41 zarah masak: http://en.wikipedia.org/wiki/​Human_mitochondrial_genetics
10:41 masak yep.
10:41 egonw ic
10:42 egonw so, the translation table is different
10:42 egonw fine
10:44 masak aye, different hash table.
10:45 edrin egonw: are you worming on mitochondria?
10:46 edrin working
10:46 egonw no
10:46 egonw @pz mitochondria
10:46 zarah [456] Use Case for the Bioinfo feature   http://tinyurl.com/b4uq67
10:46 zarah Entire list at http://tinyurl.com/cecbdm
10:46 masak sauna &
10:46 egonw zarah++
10:48 * edrin likes mitochondria
10:50 shk3 egonw: problem is that addring etc. are justing looking for closest atom/bond withoug taking distance into account
10:50 shk3 will discuss that with gilleain
10:50 shk3 when he's back
10:51 egonw ah.... that's why that distance check was there...
10:51 egonw please file a bug report
10:51 egonw gilleain knows how to fix this
10:51 egonw so do I
10:51 egonw but not time before tomorrow
10:52 shk3 the distance check is done in highlight
10:52 shk3 I think we should make this code a method like getClosestAtomInHighlightDistance or so
10:52 shk3 and use it throughout
10:53 egonw that was discussed
10:53 egonw but disfavored
10:53 shk3 hm
10:53 shk3 we will see
12:03 * egonw is heading to the room where he will give his presentation
12:04 egonw C4:301
12:16 charlgren joined #bioclipse
13:10 grandm44 joined #bioclipse
13:32 grandm44 hello
13:32 edrin hello
13:34 grandm44 I did an import of net.bioclipse.cdk.jchempain​t.editor.JChemPaintEditor, it compiles, but I get java.lang.NoClassDefFoundError: net/bioclipse/cdk/jchempai​nt/editor/JChemPaintEditor at execution
13:38 grandm44 when testing "PlatformUI.getWorkbench().getActiveWorkbenc​hWindow().getActivePage().getActiveEditor()" with "instanceof JChemPaintEditor"
13:39 shk3 do you have the plugin where JChemPaintEditor is in in your run configuration?
13:41 grandm44 in the run configuration, i have both jchempaint_feature and my custom feature, if i correctly understand your question
13:45 grandm44 Sorry, I think this a basic java problem, i'm new to java
13:48 maclean joined #bioclipse
13:48 maclean good 'noon
13:50 grandm44 hi
13:50 maclean hello
14:06 maclean left #bioclipse
14:12 egonw joined #bioclipse
14:15 grandm44 hi egonw
14:15 egonw hi grandm44
14:15 egonw gilleain implemented radical drawing for JCP
14:15 grandm44 do you have a few minutes for me?
14:15 grandm44 cool
14:16 grandm44 i will update to the latest revision
14:16 egonw no, not now... have another meeting in less than 10 minutes... sorry
14:16 egonw try tomorrow
14:16 grandm44 no problem
14:16 grandm44 good meeting
14:16 egonw if it is about BC2, just ask away
14:17 egonw I'm sure anyone else can answer
14:17 grandm44 i did a few minutes ago
14:20 egonw ah, good
14:30 jonalv joined #bioclipse
14:30 jonalv oh hai
14:30 maclean joined #bioclipse
14:30 jonalv oh hai
14:30 jonalv zarah: ping
14:30 zarah jonalv: pong
14:31 maclean o hai
14:31 jonalv ehlo
14:42 maclean @tell egonw I can't get lone pairs to show up in a cml file : is there a way to test the lone-pair generation?
14:42 zarah Consider it noted.
14:42 maclean ta luv
14:50 jonalv what features are in the Bioclipse release_ :)
14:51 * jonalv should probably know this...
14:51 jonalv but he doesn't...
15:00 maclean there may be a wiki page on it?
15:01 jonalv @pz Bioclipse 2 is not released
15:01 zarah http://tinyurl.com/bql2pv
15:02 jonalv @pz 457
15:02 zarah http://tinyurl.com/ck8suz
15:02 jonalv !!!!!!!
15:02 jonalv what is going on here?
15:10 maclean what is what going on?
15:13 * jonalv is trying Bioclipse 2 out and hunting bugs
15:13 jonalv I am very dissapointed with what I am finding :(
15:14 jonalv something is listening to mouse clicks it seems
15:14 jonalv the exceptions are flooding when I click in the explorer
15:14 maclean :(
15:15 CIA-55 bioclipse: shk3 * r8743 /bioclipse2/trunk/plugins/n​et.bioclipse.spectrum.test/ (4 files in 2 dirs): added coverate test for spectrum
15:15 shk3 grandm44 sorry, I was away
15:16 shk3 did you solve your problem?
15:17 grandm44 no problem shk3, and no i didn't solve it yet. I'm updating to the latest revision right now
15:21 shk3 I can't see any other reason than run configuration right now
15:21 shk3 if it compiles, but complains about missing classes at run time,
15:21 shk3 then run config would be my guess.
