Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-01-16

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

All times shown according to UTC.

Time Nick Message
05:29 masak joined #bioclipse
07:07 CIA-20 bioclipse: carl_masak * r4677 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
07:07 CIA-20 bioclipse: [ScriptingConsoleView.java]
07:07 CIA-20 bioclipse: * removed old TODOs
07:07 CIA-20 bioclipse: * comments and javadoc
07:07 CIA-20 bioclipse: * the comma (',') is not a binary operator
07:07 CIA-20 bioclipse: * used "" instead of null as parameter to getAllVariablesIn
07:08 CIA-20 bioclipse: carl_masak * r4678 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java:
07:08 CIA-20 bioclipse: [JsConsoleView.java]
07:08 CIA-20 bioclipse: * tab completion no longer dies if variable before dot does not exist
07:28 CIA-20 bioclipse: carl_masak * r4679 /branches/bioclipse2/core/plugins/n​et.bioclipse.scripting/src/net/bioc​lipse/scripting/JsEnvironment.java:
07:28 CIA-20 bioclipse: [JsEnvironment.java]
07:28 CIA-20 bioclipse: * javadoc
07:28 CIA-20 bioclipse: * method eval now catches and stringifies EcmaEcxeptions
07:29 CIA-20 bioclipse: carl_masak * r4680 /branches/bioclipse2/core/plugins/net.bioclipse.ui​/src/net/bioclipse/ui/views/RubyConsoleView.java:
07:29 CIA-20 bioclipse: [RubyConsoleView.java]
07:29 CIA-20 bioclipse: * non-implemented completion of things after dots
07:31 CIA-20 bioclipse: carl_masak * r4681 /branches/bioclipse2/core/plugins/net.bioclipse.c​ore/src/net/bioclipse/core/domain/BioObject.java:
07:31 CIA-20 bioclipse: [BioObject.java]
07:31 CIA-20 bioclipse: * javadoc
07:32 egonw joined #bioclipse
07:39 egonw joined #bioclipse
08:23 Annzi joined #bioclipse
09:11 jonalv joined #bioclipse
09:12 egonw_ joined #bioclipse
09:51 olas joined #bioclipse
09:51 egonw hi olas
09:52 olas hi egonw
10:12 Annzi left #bioclipse
11:17 masak & # lunch
11:17 Annzi joined #bioclipse
11:50 edrin joined #bioclipse
11:52 edrin hi
12:22 olas hi edrin
12:24 edrin hello olas
12:44 jonalv edrin, not operator today?
12:46 edrin no, you know, posing... not worth now...
12:46 edrin ;)
12:48 CIA-20 joined #bioclipse
13:30 steinbeck joined #bioclipse
13:30 egonw hi steinbeck
13:33 steinbeck Hi egonw
13:36 edrin hi egonw, hi steinbeck
13:37 edrin steinbeck: how is it in Cambridge
13:37 edrin ?
13:46 steinbeck edrin: very nice, but I cannot quite enjoy it at the moment because I'm burried in work created by my start here :-)
14:41 CIA-20 bioclipse: jonalv * r4682 /branches/bioclipse2/core/plugins/net.bioc​lipse.core/src/net/bioclipse/core/domain/ (IAASequence.java IDNASequence.java IRNASequence.java): Added IAASequence, IDNASequence and IRNASequence (I as in interface)
14:42 CIA-20 bioclipse: jonalv * r4683 /branches/bioclipse2/bioinformatics/plugins/ (12 files in 5 dirs): Created Sequence classes and some tests of them
14:48 CIA-20 bioclipse: jonalv * r4684 /branches/bioclipse2/bioinformatic​s/plugins/net.bioclipse.biojava.bu​siness.tests/tests/net/bioclipse/ (5 files in 3 dirs): renamed package
14:52 CIA-20 bioclipse: carl_masak * r4685 /branches/bioclipse2/bioinformatics/plugins​/net.bioclipse.biojava.business/src/net/bio​clipse/biojava/domain/BiojavaSequence.java:
14:52 CIA-20 bioclipse: [BioJavaSequence.java]
14:52 CIA-20 bioclipse: * removed failing @Override
14:53 CIA-20 bioclipse: carl_masak * r4686 /branches/bioclipse2/bioinformatics/plugins/​net.bioclipse.biojava.business/src/net/biocl​ipse/biojava/business/BiojavaManager.java:
14:53 CIA-20 bioclipse: [BioJavaManager.java]
14:53 CIA-20 bioclipse: * removed failing @Override
15:02 CIA-20 bioclipse: jonalv * r4687 /branches/bioclipse2/bioinformatics/plugins/ (6 files in 3 dirs): convertion to fasta test
15:11 jonalv egonw, ping
15:12 egonw pong
15:12 jonalv about the domain object extemsion point
15:13 jonalv I feel that maybe we could dicuss it a bit without the mail lagg
15:13 egonw possibly... but now I'm afraid
15:13 jonalv hehe
15:13 egonw +not
15:14 jonalv yea figures but it was still funny... :)
15:14 jonalv so whenever you have time then...
15:19 egonw ok, what the hell...
15:20 egonw can't talk straight anymore anyway...
15:20 egonw so, better spend that good time on something as BC2 :)
