Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-12-16

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

All times shown according to UTC.

Time Nick Message
05:12 mgerlich joined #bioclipse
05:12 ilogger2 joined #bioclipse
05:41 mgerlich joined #bioclipse
05:41 ilogger2 joined #bioclipse
05:56 mgerlich joined #bioclipse
05:56 ilogger2 joined #bioclipse
06:03 mgerlich joined #bioclipse
06:03 ilogger2 joined #bioclipse
06:07 sneumann_ joined #bioclipse
06:42 egonw joined #bioclipse
08:00 egonw moin
08:00 zarah ni hao egonw
08:04 sneumann_ joined #bioclipse
08:17 sneumann joined #bioclipse
08:57 masak joined #bioclipse
09:09 jonalv joined #bioclipse
09:43 jonalv How do I specify Eclipse standard icons from plguin.xml?
09:43 * egonw has no clue
09:45 * jonalv saves a copy of the icon in the plugin... It's just an icon...
11:26 egonw quiet here today
11:42 jonalv egonw: yea people are on lunch now
11:42 * jonalv is heading too, (they had boxes ):
11:55 ChanServ joined #bioclipse
12:02 CIA-81 bioclipse.structuredb: jonalv master * r6ee6cd5 / plugins/net.bioclipse.structuredb/src/net/biocli​pse/structuredb/business/StructuredbManager.java : added monitor to get a job - http://bit.ly/7YSs0A
12:02 CIA-81 bioclipse.structuredb: jonalv master * r577124f / (8 files in 3 dirs): New icons for StructureDB part of databases view - http://bit.ly/928qXw
12:16 olass joined #bioclipse
12:18 * egonw is booting Bioclipse with a latex manager
12:19 * olass wonders why
12:19 egonw converting connection tables into book source code
12:20 * egonw is a lazy bastard and prefers hacking over mindless adding '&' all over the place
12:20 egonw +ly
12:22 * egonw realizes net.bioclipse.statistics does not have a method to actually create a matrix object :(
12:23 egonw olass: is there a 2.2.x branch for bioclipse.statistics
12:23 egonw ?
12:23 olass mom
12:23 egonw does not seem so
12:23 olass let me check
12:23 egonw just want confirmation
12:24 olass you mena there is a 2.2.x
12:24 olass yes
12:24 egonw there is?
12:24 olass there is a 2.2.x
12:24 olass exists
12:24 egonw as a branch?
12:24 olass yes
12:24 egonw good
12:24 egonw I don't have it yet
12:24 olass let me check github
12:24 egonw and GitHub is down
12:24 egonw file server trouble
12:25 olass http://github.com/olas/bioc​lipse.statistics/tree/2.2.x
12:25 zarah olass's link is also http://tinyurl.com/yjkzvaf
12:25 olass works fine
12:25 egonw oh...
12:25 egonw perhaps not all users are on the same file server
12:25 egonw which would make sense, actually
12:27 * egonw is bootstrapping a matrix manager using the Bioclipse SDK
12:27 egonw (Bioclipse SDK)++
12:33 samuell joined #bioclipse
12:35 egonw olass: can I send you two patches?
12:35 olass sure
12:35 egonw it seems I was not entirely in sync with bioclipse.statistics
12:59 CIA-81 bioclipse.statistics: Egon Willighagen 2.2.x * r6583943 / (5 files): Added a Statistics Feature - http://bit.ly/82l4gR
12:59 CIA-81 bioclipse.statistics: Egon Willighagen 2.2.x * re383d41 / features/net.bioclipse.stat​istics_feature/feature.xml : Bumped version to 2.2.0.RC2 - http://bit.ly/6uLTgW
12:59 olass egonw: applied
13:00 egonw tack
13:20 egonw lovely when people bend a concept just outside the scope ... :(
13:33 egonw m = matrix.create("1 2 3 4 5", 2)
13:36 egonw grmph... need to reinstall Mylyn
13:49 sneumann joined #bioclipse
14:18 egonw @pz Statistics
14:18 zarah [1789] Statistics editor/feature is n... http://tinyurl.com/yh82k3v
14:18 zarah Entire list at http://tinyurl.com/ybt7w5t
14:21 egonw olass: emailed 5 more patches
14:31 egonw jonalv: ping
14:31 jonalv egonw: pong
14:31 egonw looking at the statistics stuff...
14:31 egonw which is seriously not Bioclipse2 material :(
14:31 egonw got a question about domain object wrt the JS console...