15:21 shk3 but you never know
15:25 jonalv who did the create from SMILES dialog?
15:25 jonalv or wizard
15:25 jonalv shk3: was that you?
15:25 jonalv and the new cml onw
15:26 jonalv and the new mdl one
15:26 jonalv they all suffer from the sampe problem
15:26 jonalv shk3: ping?
15:26 * jonalv files bug instead then...
15:29 * shk3 is hiding
15:29 shk3 might have been me
15:29 shk3 but no
15:29 shk3 not the newcml and newmdl I think
15:29 jonalv someone will get a long bug report from me anyway
15:29 jonalv they are so very wrong in so many ways...
15:30 shk3 I will have a look
15:30 shk3 but I think I didn't do them
15:34 CIA-55 bioclipse: shk3 * r8744 /bioclipse2/trunk/plugins/net.biocli​pse.spectrum/src/net/bioclipse/spect​rum/business/ISpectrumManager.java: added coverage test for spectrum
15:35 CIA-55 bioclipse: shk3 * r8745 /bioclipse2/trunk/plugins/n​et.bioclipse.specmol.test/ (4 files in 2 dirs): added coverage test for specmol
15:37 jonalv WE ARE NOT READY FOR RELEASE TOMORROW. BIOCLIPSE LOOKS TERRIBLE! :(
15:37 CIA-55 bioclipse: shk3 * r8746 /bioclipse2/trunk/plugins/net.biocl​ipse.specmol/src/net/bioclipse/spec​mol/business/ISpecmolManager.java: added coverage test for specmol
15:50 jonalv "Bioclipse can open the result as a BioResource"
15:50 jonalv I am sure the user does not want to know what a BioResource is. I am also pretty sure that BioResources does not exist in Bioclipse 2 at all. Please keep the techno mumbo jumbo to a minimum in user dialogs and if you feel forced to add it think hard one more time and then make sure that it at least is correct.
15:50 * jonalv is steadily loosing his temper...
16:07 * shk3 will try not to talk to jonalv today
16:13 shk3 I just did a bc update
16:13 shk3 lots of problems with net.bc.core.jobs stuff not found.
16:15 CIA-55 bioclipse: shk3 * r8747 /bioclipse2/trunk/plugins/net.bioclipse.tests/ (2 files in 2 dirs): added coverage test for specmol and spectrum
16:32 maclean oh ffs : does bioclipse now not even start for anyone else?
16:33 maclean or, rather, not start if based on features, but start (crippled) if based on plugins, with no contenttype detection, no js console, ...
16:35 maclean oh, wait, no I 'fixed' it.
17:00 shk3 I will leave soon and be away till monday
17:01 shk3 if you need me urgently for bioclipse, please email me
17:01 jonalv shk3: you should only have problems in old plugins which are not yet updated.
17:01 * jonalv heads home now
17:02 shk3 bye
17:02 shk3 hope it wasn't too bad today
18:37 egonw joined #bioclipse
18:54 edrin welcome back egonw
18:59 edrin egonw: available?
19:46 edrin egonw: ?
19:56 edrin left #bioclipse
20:48 olass joined #bioclipse
20:54 egonw hi olass
20:54 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
20:54 egonw @msg
20:54 zarah egonw: 6 h 11 m 38 s ago, maclean said I can't get lone pairs to show up in a cml file : is there a way to test the lone-pair generation?
20:54 olass hi egonw
20:54 olass @msg
20:54 zarah olass: You have no new messages.
20:54 egonw @tell maclean I'll look at LP in CML
20:54 zarah Consider it noted.
20:55 egonw olass: the loading with CDK is triggered via an IAdapterFactory
20:55 egonw can you tell me about those?
20:55 egonw what they are used for?
20:55 olass nope, that is Gpox's doing
20:55 egonw CDKAdapterFactory is doing the loading...
20:55 olass well, attaching functionality
20:55 egonw OK
20:55 egonw will contact him then
20:55 olass you can ask an adapterfactory for functionality for a class
20:56 olass it's the adapter design pattern
20:56 olass very much used in Eclipse
20:56 egonw what kind of functionality should I be thinking about?
20:56 olass no idea in this case
20:56 egonw I mean, itäs not format detection, right?
20:56 egonw ok
20:56 olass can you set a breakpoint anddebug?
20:56 olass what is it asked for?
20:57 olass oh, I see
20:57 egonw bug 457 and 460
20:57 olass it asks: "If I have a file, what can you give me back"?
20:58 egonw the load triggered when browsing in the navigator
20:58 egonw ok...
20:58 olass CDKAdapterFactory says: I can give you an ICDKMolecule
20:58 egonw the thing is...
20:58 egonw it actually does
20:58 egonw I mean...
20:58 olass yes
20:58 olass which is wrong
20:58 egonw it returns a instance of ICDKMolecule
20:58 olass yup, but it should not load the molecule IMO
20:58 olass else the call should not be there
20:58 olass assign bug to Gpox
20:59 egonw yes, doing that already...