15:20 egonw what's up?
15:21 jonalv can't talk staight?
15:21 egonw yeah, you get the point :)
15:21 egonw I see you have the same problem
15:22 jonalv I am trying to figure out when I would need to give a domain object via an extesnion point and how it should work
15:22 jonalv :)
15:22 egonw easiest would be too always use the EP
15:23 egonw how is a domain object loaded at this moment?
15:23 jonalv loaded?
15:23 egonw as in classloaded
15:23 jonalv they are created by methods on the managers
15:23 jonalv the managers that uses the object depends on the plugin that contains the class
15:23 egonw ok, how do you load the manager for a particular domain object
15:24 jonalv ok say that you need a biojavaManager in the biojava.ui plugin
15:25 jonalv You then ask the BundleContext for it
15:25 jonalv Preferably in the Activatr
15:25 jonalv So you implement a method in the biojava.ui.Activator that gives you the manager
15:25 egonw and how would you know about the existence of biojavaManager?
15:26 jonalv much as with the logging in bc1
15:26 egonw how would a plugin know about my gcmsManager ?
15:26 jonalv You would depend on the net.bioclipse.biojava plugin
15:26 egonw btw... biojavaManager... should that not be sequenceManager?
15:27 egonw OK...
15:27 egonw assume you know how to handle ISequence
15:27 egonw of which you know the API via the manager
15:27 jonalv We where on that track a while but I think it was to complcated to make a general sequencemanager
15:27 jonalv all frameworks are so different so the managers will be nam,ed after them
15:27 egonw you would not know anything about biojava
15:27 egonw ah...
15:28 egonw but then the idea of domain object is not working is it?
15:28 egonw a domain object like IMolecule would be implementation independent...
15:28 jonalv The idea of domain objects are more like an idea of domain interfaces
15:28 egonw but with 'domain' you really mean 'implementation' ...
15:28 jonalv all domainobjects implements a few standard iterfaces that are defined in core
15:29 jonalv And I think I am starting to see your point a little (but just a little)
15:29 jonalv Well domain objects are the implemented objects yes
15:30 jonalv No, I lost your point again...
15:46 egonw :)
15:46 egonw sorry... had some success with the metabolomics data analysis...
15:46 egonw that is.. I'm starting to understand the XCMS packge for R :)
15:47 egonw had to discuss that with my collegue next door
15:49 jonalv np
15:50 jonalv I am keeping busy coding more along our path that you are not so sure about...
15:50 jonalv :)
15:53 egonw ok
15:53 egonw ummm...
15:53 jonalv yea? :)
15:53 egonw thinking...
15:54 egonw which is difficult at the end of a day
15:54 jonalv yes I know
15:54 jonalv ...:)
15:55 egonw ok, let's talk about tomorrow or friday again...
15:55 egonw need to process your comments
15:55 jonalv oki
16:08 CIA-20 bioclipse: jonalv * r4688 /branches/bioclipse2/core/plugins/net.bioclipse.r​ecording/src/net/bioclipse/recording/Record.java: Bettered the toString method that generates the texts in the history view
16:20 jonalv The webbrowser in bioclipse 2 works great anyways... :)
16:37 egonw oh, cool
16:37 egonw and do views have access to the HTML source?
16:37 jonalv I have no idea
16:37 jonalv I just saw it was there and tried some surfing with it
16:37 * egonw feels a quick microformats/RDFa hack coming up...
16:38 jonalv yes that's something olas has been talking about too... :)'
16:40 egonw oh, boy... BC2 is going to be so cool!
16:41 jonalv I know :)
16:41 egonw Sun buys MySQL for 1 billion dollar !
16:41 jonalv yes that's interesting...
16:42 jonalv I wonder what effects it will have
16:53 CIA-20 bioclipse: jonalv * r4689 /branches/bioclipse2/core/plugins/​net.bioclipse.ui/src/net/bioclipse​/ui/views/ActionHistoryView.java: Added contextmenu and empty action for history view
17:31 Annzi left #bioclipse
19:24 edrin left #bioclipse
21:01 edrin joined #bioclipse
21:06 edrin egonw?
22:05 CIA-20 bioclipse: edrin_t * r4690 /trunk/xws-client/src/net/bioclipse/xws/client/ (XmppItem.java adhoc/Function.java adhoc/Service.java):
23:09 edrin joined #bioclipse

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