Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-11-27

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Time Nick Message
07:43 egonw joined #bioclipse
07:44 CIA-32 bioclipse: egonw * r7866 /bioclipse2/trunk/cdk-externals/trunk/ (26 files in 5 dirs): Synchronized with jchempaint-primary
07:44 CIA-32 bioclipse: egonw * r7867 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint.view/src/net/bioclipse/​cdk/jchempaint/view/SWTRenderer.java: Outcommented RunTimeException SWTRenderer
07:45 CIA-32 bioclipse: egonw * r7868 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (3 files in 3 dirs): Updated for 2D removal from class and field names
08:12 Gpox joined #bioclipse
08:13 egonw hi Gpox
08:13 egonw I got two questions
08:13 egonw 1. got element.gap cannot be resolved
08:13 egonw 2. please check commit 7867
08:14 egonw ad 2: I had to outcomment it to get it to show anything at all...
08:14 egonw hi applesauce, still here?
08:14 applesauce hey
08:14 egonw Conrad?
08:14 applesauce you must be thinking of someone else :D
08:15 egonw yes, seems so :)
08:15 egonw just checking
08:15 egonw seems you have a broad interest...
08:15 egonw any particular interest in Bioclipse?
08:15 applesauce sorry but my experience with bioclipse is all of 2 weeks :D
08:15 egonw Gpox: so, please have a look at those two things, and advice me what to do
08:15 applesauce sure open source bio is my favorite thing :)
08:16 egonw well, happy to hear that
08:16 Gpox will do
08:31 applesauce after using eclipse for java and php development it is interesting to find this project :)
08:34 egonw did you see the paper in BMC Bioinformatics?
08:35 egonw @gg bioclipse bmc bioinformatics
08:35 egonw zarah: ?
08:35 zarah egonw: yes?
08:35 egonw zarah: help
08:35 zarah egonw: avaliable commands are botsnack clear-messages google help hi karma messages pelezilla ping plan replan restart seen slap start stop tell thanks unplan
08:35 egonw @google bioclipse bmc bioinformatics
08:35 zarah egonw: http://www.bioclipse.net/
08:36 egonw mmm...
08:36 egonw not what I was looking for
08:43 egonw http://www.biomedcentral.c​om/1471-2105/8/59/abstract
08:43 zarah egonw's link is also http://tinyurl.com/5jvy9q
08:49 Gpox joined #bioclipse
09:18 CIA-32 bioclipse: egonw * r7869 /bioclipse2/trunk/cdk-externals/trunk/ (2 files in 2 dirs): Enabled and implemented addRing(IBond, int)
09:19 CIA-32 bioclipse: goglepox * r7870 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: update for changes in the cdk.renderer api
09:20 CIA-32 bioclipse: goglepox * r7871 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (3 files in 2 dirs): Moved Activator with manager to n.bc.cdk.jcp from n.bc.cdk.jcp.business
09:21 CIA-32 bioclipse: goglepox * r7872 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint.view/src/net/bioclipse/cdk/jchempaint/view/ (JChemPaintWidget.java SWTRenderer.java): Update line and text rendering
09:21 CIA-32 bioclipse: goglepox * r7873 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Fixed imports
09:22 CIA-32 bioclipse: goglepox * r7874 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Organized imports
09:22 CIA-32 bioclipse: goglepox * r7875 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint.view/src/net/bioclipse/​cdk/jchempaint/view/SWTRenderer.java:
09:22 CIA-32 bioclipse: Changed line rendering to use a Path
09:22 CIA-32 bioclipse: for extra precision.
09:25 egonw Gpox: updating cdk.control and cdk.render?
