Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-05

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

All times shown according to UTC.

Time Nick Message
05:24 CIA-40 bioclipse: egonw * r10061 /bioclipse2/trunk/plugins/net.bioclips​e.chemoinformatics.test/src/testFiles/ (. aromatic.mol): Added missing testFiles folder to SVN
05:25 CIA-40 bioclipse: egonw * r10062 /bioclipse2/trunk/plugins/ (4 files in 2 dirs): Added cdk.get/setProperty for ICDKMolecule (fixes #1004)
05:25 zarah bug #1004 | http://tinyurl.com/clmrm7
05:38 egonw joined #bioclipse
06:20 masak joined #bioclipse
06:32 Gpox joined #bioclipse
06:38 Gpoks joined #bioclipse
06:56 edrin joined #bioclipse
07:00 egonw joined #bioclipse
07:15 edrin hi egon
07:17 olass joined #bioclipse
07:17 egonw hi edrin
07:17 edrin hi olass
07:18 masak hi edrin
07:19 olass hi
07:19 zarah privet olass
07:22 olass edrin: what is jst and why jst as a manager?
07:29 edrin hi olass
07:29 edrin olass: come to xws?
07:45 edrin http://pele.farmbio.uu.se/xmpp-service​s/index.php/XMPP_services_in_Bioclipse
07:45 zarah edrin's link is also http://tinyurl.com/c5c7du
08:09 shk3 joined #bioclipse
08:24 edrin joined #bioclipse
08:25 edrin hi
08:25 zarah oh hai edrin
08:28 egonw hi shk3, edrin
08:30 shk3 hi egonw
08:36 jonalv joined #bioclipse
08:56 jonalv @ping
08:56 zarah jonalv: pong
09:00 jonalv zarah: tell egonw http://wiki.bioclipse.net/index.ph​p?title=How_to_make_a_manager#The_.40PublishedClass_and_.40P​ublishedMethod_annotations
09:00 zarah jonalv's link is also http://tinyurl.com/dypvah
09:00 zarah Consider it noted.
09:05 jonalv CAn someone direct me to a plugin test that is using the BiocipseJob? :)
09:12 egonw @tell jonalv that that wiki does not specify what the content of the "params" field should look like, and that that is what I am after
09:12 zarah Consider it noted.
09:12 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
09:14 jonalv egonw: "The two paramaters are used for documenting the manager methods and they should be used in a very special ways for our manager documentation to be consistent. The params shall be just a copy of the paramaters of the method as they are written in Java, and all the explanations about those paramaters shall be found in the methodSummary paramater of the annotation. Here follows an example just to make things clear:"
09:14 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
09:15 jonalv zarah: just tell me...
09:15 zarah jonalv: 2 m 21 s ago, egonw said that that wiki does not specify what the content of the "params" field should look like, and that that is what I am after
09:15 egonw I think I understand what it is meant to so...
09:15 egonw but please define copy...
09:16 egonw please just describe the format
09:16 egonw the params="" is also in Java
09:16 egonw with the proper context is makes sense
09:17 egonw but I am just guessing
09:17 egonw whay you mean is:
09:18 edrin where is ola?
09:18 egonw "a comma separated list of the type (without package name) and name of each parameter, separated by a space, e.g. 'IMolecule molecule' or 'ICDKMolecule mol, boolean isSexy'"
09:18 egonw jonalv: right?
09:19 jonalv egonw: yea I guess so
09:19 jonalv egonw: please update the wiki if you know a better way to write it
09:20 egonw OK, I will add that description then, and write a unit test to test for that
09:21 olass joined #bioclipse
09:26 CIA-40 bioclipse: carl_masak * r10063 /bioclipse2/trunk/plugins/net.bioclipse.script​ing/src/net/bioclipse/scripting/JsThread.java:
09:26 CIA-40 bioclipse: [JsThread] simpler array initialisation
09:26 CIA-40 bioclipse: Using autoboxing to our advantage. No need to make Java even more verbose
09:26 CIA-40 bioclipse: and circumscript than it alrady is.
09:47 olass edrin: please have a look at bug 1010 and try to fix that
09:47 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
09:56 maclean joined #bioclipse
09:59 egonw hi maclean
09:59 maclean hi egonw
09:59 masak oh hai maclean
09:59 maclean O hai
10:00 masak maclean: I made you a cheezburger... but I eated it. :/
10:00 maclean impressive combinatorics code in p6, masak
10:00 maclean :)
10:00 masak maclean: thank you. nice to have people following my bloch.
10:04 egonw lunch time
10:13 CIA-40 bioclipse: shk3 * r10064 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: better no commas in help except between parameters
11:00 olass @msg
11:01 zarah olass: 2 h 9 m 20 s ago, masak said http://www.modernperlbooks.com/mt/200​9/04/the-rapid-release-tautology.html
11:02 masak olass: I think we should eventually aim for a monthly release schedule.
