Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-03-06

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All times shown according to UTC.

Time Nick Message
06:21 masak joined #bioclipse
08:00 Gpox joined #bioclipse
08:00 Gpoks joined #bioclipse
08:01 Gpox joined #bioclipse
08:09 CIA-55 bioclipse: goglepox * r9224 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java:
08:09 CIA-55 bioclipse: Added the text 'Changed' to the editor when it is dirty
08:09 CIA-55 bioclipse: bug #167
08:09 zarah bug #167 | http://tinyurl.com/bk3y89
08:18 olass joined #bioclipse
09:10 shk3 joined #bioclipse
09:30 olass @ping
09:30 zarah olass: pong
09:30 olass was so silent here
09:30 masak olass: pong.
09:30 masak no-one but us chickens in here.
09:31 olass masak: what was the name of yesterday's game?
09:31 masak olass: druid.
09:31 olass ah
09:31 * olass liked it
09:31 masak http://www.cameronius.com/games/druid/
09:31 masak olass: and you were good at it, too!
09:32 masak olass++
09:32 olass beginners luck ;)
09:32 masak no, it was some innate ability, I believe.
09:32 masak I saw you think long and hard, and with results.
09:33 masak generally, I'm surprised by people's ability to pick up Druid.
09:33 masak that doesn't happen at all with Hex.
09:39 shk3 hi masak
09:39 shk3 hi olass
09:39 masak greetings shk3.
09:39 olass hi shk3
09:39 shk3 I am going to work on the undo/redo so that the manager stuff is undoable as well
09:39 shk3 should be finished today
09:39 olass shk3++
09:40 shk3 sorry for that discussion with file formats
09:40 masak :)
09:40 * masak likes flames to a certain extent
09:40 olass your intentions were good
09:40 shk3 well, I got the impression egonw was a bit pissed off
09:41 olass I think egonw is a bit stressed currently
09:41 shk3 I think the problem is a bit that in Bioclipse (sorry for saying this)
09:41 shk3 we do not have a real unique selling positino
09:41 shk3 someting only bc can do
09:41 shk3 or bc can do way better than others
09:41 olass we will have soon
09:41 olass but you are right
09:41 shk3 if we would have this, we could say people will use it no matter what
09:41 shk3 formats etc. are supported
09:42 shk3 but as long as we only have "standard things", they need to be polished
09:42 olass agreed
09:42 olass you need to walk before you can run
09:42 olass so we shall do our best
09:43 shk3 yes
09:43 olass undo/redo is very welcome
09:43 shk3 undo/redo is important
09:43 shk3 indeed ;-)
09:43 olass IMO a requirement
09:43 shk3 yes
09:43 shk3 also the merge of atoms is a must
09:43 olass yes
09:43 shk3 might do that next week
09:43 olass would be great
09:43 shk3 right now, you can't do a ring closure without using the templates
09:44 olass just coordinate with Gpox
09:44 olass he is actively working with JCP
09:44 shk3 btw, coordinate
09:44 shk3 I found some changes where commited to cdk code in bc
09:44 shk3 which makes it easy to synchronize stuff
09:45 shk3 I would encourage everybody to stay away from that if possible
09:45 shk3 I know it's not always possible
09:45 shk3 just a polite reminder
09:45 olass I don't understand, you need discuss this with egonw
09:46 olass he should be back soon
09:47 shk3 well, we have a copy of cdk in the cdk modules in bc
09:47 shk3 if changes get commited to these and cdk codebase, it is hard to sort out.
10:20 jonalv joined #bioclipse
10:21 jonalv oh hai
10:21 zarah hi jonalv
10:22 olass shk3: I see
10:28 shk3 yeah
10:29 shk3 as I said, not that I want to complain
10:29 shk3 I know what it is like
10:29 shk3 and merging is possible
10:29 shk3 just if possible I would suggest we change in cdk repository and copy to bc
10:42 egonw joined #bioclipse
11:47 CIA-55 bioclipse: shk3 * r9225 /bioclipse2/trunk/cdk-externals/tr​unk/org.openscience.cdk.control/sr​c/org/openscience/cdk/controller/ (15 files in 2 dirs): synchronized with jcp-primary branch
11:48 CIA-55 bioclipse: shk3 * r9226 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.jchempaint/src/net/bioclipse/cdk/jchem​paint/handlers/ChangeModuleHandler.java: changes because of synchronize of controler module
11:50 egonw shk3: please update the cdk-external plugins MANIFEST versions
11:51 egonw shk3: and next time please put in the commit message which revision you synchronized with
11:52 egonw shk3: also check your patches...