09:25 egonw if so, please hold on for one more patch
09:26 egonw which I commited to BC2 SVN, and now porting to CDK jcp-prim SVN
09:28 Gpox no hurry, i made no api changes
09:28 egonw ok, good
09:35 egonw excellent! got a full display now :)
09:35 egonw Gpox: like you showed me yesterday
09:35 CIA-32 bioclipse: shk3 * r7876 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: better test
09:38 jonalv joined #bioclipse
09:38 egonw hi jonalv
09:39 jonalv hi egonw
09:39 jonalv hi alkl
09:39 jonalv *all :)
09:40 jonalv http://www.phdcomics.com/co​mics/archive/phd112608s.gif
09:40 zarah jonalv's link is also http://tinyurl.com/5judk4
10:06 * jonalv is updateing his sytem and will go away during reboot
10:06 egonw cu later
10:07 egonw mmm... the ringPlacer doesn't give all ring atoms coordinates :(
10:13 jonalv joined #bioclipse
10:13 jonalv hi
10:13 zarah hi jonalv
10:17 egonw ok, addRing(IBond, size) works now
10:20 CIA-32 bioclipse: egonw * r7877 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint/src/net/bioclipse/cdk/jchempaint/business/ (IJChemPaintManager.java JChemPaintManager.java): Added addRing(IBond, int) to the jcp manager
10:21 CIA-32 bioclipse: egonw * r7878 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.control/src/org/opensc​ience/cdk/controller/ControllerHub.java: Fixed adding rings to bonds: the sharedAtoms container must include the bond too
10:36 gilleain joined #bioclipse
10:36 egonw hi gilleain
10:41 gilleain hi egonw
10:41 egonw I implemented the addRing(IBond bond, int size)
10:41 gilleain cool! I'll hook it up, then
10:41 gilleain how are you feeling today?
10:41 egonw let me know if you really need addPhenyl(IBond bond)
10:41 egonw sort of as expected
10:42 egonw did not get worse...
10:42 gilleain hmmm.
10:42 egonw but my nose is so irritated :(
10:42 egonw glad to work from home
10:42 egonw might catch some sleep later
10:42 gilleain good.
10:42 egonw but difficult when there is so much to do
10:42 egonw will shk3 come online today?
10:42 egonw I'd like to discuss at some points two JCP things:
10:43 egonw 1. clean up the ControllerHub
10:43 egonw that is...
10:43 egonw talk about how to distribute its content over the controller modules
10:43 gilleain he's here in meatspace
10:44 egonw meatspace :) nice
10:44 gilleain I'll try enticing him to the virtual world
10:44 shk3 joined #bioclipse
10:44 egonw hi shk3
10:45 shk3 hi egomw
10:46 egonw 2. how to handle selections
10:46 egonw will email about both in the next two hours or so
10:48 gilleain Ahh selections.
10:48 shk3 sorry, what was 1?
10:48 egonw [11:43:03] <egonw> 1. clean up the ControllerHub
10:48 egonw [11:43:25] <egonw> that is...
10:48 egonw [11:43:39] <egonw> talk about how to distribute its content over the controller modules
10:48 gilleain we were just talking about addPhenyl(IBond)
10:49 egonw you want it?
10:49 gilleain we need the functionality of adding a benzene ring to a bond, but it doesn't have to be done through that method, necessarily
10:49 egonw I think it is the easiest
10:49 egonw adding a phenyl to an empty screen was easily worked around...
10:50 egonw gilleain: btw, do you agree with the addRing(int size, Point2d) patch?
10:50 egonw (see email)
10:50 * egonw is adding addPhenyl(IBond)
10:50 gilleain I saw the change, I have no problem with it.
10:50 egonw does it make sense too?
10:50 egonw (for me it does...)
10:51 egonw it does not just have to be OK, it has to be better than what it replaced
10:51 gilleain I could see that you might want to add a disconnected ring to a non-blank canvas.
10:51 gilleain For which, you need a method that takes a point.
10:51 egonw (e.g. for drawing reaction)
10:51 gilleain eggsactly
10:52 egonw ha... you heard the radio show almost 6 years ago...
10:52 egonw about Egon?
10:52 egonw Eggon-toast?
10:52 gilleain nah, it's a fairly standard english pun
10:52 egonw E-gone-fishing?
10:53 gilleain oh, btw - did you see the change I made to atom placement? Is that okay.
10:54 egonw not sure
10:54 gilleain in the addAtom(String, IAtom)
10:54 egonw which commit?
10:54 gilleain uhhh.
10:54 gilleain so many commits to cia, it's off the next page already.
10:55 egonw that's one thing I much like of Gmail
10:55 egonw I can search my inbox
10:56 gilleain ah. r13308
10:56 gilleain I used the AtomPlacer.placeLinearChain method.
10:57 egonw ah..
10:57 egonw yes saw that...
10:57 egonw I guess that adds an angle, right?
10:57 gilleain Yes.
10:57 egonw yes, that makes sense...
10:57 egonw 60 degrees?
