Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-09-04

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
01:59 m4r1in_ joined #bioclipse
02:03 m4r1in_ joined #bioclipse
05:32 Gpoks joined #bioclipse
05:34 Gpox joined #bioclipse
05:44 egonw joined #bioclipse
06:08 Gpox joined #bioclipse
06:09 egonw @tell olas I'm on the problem...
06:09 zarah Consider it noted.
06:16 Gpox joined #bioclipse
07:20 jonalv joined #bioclipse
07:20 jonalv hi
07:20 zarah hi jonalv
07:25 edrin joined #bioclipse
07:27 egonw oh, crap
07:28 egonw this is *very* *bad* *timing*
07:28 egonw @tell olas that I cannot upload my Sybyl fixes, because SVN write access is offline today, because of system upgrade
07:28 zarah Consider it noted.
07:46 thomas_ku joined #bioclipse
07:47 edrin hi
07:47 zarah hi edrin
07:49 jonalv hi edrin
07:51 edrin hi jonalv
07:52 edrin egonw: read my mail?
07:52 egonw no, did not have time
07:53 egonw will do as the very next thing...
07:55 edrin ok
08:00 jonalv do anyone know how much memory Bioclipse has to play with? I seem to remember someone tweaking this...
08:14 egonw edrin: replied
08:30 olas joined #bioclipse
08:30 olas hi
08:30 zarah hi olas
08:30 zarah olas: You have new messages. Write '@messages' to read them.
08:30 olas @msg
08:30 zarah olas: egonw said I'm on the problem...
08:30 zarah olas: egonw said that I cannot upload my Sybyl fixes, because SVN write access is offline today, because of system upgrade
08:30 olas ack
08:30 olas hmm
08:30 * olas is comitting now
08:31 CIA-30 bioclipse: ospjuth * r6880 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (icons/doc_mol_2d.png plugin.xml): Duplicated icons, should be removed and referenced from bc.ui but no time to find out how to do that now.
08:31 olas egonw: svn commit seems to work...
08:31 olas edrin: sorry for not responding to email
08:32 olas will do that on the train home, after 17 today
08:32 olas too busy now :-)
08:32 egonw olas: indeed
08:32 egonw trying to commit again
08:33 olas egonw: did all go well with the last days?
08:33 CIA-30 bioclipse: goglepox * r6881 /bioclipse2/trunk/plugins/net.bioc​lipse.tests/META-INF/MANIFEST.MF: Removed dependency on brunn
08:34 egonw olas: at work?
08:34 egonw all CDKManger tests work now
08:34 olas at AZ
08:35 CIA-30 bioclipse: egonw * r6882 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
08:35 CIA-30 bioclipse: Fixed Sybyl atom type perception: the problem was that aromaticity detection
08:35 CIA-30 bioclipse: requires *all* atom types already to be perceived, so it's a CDK bug. The code
08:35 CIA-30 bioclipse: in CDKManager therefore works around the CDK code to be fixed, by implementing
08:35 CIA-30 bioclipse: the logic correctly
08:35 egonw olas: huh?
08:42 egonw no egonw++ ?
08:42 zarah shame on you, egonw, giving yourself karma like that
08:42 egonw zarah: he, I was only asking... !
08:42 zarah egonw: I did not understand that
08:42 egonw yeah, play the innocent
08:42 egonw @slab zarah
08:43 egonw @hit zarah
08:43 * egonw hits zarah with a trout
08:43 jonalv =)
08:43 * egonw acquired the skill of git merging on svn repositories
08:43 jonalv oh, svn merging is terrible...
08:44 egonw so, we have git do it :)
08:44 jonalv nice :)
08:47 olas egonw: have you fixed the sybyl atom typing problem?
08:47 egonw sure
08:48 egonw you know me
08:48 olas :-)
08:48 egonw see commit message for details on why it failed
08:55 edrin egonw: thanks, olas: ok
09:29 CIA-30 bioclipse: goglepox * r6883 /bioclipse2/trunk/plugins/net.bioclipse.core​/src/net/bioclipse/core/BioclipseStore.java: Removed verbose logging statement
09:43 maclean joined #bioclipse
09:44 CIA-30 bioclipse: goglepox * r6884 /bioclipse2/trunk/plugins/net.biocl​ipse.cdk.business/src/net/bioclipse​/cdk/domain/SDFAdapterFactory.java: changed assertion on number of molecules to one
09:46 CIA-30 bioclipse: goglepox * r6885 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/MoleculesEditor.java: Added check for IStructuredSelection to avoid ClassCastException
09:46 CIA-30 bioclipse: goglepox * r6886 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculesEditorLabelProvider.java: Made molecule image transparent so selection color is visible under the image
09:48 CIA-30 bioclipse: goglepox * r6887 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/sr​c/net/bioclipse/cdk/ui/model/BuilderThread.java: fixed calculation of molecule in file position
10:01 CIA-30 bioclipse: jonalv * r6888 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/ (2 files in 2 dirs): Added more exact monitor to the quick parsing of an sdf file. However it only seems to update the status bar once. No idea why... :(
10:30 CIA-30 bioclipse: goglepox * r6889 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Added option to change font size when rendering molecules
10:40 shk3 joined #bioclipse
10:44 shk3 hi all
10:44 zarah hi shk3
10:44 shk3 hi gpox
10:45 shk3 we (Gilleain and me) are wondering about jcp development
10:46 shk3 can anybody tell us about this?