11:02 olass masak: yes, I think so too
11:02 masak \o/
11:03 jonalv \o/
11:03 masak \o/
11:03 zarah \o/
11:08 Gpox ~o/
11:08 olass ~o~
11:08 masak -o-
11:09 olass proppar i öronen?
11:09 masak olass: sorry, you were saying?
11:09 olass ~o~   <  Pippi Långstrump
11:09 olass (sorry for Swe here)
11:09 masak @o@   <-- Princess Leia
11:13 jonalv olass: "Pippi Longstocking"
11:14 masak olass: "Pipi Ŝtrumpolonga"
11:14 jonalv בילבי בת-גרב
11:14 masak 長襪子皮皮
11:14 egonw Pippi Langkous
11:30 egonw olass: what about the ChEBI data plugin?
11:30 egonw maclean, shk3: is your group working on that?
11:31 olass egonw: no time for us
11:31 olass actually never heard about it
11:32 egonw olass: it's done in Chris' group...
11:32 egonw it's a single SDF
11:32 olass then they should host it IMO
11:32 olass on the EBI server
11:32 olass shk3: or what do you think?
11:36 egonw lunch I guess
11:39 egonw I hate Java regexp
11:44 masak egonw: in Soviet Russia, Java regexp hate YOU!
11:59 CIA-40 bioclipse: egonw * r10065 /bioclipse2/trunk/plugins/net.bioclipse.core/​src/net/bioclipse/core/PublishedMethod.java: Added missing JavaDoc (fixes #916)
11:59 zarah bug #916 | http://tinyurl.com/date76
11:59 CIA-40 bioclipse: egonw * r10066 /bioclipse2/trunk/plugins/net.biocl​ipse.core.tests/src/net/bioclipse/c​ore/tests/AbstractManagerTest.java: Added unit test to ensure that PublishedMethod params are properly defined (fixes #914)
11:59 zarah bug #914 | http://tinyurl.com/cjtw3g
12:07 shk3 olass: never heard about the chebi data plugin
12:08 egonw shk3: no, it does not exist yet
12:08 egonw but from your statement...
12:08 egonw I understand nothing is in the works in your group?
12:08 olass egonw: who told you it was?
12:08 egonw no one
12:08 olass :)
12:08 egonw I never said it was being worked on
12:08 shk3 don't think so
12:08 olass [13:33] < egonw> olass: what about the ChEBI data plugin?
12:09 shk3 what is it supposed to do?
12:09 egonw s/the/a/
12:09 egonw hold the ChEBI SDF
12:09 olass is there one?
12:09 egonw nothing more, nothing less
12:09 olass how big is it?
12:09 egonw http://www.steinbeck-molecular.de/steinblog/index.​php/2009/04/30/chebi-release-56-now-with-sd-file/
12:09 zarah egonw's link is also http://tinyurl.com/d7kvbt
12:10 egonw 13MB
12:10 egonw gziped
12:10 egonw ftp://ftp.ebi.ac.uk/pub/databases/chebi/SDF/
12:14 egonw I just thought it would make a nice addition to our set of data plugins
12:18 olass shk3: ask chris if you should set it up
12:18 olass would be nice
12:18 shk3 but what is the purpose?
12:20 egonw distribute and promote ChEBI and Bioclipse ?
12:20 shk3 sorry
12:20 shk3 what should it do?
12:20 shk3 which functionality should it offer?
12:21 egonw what all other data plugins do
12:21 egonw provide data
12:21 sneumann instead of a remote query ?
12:21 shk3 oh, you mean an example data plugin
12:21 shk3 with the sdf?
12:21 sneumann Would a pubchem plugin provide pubchem ?
12:21 egonw yes
12:21 egonw sneumann: no, that one provides a manager for remote calls
12:21 egonw I think SF will not be happy with 8GB data plugins :)
12:22 egonw actually...
12:22 egonw this is update site
12:22 sneumann What is the update policy for chebi plugin  ? Weekly ? Monthly ? Annually ?
12:22 egonw so update.bioclipse.net
12:22 egonw I think Ola will not be happy with 8GB data plugins :)
12:22 maclean joined #bioclipse
12:22 egonw sneumann: when they make a new release, I guess?
12:22 sneumann I'd say you can expect ChEBI to grow
12:23 CIA-40 bioclipse: carl_masak * r10067 /bioclipse2/trunk/plugins/net.bioclipse.script​ing/src/net/bioclipse/scripting/JsThread.java:
12:23 CIA-40 bioclipse: [JsThread] allowing cancelling of console js
12:23 CIA-40 bioclipse: Replaces the js environment with a fresh one when 'cancel' is pressed.