10:57 egonw umm...
10:57 egonw I mean, 120 degrees?
10:58 gilleain it has this weird distance measure argument that I don't get.
10:58 egonw file a bug report requesting JavaDoc fixing
10:58 gilleain to AtomPlacer.getNextBondVector
10:58 gilleain well, it's documented, I just don't understand it!
10:59 gilleain can I file bug reports on myself?
10:59 egonw sure
10:59 egonw I often do that...
10:59 egonw if I don't have the time to fix something immediately
10:59 gilleain No, I mean bugs in my thinking :)
10:59 egonw I prefer that over adding a comment in the source file like // FIXME: or // TODO:
11:00 egonw yeah, open a SF project gilleain
11:00 gilleain Oh. I add all sorts of FIXME
11:00 gilleain my favourite is // FIXME XXX TODO
11:02 gilleain uh-oh. addRing(IBond, int) isn't working right.
11:02 egonw mmm... it is here...
11:03 egonw mom
11:03 egonw let me check if I ported a fix to jchempaint-primary yet
11:03 egonw no, don't think I did ...
11:03 egonw hang on
11:03 gilleain ok.
11:04 egonw ok, here it comes
11:05 egonw well, on #cdk
11:05 gilleain well, yes.
11:05 gilleain :)
11:08 Julio joined #bioclipse
11:09 Julio left #bioclipse
11:26 * jonalv heads out for lunch and stuff
11:27 jonalv where stuff would be handing in the keys to my old student room :)
11:27 jonalv bbl
11:48 CIA-32 bioclipse: egonw * r7879 /bioclipse2/trunk/ (4 files in 3 dirs): Implemented addPhenyl(IBond)
12:30 egonw Gpox, gilleain, shk3: two email sent to cdk-jchempaint
12:31 gilleain okay, I'll think about it over lunch :)
12:31 egonw thanx
12:49 edrin joined #bioclipse
12:59 gilleain joined #bioclipse
13:04 * jonalv is back
13:09 CIA-32 bioclipse: jonalv * r7880 /bioclipse2/trunk/plugins/net.bioclipse.struc​turedb.tests/tests/net/bioclipse/structuredb/​persistence/dao/TextAnnotationDaoTest.java: removed unused import of a sun class
13:20 edrin hi
13:20 zarah hi edrin
13:23 egonw hi edrin
13:23 edrin hi egonw
13:26 charlgren joined #bioclipse
13:38 egonw jonalv: ping
13:42 jonalv egonw: pong
13:43 egonw where do I find numberOfEntriesInSDF?
13:43 jonalv in cdk
13:43 jonalv manager
13:43 egonw ah, tack
13:43 jonalv I thought I attached a context totthat bug...
13:44 egonw mmm... that code looks pretty efficent... I'd guessed :(
13:44 egonw ah, you did
13:44 egonw overlooked it
13:44 egonw as I though you had done that...
13:44 egonw sorry
14:07 egonw jonalv: ping
14:07 jonalv egonw: pong
14:07 egonw the numberOfEntriesInSDF was interesting
14:07 egonw the fix was suprisingly easy
14:07 egonw use BufferedInputStream
14:07 jonalv egonw: ok?
14:07 egonw that's all
14:07 jonalv aha
14:08 egonw now, it's counted in well below a second
14:08 jonalv so how fast is it now? :)
14:08 jonalv nice
14:08 egonw as in... you don't even see it counted !
14:08 jonalv w0tt
14:08 jonalv I must try that. Have you commited?
14:08 egonw about to
14:08 jonalv was that with the 1 gb file?
14:08 jonalv that would be strangely fast...
14:08 egonw don't have that one here, I think
14:09 egonw download from pele takes too long
14:09 egonw no with the 21MB one
14:09 jonalv okey
14:09 jonalv I will try with the 1 GB sized one as soon as I find it... :)
14:10 jonalv ...and you have commited... :)
14:12 egonw committing now
14:13 CIA-32 bioclipse: egonw * r7881 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Use BufferedInputStream, which cashes input being read, basically optimizing reading from disc, I think (fixes #146)
14:13 zarah bug #146 | http://tinyurl.com/627sb5
14:13 CIA-32 bioclipse: egonw * r7882 /bioclipse2/trunk/plugins/net.bioclipse​.structuredb/src/net/bioclipse/structur​edb/business/StructuredbManager.java: Better feedback
14:14 jonalv egonw: better feedback?