11:52 egonw you removed bits here and there, but did not complete those patches
11:52 egonw or add an if, without putting everything in the if-clause
11:53 egonw stain: you're in Norway today?
11:56 stain nope.. still in Manchester
11:57 egonw stain-test [n=stain@s11.no]
12:02 olass stain: oh no, they've solved you! http://www.vanish.co.uk/stain_solver.shtml
12:02 shk3 how are the versions in cdk-external plugins supposed to look like?
12:02 egonw 1.1.5.date
12:03 stain egonw: s11.no is my server :)
12:03 stain olass: my wife has one of those.. :/
12:03 egonw stain: yes, guessed that after you said to be still in Manchester :)
12:10 CIA-55 bioclipse: shk3 * r9227 /bioclipse2/trunk/cdk-externals/trunk/org.op​enscience.cdk.control/META-INF/MANIFEST.MF: synchronized with jcp-primary branch rev 14364
12:42 CIA-55 bioclipse: goglepox * r9228 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Added support for content of a AtomContainer to be selected
12:47 CIA-55 bioclipse: shk3 * r9229 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/handlers/RemoveHandler.java: using relay instead of handler to avoid individual actions to be undoable
13:07 egonw shk3: ping... is there info online on how to set up MySQL for NMRShiftDB?
13:56 shk3 yes
13:56 egonw link welcome :)
13:56 shk3 mom
13:57 shk3 http://nmrshiftdb.svn.sourceforge.net/viewvc/nmrsh​iftdb/trunk/nmrshiftdb/doc/administratorguide.pdf
14:25 shk3 I just activated the Bioclipse undo/redo menu items/buttons for jcp editor
14:25 shk3 do we still need those in the jcp toolbar?
14:27 shk3 Gpox, jonalv: what do you think?
14:29 jonalv shk3: sorry I did not understand. Where are the undo redo buttons more?
14:29 egonw jonalv: in the JCP toolbar
14:29 shk3 sorry
14:29 egonw the JCP icons
14:29 shk3 I made the standard ones work
14:30 shk3 so the jcp icons can go?
14:30 jonalv I have no idea at all...
14:30 egonw I would say yes
14:30 * jonalv is toally confused now :)
14:30 egonw they are redundant
14:30 shk3 can't see why not
14:30 shk3 but wanted to ask
14:30 shk3 but confused jonalv
14:30 egonw Gpox: ping
14:30 shk3 the normal eclipse toolbar has
14:30 shk3 tow buttons
14:30 egonw jonalv: JCP comes with its own undo/redo buttons
14:30 shk3 with arrows on them
14:30 olass we want to use Eclipse undo/redo actions/icons/menu
14:30 egonw but RCP already has those
14:30 shk3 and edit menu
14:30 shk3 has undo/redo items
14:31 shk3 these now work
14:31 olass good
14:31 shk3 (in  my copy, not committed)
14:31 olass then please remove the JCP toolbar undo/redo buttons
14:31 Gpox I don't know where those come from or what they are doing there, pleas remove them
14:31 shk3 thanks
14:31 jonalv aha
14:32 * jonalv will testrun jchemapint some day but not just now... :)
14:33 jonalv afk
14:39 shk3 no problem
15:05 CIA-55 bioclipse: shk3 * r9230 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (15 files in 6 dirs): undo/redo is via the eclipse controls
15:07 shk3 btw, the TextEditor in bc does not have undo/redo
15:07 shk3 isn't that an Eclipse component?
15:10 olass it should have
15:10 olass are you sure?
15:12 shk3 well, for me, buttons don't get active
15:14 olass they do for me
15:14 olass if you write some, undo gets active
15:15 olass of course it's inactive if you havent edited
15:15 olass does it not work?
15:15 olass here it does....
