Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-12-16

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All times shown according to UTC.

Time Nick Message
08:20 olass joined #bioclipse
08:21 olass moin
08:21 zarah hi olass
08:41 CIA-32 bioclipse: ospjuth * r8063 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MultiPageMoleculesEditorPart.java: Access method to get moleculePage from MPE.
08:41 CIA-32 bioclipse: ospjuth * r8064 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/MoleculesEditor.java: Access methods to get cTable and contentProvider from MoleculesEditor.
08:44 CIA-32 bioclipse: ospjuth * r8065 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (2 files): Interface for custom renderer2D configuration and call it in MoleculeTableContentProvider. Allows plugins to customize the renderer in a MoleculesTable.
08:45 CIA-32 bioclipse: ospjuth * r8066 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.ui.sdfeditor/META-INF/MANIFEST.MF: Export cTable packages.
08:46 egonw joined #bioclipse
08:48 egonw moin
08:48 zarah hi egonw
08:53 edrin joined #bioclipse
08:54 edrin hi
08:54 zarah hi edrin
09:11 jonalv joined #bioclipse
09:15 jonalv hi
09:15 zarah hi jonalv
09:18 shk3 joined #bioclipse
09:23 jonalv egonw: ping
09:44 egonw pong
09:46 jonalv egonw: do you have a few minutes?
09:47 egonw yes
09:47 egonw where?
09:47 jonalv I'll join you then...
10:21 Julio joined #bioclipse
10:22 gilleain joined #bioclipse
10:35 jonalv Did we have a wiki page regarding mylyn setup?
10:35 egonw yes
10:35 egonw search for mylym
10:36 egonw search for mylyn
10:54 masak joined #bioclipse
10:54 jonalv hi masak
10:54 masak net presence. nice.
10:55 gilleain sorry to hear that your laptop was nicked, masak.
10:57 masak gilleain: yeah. that sucks, to be honest.
10:57 gilleain :(
10:58 masak I am writing this from a Windows(TM) computer.
10:59 masak better than nothing, but only slightly :)
10:59 masak at least I got Emacs installed.
10:59 masak currently trying to rewire Caps Lock to mean Ctrl, because I keep thinking it does...
10:59 gilleain heh.
11:00 masak & lunch
11:00 jonalv lunch &
11:01 gilleain [1] 1169
11:01 gilleain .-bash: lunch: command not found
11:01 gilleain [1]+  Exit 127                lunch
11:22 Julio joined #bioclipse
12:13 masak gilleain: :)
13:02 masak egonw: http://wiki.bioclipse.net/i​ndex.php?title=Style_guide
13:02 zarah masak's link is also http://tinyurl.com/5wlqjo
13:02 masak I added a section about commit comments.
13:02 masak egonw: I also saw that there's another page called Coding conventions.
13:02 masak we might consider merging the two.
13:04 masak ok, going to log out now to see if I managed to turn Caps Lock into Ctrl.
13:08 masak joined #bioclipse
13:11 gilleain masak++
13:11 * gilleain cares about coding conventions...
13:13 masak ok, going to try to reboot this computer and install Debian on it...
13:13 egonw Lenny?
13:13 egonw that would make a nice OpenJDK test machine :)
13:13 jonalv egonw: yea :)
13:13 egonw masak++
13:14 jonalv we are seting it up for dual boot...
13:14 jonalv windows+debian
13:21 gilleain uh-oh. no "} else {". :(
13:44 egonw file a bug report
13:44 gilleain what?
13:44 egonw unless it is your own code :)
13:45 gilleain no, the style guide!
13:45 egonw ah...
13:45 gilleain yes, ah...
13:46 egonw "Don't talk directly to other developers via commit messages."
13:46 egonw grmph... no more chess :(
13:46 gilleain Heh.
13:47 jonalv :)
13:47 gilleain Actually, most formatting stuff is much easier in eclipse with shift-command-f.
13:47 egonw mmm... not sure I like the no-hugging clause
13:47 egonw that makes the code longer in terms of lines...
13:47 jonalv egonw: I like it
13:48 gilleain it's inconsistent with java-style brackets
13:48 gilleain like:
13:48 gilleain if (condition) {
13:48 gilleain } else {
13:48 gilleain }
13:48 gilleain but oh well.
13:49 jonalv gilleain: Why do you think that is java style?
13:49 gilleain http://java.sun.com/docs/codeconv/​html/CodeConventions.doc6.html#449
13:49 zarah gilleain's link is also http://tinyurl.com/66yy7a
13:49 jonalv personally I am very much for scanning the left side of the text and keeping things related under things related..
13:50 egonw so, the Braces sections suggests to use:
13:50 egonw if (foo) {
13:50 egonw }
13:50 egonw else {
13:50 egonw }
13:50 egonw correct?
13:51 egonw this breaks my reading of the code... actually...
13:51 egonw I understand the else as first argument
13:51 jonalv yea because when you are looking for the else clasue you scan the left side of the code and find it..
13:51 egonw but for me } indicated end, period
13:51 egonw but now it reads to me like:
13:51 egonw end.
13:51 egonw Oh, no wait... there is an else too
13:52 gilleain egonw : I agree.
13:52 egonw anyway...