14:14 egonw reading 566/3670
14:14 egonw reading 567/3670
14:14 egonw reading 568/3670
14:14 egonw reading 569/3670
14:14 egonw reading 570/3670
14:15 gilleain wow, it posts the feedback to irc?
14:15 jonalv huh?
14:15 gilleain ;)
14:15 * jonalv isn't sure that's beter... ;)
14:15 egonw well, at least it gives the number of items being read
14:16 jonalv oh okey
14:16 egonw but somewhere around molecule 600 or so...
14:17 egonw it sort of crashes
14:17 egonw btw, wishlist: allow cancelling
14:17 egonw mom, let me test something
14:17 egonw while ( iterator.hasNext() && !monitor.isCanceled()) {
14:18 egonw that might just work
14:18 jonalv egonw: where are you now?
14:18 jonalv in the import method in structuredb?
14:18 egonw StructutredbManager
14:18 egonw addMoleculesFromSDF
14:19 jonalv okey
14:19 jonalv yea that might be a good idea
14:19 jonalv I am suprised I hadn't written that already...
14:19 egonw testing
14:19 egonw so much to do, so little time (tm)
14:20 egonw yes, that seems to do the job :)
14:21 jonalv sounds good
14:21 CIA-32 bioclipse: egonw * r7883 /bioclipse2/trunk/plugins/net.bioclipse​.structuredb/src/net/bioclipse/structur​edb/business/StructuredbManager.java: Allowing canceling import... without a revert, btw. So anything added by then, remains added. Not really cancel, but more like Stop Now.
14:22 egonw ok, going to have some coffee now...
14:22 egonw bbl for fixing the full import of that file
14:23 gilleain hmmm. I wonder...
14:23 gilleain ü
14:23 gilleain î
14:23 gilleain é
14:23 gilleain thought so.
14:24 jonalv [
14:24 jonalv what are we playing?
14:24 gilleain I found yesterday that alt+e/al+u/alt+i on the mac do this great thing
14:24 gilleain where a yellow box appears with the letter decoration, and then you press the key of the letter under it
14:25 gilleain ñ
14:25 gilleain
14:26 jonalv counting number of entries in the 1gb sized sdf files takes less than 1 min on my machine...
14:27 jonalv egonw++
14:27 gilleain cool.
14:27 gilleain egonw++
14:27 jonalv now we just need to speed up the actual import into strucutredb as well... :)
14:27 gilleain :¬)
14:48 masak joined #bioclipse
14:49 jonalv masak: y0
14:49 gilleain ¥ø
14:50 masak y0
14:50 zarah hi masak
14:50 masak hi zarah
15:02 masak egonw: if it's not really Cancel, one could argue that it shouldn't really be called 'Cancel'
15:03 masak (re r7883)
15:08 egonw masak: yeah, tell the Eclipse people
15:09 masak do they call non-Cancel "Cancel" too?
15:13 egonw not sure of a progress monitor has non-cancel...
15:13 masak what I mean is,
15:13 masak 'Cancel' usually involves rollback
15:13 masak otherwise the customer feels very sad
15:14 masak so, if there's no rollback, better not to name it 'Cancel'
15:14 masak ...but 'Stop', or something
15:14 egonw yes, agreed
15:26 jonalv masak: how do we do that?
15:27 masak jonalv: what? rollback, or change from 'Cancel' to 'Stop'?
15:27 jonalv masak: change from cancel to stop
15:28 masak jonalv: my guess is we don't. not in a standard progress display.
15:28 masak my guess is that one would have to climb high in the inheritance hierarchy and derive something.
15:28 jonalv exactly
15:28 masak and it's doubtful whether one would want to do that.
15:29 masak ...which is why it's better to do rollback instead.
15:29 jonalv masak: yea...
15:29 masak but I don't know what the process is, so I don't know how to roll it back. :)
15:30 jonalv so the process is importing of molecules from sdf into the datbase
15:30 masak import them into a sandbox
15:30 egonw btw, it's amazing how well the TextEditor can handle 21MB files !
15:31 masak then, when you're done, flip a switch.
15:31 masak (oh, and make sure the sandbox gets GC'd if it's orphaned)
15:31 masak (databases can do that, right?)
