Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-11

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All times shown according to UTC.

Time Nick Message
05:25 egonw joined #bioclipse
06:57 edrin joined #bioclipse
07:04 edrin hi egonw
07:19 Gpox joined #bioclipse
07:43 edrin joined #bioclipse
08:01 egonw joined #bioclipse
08:16 shk3 joined #bioclipse
08:45 CIA-40 bioclipse: goglepox * r10203 /bioclipse2/trunk/plugins/net.bioclipse.co​re/src/net/bioclipse/core/Activator.java: Added refresh when creating 'Virtal' project
08:45 CIA-40 bioclipse: goglepox * r10204 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java:
08:45 CIA-40 bioclipse: Moved setup code for positioning to reset()
08:45 CIA-40 bioclipse: and call it from setModel()
08:45 CIA-40 bioclipse: it is also called from jcp.zap() and jcp.cleanup()
08:45 CIA-40 bioclipse: Resolves bug #969
08:45 zarah bug #969 | http://tinyurl.com/o33aae
08:51 CIA-40 bioclipse: goglepox * r10205 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint.view/src/net/bioclipse/​cdk/jchempaint/view/SWTRenderer.java:
08:51 CIA-40 bioclipse: Use line width of 1 fi widht is <1 in SWTRenderer
08:51 CIA-40 bioclipse: Line width 0 in SWT is a hint to enable fastest
08:51 CIA-40 bioclipse: possible rendering.
08:52 jonalv joined #bioclipse
08:52 egonw hi jonalv
09:01 jonalv hi egonw
09:46 CIA-40 bioclipse: goglepox * r10206 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Added check if widget is disposed before doing a resizeControll in JCP
09:47 CIA-40 bioclipse: goglepox * r10207 /bioclipse2/trunk/plugins/net.bioclipse.jmol/s​rc/net/bioclipse/jmol/editors/JmolEditor.java: (log message trimmed)
09:47 CIA-40 bioclipse: Added keylistener to jmolPanel to lisen for CTRL/COMMAND-W
09:47 CIA-40 bioclipse: This adds a key listener that listens for W with
09:47 CIA-40 bioclipse: modifier CTRL or COMMAND depending if it is mac
09:47 CIA-40 bioclipse: or not, if it is close editor is called.
09:47 CIA-40 bioclipse: This is kinda a qick fix dunno if there is a real fix
09:47 CIA-40 bioclipse: like getting those events out to eclpse.
10:25 maclean joined #bioclipse
10:38 egonw joined #bioclipse
10:44 egonw jonalv, Gpox: ola will not be around today, will he?
11:07 jonalv egonw: I don't know. I was actually wondering the same thing
11:15 egonw I think he said that we was having a long weekend holiday
11:17 Gpox i think so too, he was traveling somewhere iirc
11:21 CIA-40 bioclipse: goglepox * r10208 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui/plugin.xml:
11:21 CIA-40 bioclipse: Chaged default handler for generateInChI
11:21 CIA-40 bioclipse: from net.bc.inchi.handlers.GenerateInChI to
11:21 CIA-40 bioclipse: net.bc.cdk.business.GenerateInChI
11:21 CIA-40 bioclipse: goglepox * r10209 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/MoleculeTableViewer.java: Added hook for doubleclick action
11:22 masak joined #bioclipse
11:22 CIA-40 bioclipse: goglepox * r10210 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MultiPageMoleculesEditorPart.java:
11:22 CIA-40 bioclipse: Now changes to single structure tab when double-clicked
11:22 CIA-40 bioclipse: Fixes bug #964
11:22 zarah bug #964 | http://tinyurl.com/opfyfg
11:39 egonw lunch time
12:18 CIA-40 bioclipse: goglepox * r10211 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Fixed getAtaper(IAtomContainer.class) to sync the molecule
12:19 CIA-40 bioclipse: goglepox * r10212 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
12:19 CIA-40 bioclipse: Reverted chages for visulazing substrcture matches
12:19 CIA-40 bioclipse: in selection.
12:19 CIA-40 bioclipse: It introduced bug #1048 which this resolves
12:19 zarah bug #1048 | http://tinyurl.com/qvw8bk
12:26 shk3 joined #bioclipse
12:30 egonw joined #bioclipse
12:32 shk3_ joined #bioclipse
13:00 CIA-40 bioclipse: shk3 * r10213 /bioclipse2/trunk/plugins/net.bioclipse.reaction/: Initial import.
13:03 CIA-40 bioclipse: shk3 * r10214 /bioclipse2/trunk/plugins/net.bioclipse.reaction/ (109 files in 25 dirs): Initial import.