15:21 shk3 sorry
15:21 shk3 must have overlooked that
15:21 shk3 btw, "of course it's inactive if you haven't edit"
15:21 shk3 you could think that's default behaviour,
15:21 shk3 but no
15:21 shk3 there is some trick with that
15:37 olass is it?
16:07 |egonw| joined #bioclipse
16:13 shk3 well, there must be.
16:13 shk3 But I did not yet discover it.
16:37 CIA-55 bioclipse: ospjuth * r9231 /bioclipse2/trunk/plugins/net.​bioclipse.cdk.smartsmatching/: Initial import.
16:44 shk3 ah, you decided for a plugin in its own
16:46 CIA-55 joined #bioclipse
16:51 olass shk3: yes
17:00 |egonw| olass++
17:00 olass |egonw|: you likey?
17:00 |egonw| for the SMARTS stuff
17:00 olass have you tried it?
17:01 |egonw| no, not yet...
17:01 |egonw| just finished with one of the HCLS conf calls...
17:01 olass I'm quite happy with the result
17:01 |egonw| really cool stuff...
17:01 |egonw| and I am right on top of it:)
17:01 olass interesting
17:01 |egonw| what we have been doing with metware is really cutting edge
17:02 |egonw| and bioclipse is just around the corner
17:02 olass yup, interesting times ahead
17:02 |egonw| we can really have some impact in metabolomics, semantic web stuff, really soon :)
17:02 olass looking forward to seeing some features in BC soon
17:02 olass yes, I know, we need 2.0 release first :-(
17:02 |egonw| there are still weekends :)
17:02 olass please test the SmartsMatching
17:03 |egonw| will do
17:03 olass I need your feedback
17:03 |egonw| relocating to my own room first now
17:03 |egonw| brb
17:10 egonw joined #bioclipse
17:11 egonw back
17:12 egonw olass: please use the existing chemoinformatics category for views
17:13 olass thought I did
17:13 olass I used that in chemoinfo plugin
17:13 egonw mmm
17:13 egonw I have two cheminfo groups in the Views -> Other now ...
17:13 olass pretty sure I used taht in chemoinfo plugin
17:13 olass like 100% or so
17:14 olass maybe someone elese has another category?
17:14 egonw yes, that would be the alternative :)
17:14 egonw 2D-Structure
17:14 egonw that's the view in the other folder
17:15 egonw can you please file a bug report against me to sort it out...
17:15 * egonw is opening the 800MB StarLite db in Bioclipse
17:15 egonw with interesting results...
17:16 egonw guys: brilliant work!
17:16 egonw works like a charm :)
17:16 olass nice
17:18 egonw oh... I cannot run the SMARTS against a SDF?
17:18 olass can I?
17:18 CIA-55 bioclipse: ospjuth * r9233 /bioclipse2/trunk/plugins/net.bioclipse.cdk.smar​tsmatching/src/net/bioclipse/cdk/smartsmatching/ (2 files in 2 dirs): Caught NPE on exit and enabled editing of SMARTS in Properties view. Solves #679.
17:19 olass egonw: no
17:19 egonw mmm... that sucks
17:19 olass only for single files
17:19 olass highlighting in MolTable is not 100% sorted out
17:19 olass but should not be overly difficult to sort out
17:19 olass need Gpox help for it though
17:20 olass so scheduled for next week
17:20 olass tuesday
17:20 egonw ERROR - SmartsMatchingPrefs part: CF3could not be parsed into name and smartsstring. Skipped.
17:20 egonw ERROR - SmartsMatchingPrefs part: FC(F)Fcould not be parsed into name and smartsstring. Skipped.
17:21 olass but manager methods for querying SDFiles for a SMARST would be desired until then...
17:21 egonw mmm... can't get it to work
17:21 olass doesn't work out of the box?
17:22 egonw nope
17:22 * olass will clear workspace and try from scratch
17:23 olass did you add someting?
17:23 olass works here...
17:23 egonw it does not seem able to compile the SMARTS I enter...
17:23 olass oh, so you added stuff
17:23 olass did you not just try it?
17:24 olass what did you enter?
17:24 olass did you not enter a name?
17:24 egonw see above erros
17:24 egonw I tried:
17:24 egonw CC
17:24 egonw FC(F)F
17:24 olass and name?
17:24 egonw and an amide
17:24 egonw test
17:24 egonw amide
17:24 egonw and
17:24 egonw CF3
17:25 olass what did it say about saving?
17:25 olass here it works...
17:25 egonw saving?
17:26 egonw I got a NPE when I exited Bioclipse
17:26 egonw from the SMARTS widget
17:26 olass ah, please update
17:26 olass r9233
17:26 egonw INFO - SmartsMatching default preferences initialized
17:26 egonw ERROR - SmartsMatchingPrefs part: Aromaticcould not be parsed into name and smartsstring. Skipped.
17:26 egonw ERROR - SmartsMatchingPrefs part: [a]could not be parsed into name and smartsstring. Skipped.
17:26 egonw ERROR - SmartsMatchingPrefs part: Fragment 1could not be parsed into name and smartsstring. Skipped.
17:26 egonw ERROR - SmartsMatchingPrefs part: [CH2](*(N))could not be parsed into name and smartsstring. Skipped.
17:26 egonw ERROR - SmartsMatchingPrefs part: Fragment 2could not be parsed into name and smartsstring. Skipped.
17:26 egonw ERROR - SmartsMatchingPrefs part: [N](*(*(O)))could not be parsed into name and smartsstring. Skipped.
17:26 egonw
17:26 egonw OK, hang on
17:26 olass hmm
17:27 olass very strange
17:27 olass maybe bad choice of delimiter strings for linux
17:28 egonw yes, could be
17:28 egonw brb
17:30 olass I choose delimiters § and £ as I was pretty sure they are not valid SMARTS chars...
17:32 olass egonw: please advice on other delimiters
17:33 olass how about ?
17:39 egonw wrap things in quotes?
17:39 egonw I don't know...
17:39 egonw use XML
17:39 olass no
17:39 olass too much overweight
17:39 olass ok, will play around
17:39 egonw why not use the RCP Prefs?
17:39 olass which is?
17:39 egonw I don't care... but right now it doesn't work...
17:39 olass ok
17:39 egonw pref pages
17:39 olass ?
17:40 olass please explain what you mean
17:40 olass (I have no preference page)
17:40 egonw mom
17:40 egonw you should be able to use the preferenceStore anyway, I think
17:41 egonw Activator.getDefault().getPreferenceStore()
17:41 olass that is not the problem
17:41 egonw add an Activator for your plugin
17:41 olass of course I am using that
17:41 olass it's the splitting of String that fails
17:41 olass no worries, will try some more
17:42 egonw encode them into hexadec
17:42 egonw and use a comma
17:42 egonw whatever...
17:45 CIA-55 bioclipse: ospjuth * r9234 /bioclipse2/trunk/plugins/net.bioclipse.cdk.s​martsmatching/src/net/bioclipse/cdk/smartsmat​ching/prefs/SmartsMatchingPrefsHelper.java: Added more logging for preference parsing and changed delimiters.
17:45 olass egonw: please update and try again in a clear workspace. I think I solved the problem. If not, please send me log output
17:45 egonw ok, got 5 minutes
17:46 egonw the I'm going home
17:50 egonw ok, compile helped...
17:51 egonw but does not find the right amount of matches...
17:51 egonw have to catch my bus now
17:51 egonw but, it's a nice view... now that it works
17:51 egonw please include in the cheminfo feature
17:52 egonw DEBUG - Read Smarts prefs string: CF3-SPSP-FC(F)F-SP
17:52 egonw DEBUG - Part 0 extracted: CF3-SPSP-FC(F)F-SP
17:52 egonw can't see what SMARTS it used for the matching...
17:52 egonw maybe something goes wrong there...
17:52 egonw bye for now!
18:12 CIA-55 bioclipse: ospjuth * r9235 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Added smartsmatching to cheminfo feature.
18:12 CIA-55 bioclipse: ospjuth * r9236 /bioclipse2/trunk/plugins/net.bioclipse.cdk.s​martsmatching/src/net/bioclipse/cdk/smartsmat​ching/prefs/SmartsMatchingPrefsHelper.java: Updated delimiter. More stable now.
18:48 egonw joined #bioclipse
18:48 egonw moin
18:48 zarah hello egonw, you fantastic person you
22:42 olass joined #bioclipse

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