15:32 egonw jonalv: that hydrogen removal problem is interesting...
15:32 egonw this is the molecule it fails on:
15:32 egonw 783
15:32 egonw -OEChem-10090810202D
15:32 egonw 2  1  0     0  0  0  0  0  0999 V2000
15:32 egonw 2.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
15:32 egonw 3.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
15:32 egonw 1  2  1  0  0  0  0
15:32 egonw M  END
15:32 egonw interesting case, not? :)
15:32 masak nopaste!
15:33 egonw where?!?!
15:33 egonw nevermind
15:33 masak http://gist.github.com/
15:33 egonw interesting case, not? :)
15:33 jonalv egonw: I am not that used to reading mdl files... I see a lot of 0s though...
15:33 egonw check the atom elements
15:33 egonw it's removing hydrogens!
15:34 jonalv so nothing get left?
15:34 egonw right :)
15:34 egonw should not throw an exception, of course...
15:34 jonalv what file was this from?
15:35 egonw small.sdf
15:35 jonalv so small.sdf contains H2?
15:35 egonw yes :)
15:35 jonalv lol
15:35 egonw speaking of small
15:35 jonalv yea
15:35 masak does it remove exactly the present amount of hydrogens, or more than the present amount of hydrogens?
15:36 egonw no idea
15:36 egonw will write a unit test for the CDK
15:36 masak heh
15:37 charlgren egonw, masak: Do you know how to get the absolute path of a file with java? Not just relative to the package, but the system root? For portability.
15:37 masak charlgren: feels familiar. let me have a look at the Java API and see if I can remember.
15:38 charlgren masak: would be nice
15:38 jonalv I totally failed so I thought perhaps one of you guys might know...
15:38 * jonalv feels a bit silly... :)
15:38 masak charlgren: http://java.sun.com/j2se/1.5.0/docs/a​pi/java/io/File.html#getAbsoluteFile()
15:39 zarah masak's link is also http://tinyurl.com/4662p
15:39 masak have you tried that one?
15:39 masak http://java.sun.com/j2se/1.5.0/docs/a​pi/java/io/File.html#getAbsolutePath()
15:39 zarah masak's link is also http://tinyurl.com/4662p
15:39 masak ...perhaps better if you want the path itself.
15:40 charlgren masak: mabe with the constructor taking uri, otherwise you have to specify the absolute path in the constructor
15:40 masak charlgren: sorry, was that a question? I don't understand.
15:41 jonalv uhm masak how do we get the file in the first place?
15:41 charlgren masak: not sure
15:41 masak oh! you don't have the File!
15:41 masak well, what _do_ you have?
15:41 jonalv we know what package the file is in. (I think)
15:42 masak as in Java package?
15:42 charlgren File("myFile.txt") creates a new file in /home/jonas
15:42 charlgren I need to get the path of an existing file
15:42 masak um.
15:43 masak I've never done exactly that.
15:43 charlgren can get the path relative to package root
15:43 masak but I still think your best shot is to go via File objects
15:43 charlgren it sounds reasonable
15:43 masak play around with it and see if you can turn your relative path into a File somehow.
15:44 masak and then, hopefully, Java will know the absolute path.
15:44 charlgren will do so
15:50 egonw jonalv: ok, it now parses the full 21MB in a few minutes
15:50 egonw and gets really slow at the end
15:50 jonalv the import?
15:50 egonw either those molecules are really large
15:50 egonw yes
15:50 jonalv nice
15:50 egonw or there is some memory leaking
15:50 jonalv what have you changed? :)
15:50 jonalv I think there is some memory leaking...
15:50 jonalv HAve you tried a bigger file?
15:51 egonw no
15:51 egonw double clikcing the 'small' crashes bioclipse
15:51 egonw ooh... with a nasty seg fault in the JRE :)
15:51 jonalv as in opening it in the sdf editor?
15:52 egonw # Java VM: Java HotSpot(TM) Server VM (11.0-b15 mixed mode linux-x86)
15:52 egonw # Problematic frame:
15:52 egonw # C  [libc.so.6+0x785dd]  memmove+0x4d
15:52 egonw right
15:52 jonalv aouch..
15:52 jonalv can you reproduce that?
15:52 egonw no idea
15:52 egonw will try
15:52 masak egonw++ # nasty segfault!