13:20 CIA-40 bioclipse: goglepox * r10215 /bioclipse2/trunk/plugins/ (4 files in 4 dirs):
13:20 CIA-40 bioclipse: Added popupmenu item for opening 2D-strcuture tab
13:20 CIA-40 bioclipse: Also linked double-click to this command
13:22 CIA-40 bioclipse: shk3 * r10216 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business/src/net/bioclipse/cdk/ (4 files in 2 dirs): added reaction domain objects and manager methods
13:23 CIA-40 bioclipse: shk3 * r10217 /bioclipse2/trunk/plugins/net.bioc​lipse.chemoinformatics/plugin.xml: added content type for rxn
13:23 CIA-40 bioclipse: shk3 * r10218 /bioclipse2/trunk/plugins/net.bioclipse.cml/ (2 files in 2 dirs): added content types for cml reactions
13:30 shk3__ joined #bioclipse
13:34 CIA-40 bioclipse: shk3 * r10219 /bioclipse2/trunk/plugins/ne​t.bioclipse.data.reaction/: Initial import.
13:35 CIA-40 bioclipse: shk3 * r10220 /bioclipse2/trunk/plugins/n​et.bioclipse.data.reaction/ (22 files in 10 dirs): Initial import.
13:36 CIA-40 bioclipse: shk3 * r10221 /bioclipse2/trunk/plugins/net.bi​oclipse.data.reaction/.project: wrong project name
13:54 CIA-40 bioclipse: shk3 * r10222 /bioclipse2/trunk/plugins/net.b​ioclipse.cdk.business.test/src/ (3 files in 2 dirs): added tests for reaction loading
14:06 CIA-40 bioclipse: shk3 * r10223 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: reaction loading seems to be ok
14:28 shk3_ joined #bioclipse
14:55 CIA-40 bioclipse: goglepox * r10224 /bioclipse2/trunk/ (2 files in 2 dirs):
14:56 CIA-40 bioclipse: Removed SelectionGenerator
14:56 CIA-40 bioclipse: Changed references to SelectAtomGenerator and
14:56 CIA-40 bioclipse: SelectBondGenerator.
14:56 CIA-40 bioclipse: Resolves bug #988
14:56 zarah bug #988 | http://tinyurl.com/p387z3
14:57 CIA-40 bioclipse: goglepox * r10225 /bioclipse2/trunk/plugins/ (4 files in 3 dirs):
14:57 CIA-40 bioclipse: Aded InChI dialog
14:57 CIA-40 bioclipse: This also adds the posibility to copy inchi with
14:57 CIA-40 bioclipse: CMD-C
15:03 egonw Gpox++
15:18 CIA-40 bioclipse: shk3 * r10226 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): loadreactions loads multiple reactions
15:20 masak should the cdx namespace be included in a shipped Bioclipse?
15:27 shk3__ joined #bioclipse
15:27 egonw it's in the CDK feature
15:35 CIA-40 bioclipse: shk3 * r10227 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: use biolist
15:39 CIA-40 bioclipse: goglepox * r10228 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java:
15:39 CIA-40 bioclipse: Added diry checks when doing undo redo.
15:39 CIA-40 bioclipse: Resolves bug #760
15:39 zarah bug #760 | http://tinyurl.com/q8sam2
15:46 jonalv out of 208 New world order plugin tests we now have 35 errors and 2 failures
15:50 CIA-40 bioclipse: goglepox * r10229 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint/src/net/bioclipse/cdk/jchempaint/undoredo/ (SWTLoadNewModelEdit.java SWTUndoRedoFactory.java):
15:50 CIA-40 bioclipse: Implemented SWTUndoRedoFactory.getLoadNewModelEdit()
15:50 CIA-40 bioclipse: Fixes bug #987
15:50 zarah bug #987 | http://tinyurl.com/r4evyj
15:55 egonw jonalv++
15:56 CIA-40 bioclipse: shk3 * r10230 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (3 files in 3 dirs): better use of manager in editor
16:25 shk3_ joined #bioclipse
17:04 ilogger2 joined #bioclipse
17:12 edrin left #bioclipse
17:18 shk3__ joined #bioclipse
17:22 CIA-40 bioclipse: shk3 * r10231 /bioclipse2/trunk/plugins/net.bioclipse.seneca/ (plugin.xml src/net/bioclipse/seneca/editor/JudgePage.java): small cosmetic changes
17:43 CIA-40 bioclipse: egonw * r10232 /bioclipse2/trunk/_playgro​und_/net.bioclipse.medea/: Copied medea plugin, for updating against Seneca in BC2
17:44 CIA-40 bioclipse: egonw * r10233 /bioclipse2/trunk/_playground​_/net.bioclipse.medea.case/: Copied medea CASE plugin, for updating against Seneca in BC2
17:47 CIA-40 bioclipse: steinbeck * r10234 /bioclipse2/trunk/features/net.biocl​ipse.speclipse_feature/feature.xml: Added all relevant plugins for SENECA to be included in the Speclipse feature
20:44 egonw joined #bioclipse
20:50 rojasm joined #bioclipse
20:51 * rojasm updating medea and more plugins
20:51 egonw ah, did not commit yet
20:51 egonw polishing some last missing dependencies...
