Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-08-07

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All times shown according to UTC.

Time Nick Message
00:25 nielsout joined #bioclipse
00:28 nielsout changed the nick to nout
00:28 Nielsout joined #bioclipse
00:30 nout argh nickserv is confusing :)
06:14 masak joined #bioclipse
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07:59 EskilA Hello
08:07 masak good morning
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09:03 jonalv egonw: ping
09:04 egonw pong
09:04 jonalv egonw, I am wondering about your suggestion to keep the MatrixModel class as it is now and use the Nebula projects Grid plugin
09:05 jonalv The Matrixmodel as it looks now is a KTable thing
09:05 egonw ok
09:06 jonalv Are there some sort of compatibility issues here?
09:06 egonw ack... my mistake...
09:06 egonw replace matrixmodel with MatrixResource
09:06 jonalv I checked the dexcriptor plugin for code that uses the MatrixModel but didn't find any
09:08 jonalv But the Matrixmodel really shouln't need to be used outside the matrixeditor or should it?
09:08 egonw correct
09:09 egonw the MatrixResource is the code I wanted to mention...
09:09 egonw if you can make a Nebula-grid based editor that uses MatrixResource as sole data model, than I'm happy...
09:09 egonw the MatrixModel is just the translation layer to convert KTable calls to MatrixResource calls...
09:10 jonalv Yep that makes sence. I am afraid that there will be a similar layer for the Grid widget but I think it will be a little bit more light weight
09:10 egonw that's fine...
09:11 egonw as long as you do not have to make a copy of the data
09:11 jonalv Hm that's true. I will have to check that out
09:27 jonalv egonw, hm seems to me as the grid widget uses rowObjects which needs to get their values set as strings. Do you mean that this is to much heavy copying of string references? I wonder...
09:28 egonw yeah, we need to subclass those rowObjects to interface with MatrixResource
09:29 jonalv but why? It seems to me as that would be a bit daring...
09:29 jonalv They depend on an arraylist of texts in the griditem
09:30 jonalv Not using that seems a bit to much as meddling with things that should not be meddled with to me...
09:30 egonw that sucks...
09:30 egonw you really do not want to copy the data...
09:31 jonalv but you have to make them inteo Strings sometime
09:31 egonw sure
09:31 egonw but on the fly please...
09:31 jonalv might aswell do it when creating the rows as when presenting them
09:31 egonw you can't store a 10GB table in memory
09:31 jonalv (becasue the values are doubles I hope?)
09:31 egonw or even just a 500MB matrix
09:32 egonw not if you have to copy/paste that just for the editor
09:32 jonalv hm no there need to be some sort of lazy initialisation of the rows...
09:32 jonalv wonder if that can be done...
09:33 jonalv but wait a minute here a 10 GB table in a table editor?
09:33 jonalv just scrolling that is crazy at some level...
09:34 egonw 10GB is a bit of an exaturation...
09:34 egonw think of a table of 500MB...
09:34 egonw that's not that much for a QSAR table...
09:34 egonw < 5000 molecules...
09:35 jonalv it still feels strange to show all of it at the same time in spreadsheet
09:35 jonalv can't they be sorted up inte minor sets somehow
09:35 jonalv I mean just browsing such a table and find what you are looking for by scrolling is gonna be a pain
09:36 egonw yeah, but it is something you want to do now and then...
09:36 egonw especially in QSAR studies
09:37 jonalv hm in that case this might be a  bit troublesome
09:37 jonalv Have you tested that KTable only loads the cells shown on screan?
09:37 egonw no
09:38 jonalv hm
09:38 egonw did not have a larger matrix yet...
09:40 jonalv Okey, shouldn't be to hard to fake one just to try...
09:41 jonalv It still feels strange to browse it all at the same time...
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10:20 jonalv egonw, I am not sure it's such a good idea to load one cell at the time from a database either
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10:31 edrin hi
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12:12 jonalv Can anyone explain this .jam format that the matrix editor uses?
12:17 egonw yes
12:17 egonw it's a crappy simple format I made up
12:17 jonalv that's great :)
12:17 egonw (acutally, it's supported by jama)
12:18 egonw did not really make it up...
12:18 jonalv okey
12:18 egonw anyway, it's not important
12:18 egonw .csv is better
12:18 jonalv okey I just wanted to test the editor and see some values on my screan so I would like to know how such a file need to look
12:37 shk3 hi masak
12:37 masak shk3: hello!
12:37 masak have you safely arrived at your new place?