15:53 egonw ummm... egonw--
15:53 egonw it's jonalv's code
15:53 egonw jonalv++
15:53 jonalv so you get ++ fro seqfaults? :)
15:54 egonw no, for finding a bug in SUn's JVM :)
15:56 CIA-32 bioclipse: egonw * r7884 /bioclipse2/trunk/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/DBMolecule.java: Catch any exception; no SMILES is not the end of the world. Jonalv, or is it for StructureDB? Please check this patch...
15:57 jonalv egonw: oki that might actually make sence. Just look out for masak's oppinions regarding catching the base class Exception
16:00 jonalv masak?
16:00 * masak backlogs
16:00 jonalv zarah: ping masak wake up
16:00 zarah Consider it noted.
16:00 masak @clear
16:00 zarah masak: Messages cleared.
16:01 masak ah! catching Exception. yes, that's kinda frowned upon.
16:01 masak please don't do that.
16:01 egonw jonalv: feel free to reopen and make me catch NullPointerException
16:01 egonw nevermind
16:01 egonw hang on
16:01 * egonw thinkgs masak should write a PMD test for this
16:01 masak catching Exception is like saying "um, if something happens..."
16:02 masak egonw: I think there is one already.
16:02 egonw ah, then why don't we run it?
16:02 gilleain System.err.println("Something happened!");
16:02 egonw (rethorical)
16:02 egonw smiles = "";
16:02 masak egonw: do we runt PMD at all right now?
16:02 egonw ah, file a bug report
16:03 jonalv masak: do we run any nightly stuff at all?
16:03 masak jonalv: not as far as I know.
16:03 egonw no
16:03 egonw not yet
16:04 CIA-32 bioclipse: egonw * r7885 /bioclipse2/trunk/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/DBMolecule.java: Fixed my bad code, and made a mental code DON'T EVER CATCH Exception WHEN MASAK IS AROUND :)
16:04 CIA-32 bioclipse: goglepox * r7886 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (6 files in 2 dirs):
16:04 CIA-32 bioclipse: Added some more items to the popupmenu
16:04 CIA-32 bioclipse: and rewrote the handlers to use the jcp-manager
16:04 masak egonw: damn straight.
16:04 egonw :)
16:05 CIA-32 bioclipse: goglepox * r7887 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint.view/src/net/bioclipse/cdk/jchempaint/view/ (JChemPaintWidget.java SWTFontManager.java SWTRenderer.java): Implemented font manager for SWT and added rendering of formal charges
16:05 masak and try to keep a serious tone in commit messages, please :)
16:05 masak they're for ever and ever.
16:06 egonw ah, we don't even have f**k in our commit messages or comments yet
16:06 egonw we're pretty polite, I think :)
16:06 masak (as are logs)
16:06 egonw ok, guys...
16:06 egonw going home (5 meters away)
16:06 egonw and lite up the fire
16:06 masak egonw: yes, we're polite
16:06 egonw bye for now, cu tomorrow
16:06 egonw well, I try to be
16:06 masak egonw: bye
16:06 gilleain bye
16:07 egonw doesn't always work out as well as I like
16:07 masak it's trying that counts :)
17:04 CIA-32 bioclipse: gilleain * r7888 /bioclipse2/trunk/plugins/net.bioc​lipse.seneca/src/net/bioclipse/sen​eca/views/BestStructureView.java: Minor fix.
17:13 Gpox gilleain++
17:14 gilleain what did I do?
17:16 masak gilleain: fixed something minor, perhaps?
17:16 gilleain :)
17:16 Gpox just a minor fix :)
17:16 masak :)
17:16 CIA-32 bioclipse: shk3 * r7889 /bioclipse2/trunk/plugins/net.bioc​lipse.spectrum/src/net/bioclipse/s​pectrum/editor/MetadataUtils.java: cleanup
17:21 CIA-32 bioclipse: goglepox * r7890 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/handlers/ManagerHandler.java: New commands handler that calls a manager method with reflection
17:21 CIA-32 bioclipse: goglepox * r7891 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Added a few menu items using the new manger command
17:41 CIA-32 bioclipse: goglepox * r7892 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Added more menu itmes
18:10 CIA-32 bioclipse: jonalv * r7893 /bioclipse2/trunk/plugins/net.bioclipse.tests/: modified svn:ignore
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