10:47 shk3 Gpox?
11:13 Gpox not much, i did a quick and dirty port of the renderer to SWT
11:14 maclean And there is also this code from Niels Out?
11:14 shk3 So you are working in the renderer classes in cdk trunk?
11:14 shk3 and where is this port to be found?
11:16 Gpox the code i ported was from Niels, it is in SWTRenderer in net.bioclipse.cdk.jchempaint.widget
11:16 Gpox and it is almost a straight search and replace for Graphcis to GC
11:16 maclean Ah, okay. And is anyone working on the Swing code?
11:17 maclean (or planning to)
11:18 shk3 let us check if my understanding is correct:
11:18 shk3 there will be/is a widget-independent renderer in org.openscience.cdk.renderer
11:18 shk3 this is part of cdk
11:19 shk3 the jchempaint project in cdk will wrap swing round this
11:19 shk3 bioclipse will wrap swt round it.
11:19 shk3 Is this correct?
11:20 Gpox i think so
11:20 shk3 ah
11:20 Gpox right now the rendering code is very much Java2D dependant
11:21 maclean So, the parts in the render package will be graphics-independant, allowing the AWT(swing) and SWT to build on them.
11:21 shk3 hm, does this mean we can't/shoudn't use java2D in the rendere?
11:22 maclean That kind of means using some kind of intermediate graphical model (AtomShapes?) that are passed to each for rendering.
11:23 maclean I should take a look at the ControllerHub stuff.
11:24 Gpox there is a lot of graphics indepedent code that could be shared if it is untangeld
11:24 maclean sure, I expect that there is. I was just thinking aloud about the architecture.
11:25 maclean Yes, there's this cdk.controller package.
11:26 maclean With Controller2DHub, that "will central interaction point between a mouse event throwing
11:26 maclean * widget (SWT or Swing) and the Controller2D modules"
11:26 CIA-30 bioclipse: jonalv * r6890 /bioclipse2/trunk/plugins/net.bi​oclipse.structuredb/plugin.xml: [structuredb] Made gui actions delete label and delete database active also for multiple selections
11:34 egonw joined #bioclipse
11:36 shk3 we just had an internal discussion on a possible architecture.
11:37 shk3 gilleain will write this down and send it to the list.
12:52 jonalv joined #bioclipse
13:04 steinbeck joined #bioclipse
13:07 steinbeck left #bioclipse
13:07 olas joined #bioclipse
13:08 olas hi
13:08 zarah hi olas
13:08 olas @msg
13:08 zarah olas: You have no new messages.
13:08 olas zarah: why not?
13:08 zarah olas: you've just exceeded my capabilities :/
13:08 olas zarah: how come?
13:08 zarah olas: you've just exceeded my capabilities :/
13:08 olas zarah: you said that already!
13:08 zarah olas: that was not so easy for a little bot to understand
13:08 maclean /rnsg olas: Do stuff!
13:08 olas zarah: you are a grownup bot now
13:08 zarah olas: are you making fun of me?
13:08 maclean Better?
13:09 maclean :)
13:09 olas :-)
13:09 olas @clear-msg
13:09 zarah olas: Messages cleared.
13:09 olas @clear-msg
13:09 zarah olas: Messages cleared.
13:10 olas I'll be off now to the train
13:11 olas might be online later
13:11 olas on the train
13:11 olas else I'll be back tomorrow
13:11 olas bye
13:11 olas left #bioclipse
13:25 edrin me, too
13:53 masak joined #bioclipse
14:00 thomas_ku joined #bioclipse
14:18 masak joined #bioclipse
14:32 CIA-31 joined #bioclipse
14:38 jonalv joined #bioclipse
15:37 shk3 egonw!
15:43 CIA-30 joined #bioclipse
15:51 egonw hi shk3
15:51 * egonw is busy packing up the house
15:54 shk3 i am surprised you prefer this to some hacking
15:58 egonw well, hacking := do things with stuff for which the stuff was never intended...
15:58 egonw now, books were never intended to be packed together in boxes
15:59 egonw so, sort of, I guess :)
15:59 egonw cu later
18:24 egonw joined #bioclipse
18:58 ChanServ joined #bioclipse
18:58 egonw joined #bioclipse
20:48 egonw_ joined #bioclipse
20:55 ChanServ joined #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary