Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-07-15

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All times shown according to UTC.

Time Nick Message
05:42 olass joined #bioclipse
06:29 egonw joined #bioclipse
06:32 Gpox joined #bioclipse
07:01 CIA-71 bioclipse.core: Arvid Berg master * rb714b81 / plugins/net.bioclipse.browser/META-INF/MANIFEST.MF : Removed version from log4j in Import-Package - http://bit.ly/dpeqfh
09:12 s_wolf joined #bioclipse
09:18 zarah joined #bioclipse
09:42 abereles joined #bioclipse
09:43 abereles greetings
09:43 abereles i just tried out the sdk and added a stubbed manager
09:43 abereles it shows up in help
09:44 abereles i would like to try "hello world" but am not sure how...
09:47 egonw hi abereles
09:47 egonw abereles: did you try to boot Bioclipse via bioclipse.product with your manager?
09:47 egonw is it available from the JavaScript console?
09:49 abereles it shows up in help, what is another way to show that it is there?
09:49 egonw what is the 'alias' for the manager?
09:49 egonw umm... what's the name for that again...
09:49 abereles clustering
09:49 egonw ok, try on the console:
09:49 egonw clust
09:49 egonw and then type TAB
09:50 egonw does it autocomplete?
09:50 abereles yes
09:50 egonw great
09:50 egonw ok, that's one big hurdle out of the way :)
09:50 abereles yeah, the sdk worked well
09:51 egonw happy to hear that...
09:51 egonw please do feel free to put feature requests on bugs.bioclipse.net
09:51 egonw ok.. next
09:51 egonw one sec
09:51 egonw OK, check: http://wiki.bioclipse.net/index.p​hp?title=How_to_make_a_manager_2
09:51 zarah egonw's link is also http://tinyurl.com/ouun2r
09:51 egonw most info is there...
09:51 egonw the summary is:
09:51 abereles i have been reading that
09:52 egonw 1. design the API in the IClusteringManager
09:52 egonw 2. implement that in ClusteringManager
09:52 egonw (assuming those are the names of the interface and class)
09:52 abereles right
09:52 egonw mom, let me look up a simple example...
09:53 egonw http://github.com/egonw/bioclipse.social/blob/​master/plugins/net.bioclipse.twitter/src/net/b​ioclipse/twitter/business/ITwitterManager.java
09:53 zarah egonw's link is also http://tinyurl.com/2ur4v3y
09:53 egonw that's the interface
09:53 egonw and
09:53 egonw http://github.com/egonw/bioclipse.social/blob/​master/plugins/net.bioclipse.twitter/src/net/b​ioclipse/twitter/business/TwitterManager.java
09:53 zarah egonw's link is also http://tinyurl.com/33mzmxu
09:53 egonw is the implementation
09:54 egonw that's probably the most basic example
09:54 egonw setStatus() takes a String and sends it of to Twitter
09:54 egonw the @PublishedMethod
09:54 egonw ensures the method is available on the JS console
09:54 egonw and the methodSummary is for the help system
09:54 abereles given that something shows up in help
09:54 abereles how is it invoked?
09:55 egonw man twitter.setStatus
09:55 egonw how the method is invoked?
09:55 egonw twitter.setStatus("Greetings from Bioclipse!")
09:56 abereles so you can invoke a method from the js console
09:56 egonw indeed
09:56 abereles so if i add a hello world method to clustering, i can invoke it thusly
09:56 egonw yes
09:56 abereles is it reasonable to simply try that now?
09:57 egonw yes, good idea
09:57 egonw gives you a feeling for things
09:57 abereles ok, i will do so; thanks for help, will let u know
09:57 egonw yes, please do
09:57 egonw the wiki demoes more complex situations
09:57 egonw e.g. how to deal with long running methods
09:58 egonw which require a separate thread, etc
09:58 abereles very happy with bioclipse so far, altho as i said to ola, a non-trivial bit of code
09:58 egonw true
09:58 abereles i been reading about threads and osgi and spring
09:58 abereles all good stuff
09:58 egonw hopefully, setting up a development environment will get much easier soon, with that Buckminster thing :)
09:59 abereles yes, but the attempts to get it running got me somewhat familiar with the application
09:59 egonw :)
10:00 egonw good, you're a positively minded person :)
10:00 abereles i love code
10:01 abereles and i am sure the sort of stuff bioclipse is built with will be applicable elsewhere; i know spring sort of but not to the extent it is being used in your app
10:04 egonw neither do I :)
10:05 abereles i think that many of the explanations of spring found on the web are unclear; lars vogel did a good introductory job
14:11 CIA-71 bioclipse.core: Ola Spjuth master * re2514d3 / plugins/net.bioclipse.core/src/net​/bioclipse/core/util/FileUtil.java : Added a convenience method to translate plugin-relative paths to absolute paths. - http://bit.ly/bVpGPQ
16:47 egonw joined #bioclipse
17:38 egonw @pz atom type
17:38 zarah [1990] ConcurrentModification error w... http://tinyurl.com/3x3ke9h
17:38 zarah [1993] Jchempaint editor empty after ... http://tinyurl.com/2weuuv9
17:38 zarah [1428] Wrong formula given               http://tinyurl.com/yd24akx
17:38 zarah [1934] QSAR-XMPP fails when molecules... http://tinyurl.com/2e68p7a
17:38 zarah [836] Generate3D on ATP.mol in sample... http://tinyurl.com/32qhtsb
17:38 zarah Entire list (12) at http://tinyurl.com/3aauttj
19:30 craxydude joined #bioclipse
20:47 * olass will go offline now and will be back on monday morning
21:20 egonw joined #bioclipse

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