20:59 olass Looked at all the newwizards
20:59 olass IMO, there should be only one
20:59 olass New Molecule
20:59 olass it should encompass them all
21:00 olass in there you select weather to save as MDL or CML (really no point in having separate wizards for that)
21:00 olass And you should also be able to instantiate the new CML or MDL file with a SMILES
21:00 olass so only one wizard needed
21:00 olass will file that as a bug
21:00 egonw well...
21:00 egonw see my comment in the bug report
21:00 olass bug #?
21:00 egonw jonathan already did that
21:01 olass oh
21:01 egonw 461
21:01 olass what do you have against "New Molecule"?
21:02 egonw I am not really in favor of adding SMILES to the New CML wizard...
21:02 egonw I am not going to promote SMILES
21:02 egonw if people really want to use it, fine...
21:02 egonw but I have no interest in supporting that...
21:02 olass egonw: be pragmatic
21:02 egonw if people like to support that, fine...
21:02 olass if people want it, we provide it
21:02 egonw no, not about things which are intrinsically broken
21:02 egonw I'll be as pragmatic as allowing that functionality in the cheminfo feature
21:03 egonw but will never suggest people to use it
21:03 olass egonw: in a foul mood today?
21:03 egonw no, not really...
21:03 egonw just to tired to worry about crap others invent
21:03 olass think from a user perspective
21:03 egonw that's what I am doing...
21:03 olass well, people use SMILES, right?
21:03 olass you agree with me?
21:04 egonw I'm not doing user a favor with promoting things we know are broken...
21:04 olass is the SMILES reader broken?
21:04 egonw no
21:04 egonw SMILES is broken
21:04 egonw OpenSMILES is better
21:04 olass it's not broken
21:04 egonw it is
21:04 olass it's just not perfect
21:04 olass that is not broken
21:04 olass it does what it says
21:04 egonw no, it does not
21:04 olass the definition might be incorrect
21:05 egonw OpenSMILES is having a though time actually deciding what SMILES says
21:05 egonw no one knows for sure
21:05 egonw at least OpenSMILES defines what it being said...
21:05 egonw but CDK does not support OpenSMILES
21:05 egonw only SMILES
21:06 olass are you opposing the fact that many many people use smiles?
21:06 olass hmm, denying is a better word
21:06 egonw many many people like to watch sitcoms...
21:06 egonw no, not denying anything...
21:06 olass yes, and TV3 delivers them
21:06 olass because users WANT IT
21:07 egonw people also want to kill each other
21:07 egonw human nature
21:07 olass that is not true
21:07 egonw what's your point?
21:07 egonw we're scientists...
21:07 egonw not games salesmen
21:07 olass we will loose users if we donät provide what users want
21:07 olass if people don't want smiles, then we remove it OK?
21:08 egonw we will loose users if we don't provide scientifically sound software...
21:08 egonw would oyu prefer that?
21:08 olass seriously...
21:08 egonw indeed
21:08 egonw the CDK SMILES parser is actually not that good
21:08 olass you ARE in a foul mood today
21:08 olass that is a better argument
21:08 egonw no, just being sincere
21:08 egonw no, it's not
21:08 olass yes it is
21:09 olass you are thinking from your perspective, not a user
21:09 egonw define our user
21:09 olass you say you know better than the user and want to oppose restrictions on him for his own good
21:09 olass I hate that
21:09 egonw an idiot who does not care about the chemistry he is studying?
21:09 olass let him make bad decisions if he likes to
21:10 egonw no, if people like to add SMILES support to bioclipse, fine...
21:10 egonw I will not put priority on that myself
21:10 olass should we remove SDFiles as well?
21:10 olass SDF is a crappy format
21:10 olass I agree with you
21:10 olass but people still use it
21:10 olass hence we're stuck with it
21:10 olass and we have to do our best
21:10 olass but OK
21:11 olass left #bioclipse
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21:18 egonw joined #bioclipse
21:20 egonw joined #bioclipse
21:20 maclean joined #bioclipse
21:21 egonw hi maclean
21:21 maclean hi egonw
21:21 zarah maclean: You have new messages. Write '/msg zarah @messages' to read them.
21:21 maclean @messages
21:21 zarah maclean: 27 m 1 s ago, egonw said I'll look at LP in CML
21:22 egonw thanx for your fixes to compensate for the change of behavior of getClosestAtom and friend
21:22 maclean no problem
21:22 maclean shk3 suggests getClosest...WithinHighlight() methods
21:22 egonw yes, he told me...
21:22 maclean but, not right now
21:23 maclean (lots else to do :)
21:23 egonw Arvid disfavored that approach
21:23 maclean oh?
21:24 egonw let's discuss on the list, because I'm not sure anymore myself... I think Arvid had a point, but there is a lot of distance checking code around now...
21:24 * egonw is going to get sleep now...
21:24 maclean ok, sleep well
21:24 egonw olass: I left a comment in bug 461 on the issue we just discussed
21:24 olass me too :-)
21:25 * olass is trying to find a stamp
21:25 olass good night egonw
21:25 egonw ok, cu tomorrow
21:25 olass bye

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