20:51 egonw hang on
20:52 rojasm I am at least importing the plugin
20:54 egonw ack
20:56 egonw OK, closing in on the last compile problems
20:58 egonw rojasm: oh, btw
20:58 egonw Chris asked if we could meed with Asad on Wed
20:59 egonw as he will be busy on Wed
20:59 egonw I said I had no clue, since you made the appointment with Asad
21:00 rojasm I think that he would not thought a bad idea
21:00 rojasm I will sent a email him
21:00 rojasm send
21:00 egonw ok
21:01 rojasm what time do you think it could be the best
21:02 egonw I leave that to you...
21:02 egonw my taxi leaves at 15:30 or so...
21:02 egonw let me check
21:07 rojasm I guess I should leave at 16:00 but I could came with you than
21:08 egonw ah, your taxi would go at 17:15
21:08 egonw mine at 16:15
21:09 egonw would give some extra time at the airport to chat
21:09 egonw but you would need to cancel your taxi tomorrow then...
21:15 CIA-40 bioclipse: egonw * r10235 /bioclipse2/trunk/ (8 files in 6 dirs): Many compile fixes
21:17 rojasm ya. I will notify it tomorrow
21:19 rojasm I will ask Asad to change the meeting for Wednesday at 12:00
21:19 egonw ok
21:25 rojasm I sent already him a email about that
21:27 * egonw is fixing the last few compile errors
21:27 rojasm also are you working with the medea from bioclipse1?
21:27 egonw either stefan or gilleain was not entirely convinced by my design :)
21:27 egonw two plugins:
21:27 egonw medea
21:27 egonw medea.case
21:28 egonw working on both
21:29 paulymer__ joined #bioclipse
21:29 egonw hi paulymer__
21:30 paulymer__ hi
21:30 zarah privet paulymer__
21:30 paulymer__ ??
21:30 egonw zarah is our bot
21:30 egonw does some useful things
21:30 egonw privet == hi
21:30 paulymer__ ahhh
21:30 egonw not sure which langauge again :)
21:30 paulymer__ privet zarah.... :)
21:34 CIA-40 bioclipse: egonw * r10236 /bioclipse2/trunk/_playgroun​d_/net.bioclipse.medea.case/ (4 files in 3 dirs): Worked out last compile errors: Seneca in BC2 does not have judge factories anymore, and some more missing deps etc
21:36 egonw rojasm: OK, one down
21:36 egonw not sure if it works properly yet
21:36 egonw but at least compiles
21:36 egonw rojasm: I think Fragmenter is something you need to look at
21:37 egonw in net.bioclipse.medea
21:37 rojasm I am checking now
22:07 rojasm egonw: I have problem with the plugin cdk.bussines. Exactly with the
22:07 rojasm import ui.InChIDialog;
22:07 rojasm do you know why? some missing update
22:08 * egonw is updating
22:08 egonw that one is new I think
22:08 egonw I saw a commit today about an inchi dialog
22:09 rojasm in the class GenerateInChI
22:25 CIA-40 bioclipse: miguelrojasch * r10237 /bioclipse2/trunk/_playground_/​net.bioclipse.medea/plugin.xml: update popmenu to visualize the learning action and the prediction action
22:26 * egonw is impressed by that patch
22:34 egonw_ joined #bioclipse
22:35 * egonw_ trying to get his souund to work
22:45 egonw_ rojasm: what kind of problem is that InChIDialog giving you?
22:45 paulymer__ left #bioclipse
22:47 paulymer_ joined #bioclipse
22:49 egonw_ @pz wedge
22:49 zarah egonw_: I couldn't find anything on 'wedge' in the database.
22:49 egonw_ @pz bond
22:50 zarah [636] Selection 'blob' hides element ... http://tinyurl.com/opcsx7
22:50 zarah [597] Properly synchronize the editor... http://tinyurl.com/b8rd5s
22:50 zarah [590] Choose direction when adding an... http://tinyurl.com/dh6kcq
22:50 zarah [676] Selection behavior in JChemPaint   http://tinyurl.com/ryhwpq
22:50 zarah [265] Set the bond color in the Rende... http://tinyurl.com/rc54b5
22:50 zarah Entire list (18) at http://tinyurl.com/p23qmz
22:50 egonw_ @pz 852
22:50 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=852
22:56 paulymer_ left #bioclipse
22:59 egonw_ rojasm: going offline
22:59 egonw_ cu tomorrow!
23:01 rojasm see you tomorrow
23:01 CIA-40 bioclipse: miguelrojasch * r10238 /bioclipse2/trunk/_playground​_/net.bioclipse.medea.test/: Initial import for medea test.
23:01 rojasm what time do you go to there
23:01 rojasm will you take breakfast before?
23:02 CIA-40 bioclipse: miguelrojasch * r10239 /bioclipse2/trunk/_playgroun​d_/net.bioclipse.medea.test/ (15 files in 9 dirs): Added new classes
23:34 paulymer_ joined #bioclipse

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