13:52 egonw I like that page split up into two sections...
13:52 egonw a formatting section
13:52 egonw a good coding practices section
13:53 egonw I hate to see 'write good commit messages' hidden behind a Braces section
13:53 jonalv I sort of think people could be free to either hug or not hug elses...
13:53 egonw the first is really more important than where to put a closing/opening brace
13:53 gilleain hmmm.
13:54 gilleain as long as someone has a consistent style, I don't mind
13:54 * jonalv removes the section on hugging
13:54 egonw masak: and where's the 'don't catch Exceptions' ?
13:54 gilleain (well, I do, secretly :)
13:55 gilleain (but I can keep it to myself...)
13:55 egonw huh? what?
13:55 egonw did someone say something?
13:55 gilleain :)
13:58 gilleain hmm. counting all C17H30 structures with molgen would take 12 hrs.
13:59 jonalv "egonw: That's not coding style that's just common sence"  masak said
13:59 gilleain C18H32 about 2 days.
13:59 jonalv gilleain: wow
13:59 gilleain and C19H34 a week and 2 days.
14:00 * gilleain is starting to understand explosive combinatorics :)
14:00 egonw jonalv: hahahaha
14:00 egonw gilleain: and this does not even have unsaturations and non-carbon heavy atoms :)
14:01 gilleain indeed.
14:01 gilleain 33 years for C24...
14:01 jonalv gilleain: more wow
14:01 jonalv :)
14:01 gilleain :)
14:02 gilleain I guess I should be careful with my command line arguments.
14:03 egonw this is why Christoph is so keen on GA/SA in CASE
14:03 gilleain exsactly.
14:19 egonw OK, 12 compile errors left...
14:19 * egonw is preparing a big patch for CDK1.2.x
14:19 egonw with unit test cleaning and improvements
14:41 jonalv would anyone happen to have some thoughts on how you want to  query a structuredb instance from the gui?
14:42 egonw draw a SMARTS substructure
14:42 jonalv egonw: uhm do we have a widget that can do that?
14:42 egonw no, not yet
14:43 egonw he, it's a PhD you are doing...
14:43 egonw don't expect paved routes
14:43 egonw :)
14:43 jonalv :)
14:43 jonalv yea yea
14:43 gilleain a custom renderer, you say?
14:43 gilleain sounds like an interesting problem :)
14:44 jonalv egonw: But what about just "standard" substructures?
14:44 egonw gilleain: right
14:44 egonw instead of drawing IAtom's... one would be drawing IAtomQueryäs
14:44 egonw instead of drawing IAtom's... one would be drawing IAtomQuery's
14:44 gilleain if only we had a flexible rendering/controller architecture.
14:44 egonw mmm...
14:44 gilleain j/k
14:44 egonw maybe there was a grand scheme behind all that after all .... mmmm ....
14:45 jonalv guys you lost me...
14:45 egonw jonalv: please come over
14:45 jonalv Didn't you just redo jchempaint into have that?
14:45 jonalv |haivi
14:45 gilleain jonalv : yes, yes we did :)
14:45 jonalv |having
14:45 jonalv egonw: okey I will be right over
15:42 masak joined #bioclipse
15:43 egonw ha, lenny boots?
15:43 masak egonw: it does.
15:43 masak hello from Debian.
15:44 jonalv masak: hello Debian
15:45 masak jonalv: OH HAI, Darwin.
15:45 jonalv masak: metacity I presume?
15:45 masak dunno. some Gnome crap. trying to change it as we speak.
15:57 masak ok, rebooting X.
16:05 shk3 when I open an sd file, the toolbar contains the jcp buttons.
16:05 shk3 lasso, +1, -1 etc.
16:06 shk3 is this intended?
16:06 shk3 is the sdf editor for structure editing?
16:15 gilleain I don't know, but I did notice that the buttons are slightly different to the buttons in the jcp (slightly better, too, I thought...)
16:21 egonw jonalv: http://pubs.acs.org/doi/abs/10.1021/ci8003013
16:21 zarah egonw's link is also http://tinyurl.com/6pm9q7
16:24 jonalv egonw: I think I will need to add a IntegerAnnotation to Structuredb... :(
16:24 egonw oh, sure
16:26 * jonalv must have a word with olass about this...
16:27 jonalv I just wonder why noone thought about it earlier...
16:28 gilleain Adel again eh?
16:29 jonalv gilleain: ?
16:30 gilleain !!! "From the algorithms theory perspective these results mean that subgraph isomorphism is a polynomial time problem," !!!
16:30 gilleain ...
16:32 egonw yeah, was wondering about that...
16:32 gilleain jonalv : well, he's just down the corridor, for starters.
16:32 egonw did they expect linear??
16:32 gilleain also, he's known as a bit of a magician.
16:33 jonalv gilleain: okey
16:33 gilleain egonw : subgraph isomorphism is NPC.
16:33 gilleain So I think that they are suggesting that P=NP.
16:34 gilleain (I hope that that is _not_ what they are claiming)
16:34 egonw anyway... must be an interesting read
16:34 egonw it just poped up over at FriendFeed
16:34 gilleain Although I don't understand that complexity stuff to really comment, tbh.
17:00 egonw bye all
17:00 egonw dinner time
17:48 edrin left #bioclipse
20:58 egonw joined #bioclipse

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