12:38 shk3 yes, thanks
12:39 shk3 the 2dviewer looks good now
12:39 shk3 thought the pack() would be necessary, but it seems to make things worse
12:39 masak thx. haven't really done much with it the last week
12:39 masak I'm still mulling over how to fix the properties
12:40 masak there are some things I still haven't grokked about the possibleKeys variable
12:41 shk3 well, my idea was that different files might have different properties (in e. g. cml, you can have arbitrary properties).
12:41 masak yes
12:41 shk3 so we need to look first through all the files which properies exist.
12:41 masak sounds reasonable
12:41 masak since we do it 2-pass anyway
12:43 masak I seem to recall that there was another improvement to 2dviewer that we talked about, but I cannot remember what it was
12:43 shk3 hm, I intended sorting
12:44 masak ah! yes
12:44 masak that was probably it
12:44 shk3 you need a mvc table for it, if I remember correctly
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12:44 shk3 but shouldn't be too hard
12:45 olas left #bioclipse
12:45 masak an MVC would likely fix some other problems as well
12:45 olas joined #bioclipse
12:45 olas morning
12:45 masak olas: y0
12:45 masak shk3: like the last updating bugs
12:45 olas whazzup!
12:45 masak :)
12:46 CIA-32 bioclipse: ospjuth * r3639 /trunk/playground/plugins/net.bioclip​se.biomoby/src/net/bioclipse/biomoby/​views/MobyViewContentProvider.java: Put content provider in separate class
12:46 CIA-32 bioclipse: ospjuth * r3640 /trunk/playground/plugins/net.biocli​pse.biomoby/src/net/bioclipse/biomob​y/views/MobyViewLabelProvider.java: Put label provider in separate class
12:46 masak olas: looking into how to programmatically extract experiment data from BASE2
12:47 olas cool
12:47 CIA-32 bioclipse: ospjuth * r3641 /trunk/playground/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/biom​oby/model/IMobyViewListener.java: Added interface to listen for updates to model
12:47 olas any progress?
12:47 masak olas: well,
12:47 CIA-32 bioclipse: ospjuth * r3642 /trunk/playground/plugins/net.bioclipse.biomoby/sr​c/net/bioclipse/biomoby/model/MobyViewEvent.java: Added dummy event
12:47 masak since this morning I decided that maybe I didn't really need a full-fledged BASE2 plugin
12:48 masak and after lunch realized that I probably need to anyway
12:48 olas why so?
12:48 olas explain
12:48 CIA-32 bioclipse: ospjuth * r3643 /trunk/playground/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/biom​oby/model/MobyViewServiceType.java: Added a ServiceType to serve as categorization of services
12:48 masak olas: it's supposedly the way BASE2 interacts with other apps
12:49 CIA-32 bioclipse: ospjuth * r3644 /trunk/playground/plugins/net.bioclipse.​biomoby/src/net/bioclipse/biomoby/model/ (MobyViewContainer.java MobyViewObject.java): Updated root objects for new event handling
12:49 olas I see
12:49 olas Have you asked on base2 mailing list?
12:50 CIA-32 bioclipse: ospjuth * r3645 /trunk/playground/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/biom​oby/model/MobyPropertySource.java: Added propertySource:name and id properties
12:50 CIA-32 bioclipse: ospjuth * r3646 /trunk/playground/plugins/net.bioclipse.biomoby/s​rc/net/bioclipse/biomoby/BioclipseMobyModel.java: Updated to use cached impl of BioMoby central completely
12:51 CIA-32 bioclipse: ospjuth * r3647 /trunk/playground/plugins/net.bioc​lipse.biomoby/src/net/bioclipse/bi​omoby/model/MobyViewCentral.java: Use new moby model
12:51 CIA-32 bioclipse: ospjuth * r3648 /trunk/playground/plugins/net.bioclipse.biomoby​/src/net/bioclipse/biomoby/views/MobyView.java: Updated MobyView to use new model with listeners
12:51 masak olas: not really, I'm going to look now with a view of asking an well-posed question
12:52 CIA-32 bioclipse: ospjuth * r3649 /trunk/playground/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/biom​oby/model/MobyViewAuthority.java: Updated due to API change in super()
12:52 olas masak: sounds good
12:52 masak olas: been saving up on commits?
12:53 masak what's moby?
12:55 jonalv olas, hi are you in Uppsala anyday this week?
12:58 olas jonalv: wed and thurs
12:58 jonalv maybee I can get an hour on any of those days?
12:59 olas sure
13:07 olas for biomoby in BC: http://wiki.bioclipse.net/in​dex.php?title=BioMoby_plugin
13:07 olas gotta run now
13:07 lambdabot2 Title: BioMoby plugin - BioclipseWiki
13:07 olas ciao
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19:16 CIA-32 bioclipse: edrin_t * r3650 /trunk/plugins/net.bioclipse.webservices/src​/net/bioclipse/plugins/bc_webservices/wizard​s/wizardpages/OpenResourceWizardPage.java: removed not used variables

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