14:32 * jonalv isn't exactly suprised
14:32 egonw :
14:32 egonw I have a NWO manager method return a IMatrixFoo object
14:32 * jonalv prepares for the worst
14:32 egonw but IMatrixImplementationResource does not extend IBioclipseObject
14:32 jonalv egonw: IMatrixFoo?
14:32 egonw that is causing this error, correct? :
14:33 egonw Can't find method $Proxy38.writeMatrix(string,ne​t.bioclipse.model.JamaMatrix)
14:33 egonw jonalv: IMatrixImplementationResource
14:33 jonalv egonw: I am not sure
14:33 egonw jonalv: that is.. the proxy expects a domain object to be IBioclipseObject to properly be passed around between managers, correct?
14:34 jonalv egonw: I am not 100% sure. That might be the case but I am leaning towards no
14:34 egonw I'll try...
14:34 egonw tack
14:35 jonalv egonw: I am afraid there is something else that is wrong
14:35 egonw what makes you think that?
14:36 egonw (might serve as clue to a fix...)
14:36 jonalv I think it should be bale to handle classes not extending IBIoObject it handles Strings...
14:36 egonw bale?
14:36 jonalv |able
14:36 egonw yes, but then as String...
14:36 egonw so, having the exact type
14:36 jonalv Strings are Objects
14:37 egonw but the other manager does not eat JamaMatrix
14:37 egonw but IMatrixImplementationResource
14:37 jonalv Maybe I don't have the complete picture here
14:37 egonw no worries...
14:38 egonw I have enough clues
14:38 jonalv oki
14:38 egonw tack!
14:51 egonw bioclipse.statistics is a mess :(
14:51 jonalv egonw: where are we usign it?
14:52 egonw qsar at least
14:52 egonw wanted to use it to visualize SPARQL query results too...
14:52 egonw and for connection tables right now :(
14:52 * jonalv is thinking maybe masak should clean up i nthat mess when doin BioclipseP
14:52 masak gladly.
14:54 egonw it statistics IBioObject is also a IResource
14:54 egonw s/it/the/
14:54 egonw lovely
15:08 CIA-81 bioclipse.structuredb: jonalv master * r2faf22e / (2 files in 2 dirs):
15:08 CIA-81 bioclipse.structuredb: Dialog with apply to all when deleting labels
15:08 CIA-81 bioclipse.structuredb: Fixes bug: #1650 - http://bit.ly/8jJDbb
15:08 zarah bug #1650 | http://tinyurl.com/yc6xsq9
15:09 mgerlich joined #bioclipse
15:09 ilogger2 joined #bioclipse
15:17 egonw cool.... got it working now:
15:18 egonw latex.write(matrix.create("1 2 3 4", 2), "/Virtual/matrix.tex")
15:25 sneumann lovely. R has that in the hmisc package ;-)
15:25 egonw yes, crucial bit of functionality in every tool
15:26 egonw will not be part of 2.2 though
15:46 mgerlich joined #bioclipse
15:46 ilogger2 joined #bioclipse
15:54 egonw joined #bioclipse
15:55 masak joined #bioclipse
16:00 masak joined #bioclipse
16:18 mgerlich joined #bioclipse
16:18 ilogger2 joined #bioclipse
16:18 mgerlich joined #bioclipse
16:18 ilogger2 joined #bioclipse
16:29 egonw @pz sdk
16:29 zarah [947] Bioclipse SDK                      http://tinyurl.com/y8f8gao
16:29 zarah [1562] Set up http://sdk.update.biocl... http://tinyurl.com/ycoox2j
16:29 zarah [1737] The pluginstests wizard genrea... http://tinyurl.com/yfoovjw
16:29 zarah [1574] QSAR tests should be in the NW... http://tinyurl.com/y9onyz6
16:29 zarah [1491] New Bioclipse Data Pluging Wizard http://tinyurl.com/y97xfvj
16:29 zarah Entire list at http://tinyurl.com/ykpwewm
17:27 CIA-81 bioclipse.statistics: Egon Willighagen 1-matrixManager * rd9c856d / plugins/net.bioclipse.statistics.bus​iness/src/net/bioclipse/statistics/b​usiness/business/MatrixManager.java : Fixed indices: MatrixResource starts at 1, double[][] at 0 - http://bit.ly/67P28D
19:23 CIA-81 bioclipse.statistics: Egon Willighagen 1-matrixManager * r88dff69 / (2 files): Added methods to set column and row labels - http://bit.ly/7TY5yt
22:29 egonw joined #bioclipse
23:41 egonw joined #bioclipse

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