Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-01-30

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All times shown according to UTC.

Time Nick Message
06:18 egonw_ joined #bioclipse
07:20 rojasm joined #bioclipse
07:50 rojas1 joined #bioclipse
08:20 olas joined #bioclipse
08:20 olas hi all
08:42 egonw_ hi olas
08:44 CIA-21 bioclipse: carl_masak * r4833 /trunk/plugins/net.bioclipse/src/net/​bioclipse/views/BioResourceView.java:
08:44 CIA-21 bioclipse: [BioResourceView.java]
08:44 CIA-21 bioclipse: * removed unused imports
08:44 CIA-21 bioclipse: * added generics and casts to remove warnings
08:44 masak joined #bioclipse
08:52 jonalv joined #bioclipse
09:02 steinbeck joined #bioclipse
09:04 Annzi joined #bioclipse
09:37 egonw__ joined #bioclipse
10:09 rojasm joined #bioclipse
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12:09 edrin joined #bioclipse
12:20 CIA-21 bioclipse: carl_masak * r4834 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (5 files in 3 dirs):
12:20 CIA-21 bioclipse: * assays not in any specific experiment now end up in their own
12:20 CIA-21 bioclipse:  pseudo-experiment "Other assays"
12:45 edrin http://xkcd.com/374/
12:45 edrin and
12:46 edrin http://xkcd.com/377/
12:54 masak edrin: serves the guy right
12:58 CIA-21 bioclipse: carl_masak * r4835 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (7 files in 2 dirs):
12:58 CIA-21 bioclipse: * Database now loads all its descendants lazily
12:58 CIA-21 bioclipse: * coming up: more fine-grained lazy loading
13:01 viklund joined #bioclipse
13:06 CIA-21 bioclipse: carl_masak * r4836 /trunk/playground/plugins/net.bioclips​e.base2/src/net/bioclipse/base2/model/ (Database.java Project.java): * Projects now load lazily
13:07 * egonw_ is longing very much for a developers-meeting-on-irc-a​bout-bioclipse2-with-demos
13:07 * egonw_ is longing very much for a developers-meeting-on-irc-about-biocli​pse2-with-demos-as-technology-preview
13:08 egonw_ e.g. I'd love to learn how I can set up a temporary database
13:12 olas jonalv: what do you think?
13:13 egonw_ and the way we can define custom projects (like the QSAR project type)
13:13 * jonalv doesn't know
13:13 egonw_ and a hands-on how to hook in script commands
13:14 jonalv What should I think about what?
13:14 * jonalv feels a bit lost here...
13:15 jonalv a temporary database?
13:15 jonalv do we support that?
13:15 egonw_ good question...
13:16 * jonalv is currently fighting to get our BioObjects recordable by making AOP proxies of them
13:16 jonalv it looks good
13:16 jonalv I am about to start writing javascript generation code for it now...
13:17 jonalv Will commit when things work a litttle bit better
13:17 jonalv I think I might currently be breaking some functionality...
13:18 CIA-21 bioclipse: Annzi * r4837 /branches/bioclipse2/chemoinformatics/ne​t.bioclipse.moss/src/net/bioclipse/moss/ (6 files in 2 dirs):
13:23 jonalv commit comming up
13:24 jonalv Bioclipse 2 developers please update and run some tests because I have changed inner magic
13:27 olas ooh
13:27 jonalv hm I seem to lack net.bioclipse.logging...
13:27 * olas is expecting miracles
13:27 jonalv I need to do some merging here then the commit will come
13:29 jonalv well there is no miracles here yet. Need some hard work first
13:34 jonalv please remember me to update once in a while... :)
13:35 egonw_ yeah, commits without updates just in front of it, should be technically impossible
13:35 olas true
13:35 jonalv well they sort of are... right?
13:37 CIA-21 bioclipse: carl_masak * r4838 /trunk/playground/plugins/net.bioclipse.base2/​src/net/bioclipse/base2/db/Base2Database.java:
13:37 CIA-21 bioclipse: [Base2Database.java]
13:37 CIA-21 bioclipse: * Better exception descriptions
13:38 CIA-21 bioclipse: jonalv * r4839 /branches/bioclipse2/ (17 files in 10 dirs): First code for making BioObjects recordable by proxies. Things may have gone broken. Please look for bugs and tell me.
13:47 CIA-21 bioclipse: jonalv * r4840 /branches/bioclipse2/ (4 files in 4 dirs): moved BioObjectList into core.domain
13:53 EskilA_ joined #bioclipse
13:55 CIA-21 bioclipse: carl_masak * r4841 /trunk/playground/plugins/net.bioclips​e.base2/src/net/bioclipse/base2/model/ (Experiment.java Project.java):
13:55 CIA-21 bioclipse: * Experiments now load lazily
13:55 CIA-21 bioclipse: * ...except if you expand "Other assays"
13:56 CIA-21 bioclipse: carl_masak * r4842 /trunk/playground/plugins/net.bioclipse.base2​/src/net/bioclipse/base2/model/Database.java:
13:56 CIA-21 bioclipse: [Database.java]
13:56 CIA-21 bioclipse: * Removed unused imports
14:05 CIA-21 bioclipse: ospjuth * r4843 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (META-INF/MANIFEST.MF plugin.xml): Removed use of namespace EP and imported net.bioclipse.logging again.
14:06 CIA-21 bioclipse: ospjuth * r4844 /branches/bioclipse2/chemoinformatics/ne​t.bioclipse.cdk.ui/META-INF/MANIFEST.MF: Imported net.bioclipse.logging again.
14:07 CIA-21 bioclipse: ospjuth * r4845 /branches/bioclipse2/chemoinformatics/n​et.bioclipse.qsar/META-INF/MANIFEST.MF: Imported net.bioclipse.logging again.
14:08 steinbeck joined #bioclipse
14:10 CIA-21 bioclipse: carl_masak * r4846 /trunk/playground/plugins/net.bioclipse.base2​/src/net/bioclipse/base2/views/TreeView.java:
14:10 CIA-21 bioclipse: [TreeView.java]
14:10 CIA-21 bioclipse: * added the mocked database alongside the real one
14:10 CIA-21 bioclipse: * still hardcoded, though
15:26 CIA-21 bioclipse: ospjuth * r4847 /branches/bioclipse2/misc/ne​t.bioclipse.data.sampledata/ (3 files in 3 dirs): Imported net.bioclipse.logging again and updated BioclipseException location.
15:37 rojasm left #bioclipse
15:48 CIA-21 bioclipse: carl_masak * r4848 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (7 files in 3 dirs): * added new level to the data model: DataFile
15:49 egonw_ masak: what does that last thingy do?
15:50 egonw_ thingy=commit
15:50 CIA-21 bioclipse: ospjuth * r4849 /branches/bioclipse2/chemoinformati​cs/net.bioclipse.cdk.ui/plugin.xml: Use a contenttype instead of hardcoding file extensions into editor.
15:50 egonw_ that is: what is a "DataFile"?
15:51 egonw_ oh... that sounds yummy too !
15:52 olas yup
15:52 olas on the way
15:52 olas will try to create a manager for CDK now that will be able to extract SMILES from a mol-file :-)
15:52 olas need that for the MOSS project
15:59 Annzi left #bioclipse
16:06 egonw_ indeed
16:06 egonw_ MOSS should really use some patch to be able to read CML...
16:06 egonw_ but it's a start anyway...
16:42 CIA-21 bioclipse: carl_masak * r4850 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
16:42 CIA-21 bioclipse: [ScriptingConsoleView.java]
16:42 CIA-21 bioclipse: * added TODO
16:42 CIA-21 bioclipse: * rebound HOME button to work as expected
17:31 Annzi joined #bioclipse
17:37 CIA-21 bioclipse: jonalv * r4851 /branches/bioclipse2/ (5 files in 3 dirs):
17:37 CIA-21 bioclipse: Removed ISequenceCollection. And made changes in sequenceContentprocider and
17:37 CIA-21 bioclipse: Sequencelabelprovider so that the objects in bioobjectlist only are retrieved
17:37 CIA-21 bioclipse: once. This is in order to get nicer recording. Perhaps we can figure out some
17:37 CIA-21 bioclipse: better way to do the recording/script generation because this restrictions feel
17:37 CIA-21 bioclipse: a bit sad...
17:37 CIA-21 bioclipse: olas: please check my changes since it was your code originally
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19:29 edrin left #bioclipse
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