12:23 CIA-40 bioclipse: Currently loses the three functions {clear, print, say} defined through
12:23 CIA-40 bioclipse: the js console view.
12:23 maclean egonw: why would you imagine that there is a ChEBI plugin?
12:23 egonw I'd say you're quite right
12:23 egonw I imagine there *could* be a ChEBI plugin
12:23 maclean there is the sdf file release, and no more :)
12:23 egonw and think that it would be nice
12:24 maclean I can imagine all sorts of plugins!
12:24 sneumann Why not provide a ChEBI plugin "that one provides a manager for remote calls"
12:24 egonw maclean++
12:24 CIA-40 bioclipse: carl_masak * r10068 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): (log message trimmed)
12:24 CIA-40 bioclipse: moved topLevelCommands JsConsoleView -> JsThread
12:24 CIA-40 bioclipse: The topLevelCommands {clear, print, say} are now initialized when the
12:24 CIA-40 bioclipse: JsThread (re)boots and gets itself a fresh JsEnvironment. Since JsThread
12:24 CIA-40 bioclipse: doesn't know about JsConsoleView, the data structure was moved to the
12:24 CIA-40 bioclipse: former. This way, the commands are not lost after a forced cancel/reboot.
12:24 CIA-40 bioclipse: It is possible that topLevelCommands should really reside in JsEnvironment
12:24 shk3 sneumann: somebody would have to do it
12:24 egonw a plugin has advantages because of automatic updates?
12:24 * masak resolves #625
12:25 egonw and we need advertisement of the whole plugin concept?
12:25 shk3 i will talk to chebi people
12:25 egonw and a ChEBI plugin would combine two things done in Chris' group?
12:25 egonw it would demo our MolTable feature of BC2?
12:25 maclean I'm not saying it's not a good idea, egon.
12:25 egonw and JChemPaint?
12:26 maclean I'm saying that no-one has any plans to do it
12:26 egonw and test things more properly
12:26 egonw maclean: I never said anyone had plans
12:26 egonw I only *asked* if you already had plans...
12:26 egonw but that was before you joined
12:26 egonw yes, I did make a typo s/the/a/
12:26 egonw which suggested there already was a finished plugin
12:27 maclean Ah, okay then. So the answer is : "no".
12:27 egonw but never suggested anyone was already *working* on it
12:27 egonw maclean: good :)
12:27 maclean But not : "no way" :)
12:27 masak NO WAI
12:27 maclean WAI
12:27 egonw sneumann: yes, a ChEBI plugin that would do remote searches would be nice too
12:27 egonw but more work than distributing a mere SDF
12:28 egonw even with updates (which remote searching would need too), it is little work
12:28 egonw update version number, and SDF
12:28 egonw done
12:29 egonw meanwhile... PubChem-CDK has now close to 2M compounds
12:29 egonw of which about 700k atom typed
12:31 edrin @pz
12:31 zarah edrin: Pelezilla is at http://bugs.bioclipse.net
12:31 * egonw loves scripts just doing their thing...
12:31 olass mine seldom do :(
12:32 maclean I thought of a good test-project for demonstrating bioclipse capability the other day
12:33 * egonw listens
12:33 maclean it would open a set of proteins from a directory in jmol, run a jmol-script on each and make a snapshot-image
12:34 maclean self-contained, project-like, and of fairly general interest
12:34 maclean I guess the same could be done with jcp..
12:34 maclean it's maybe more of a tutorial thing, I don't know.
12:36 edrin maclean: this can be easily done with just a small javascript
12:36 maclean well yes
12:36 maclean but it requires the 'infastructure' of a project directory, separate pdb and image sub-directories...
12:37 maclean the point is that it is not necessarily clear for users how to start with bioclipse
12:37 edrin indeed
12:37 maclean the "why would I use this program" problem
12:38 masak better than the "what a piece of crap" problem, at least.
12:38 maclean :D
12:38 maclean I mean >:-(
12:39 edrin this script walks recursively through all services of an xmpp server and creates bindings for all functions :) http://gist.github.com/106630
12:39 edrin don't run it, it would take ~1h
12:40 edrin because it creates bindings for CML ~20x
12:41 egonw fika here, bbl
12:42 egonw maclean: sounds like an interesting cheat sheet!
12:42 egonw bbl
12:42 maclean true
12:43 maclean edrin : heh "here is a cool script, but don't run it!" - that's like a big button marked "don't press!" :)
12:43 edrin hehe
12:44 maclean edrin : what do you imagine that the average user would use the xmpp stuff for? Like quite basic, but still useful activity?
12:44 edrin maclean: we would be happy if you could try all the scripts here http://pele.farmbio.uu.se/xmpp-service​s/index.php/XMPP_services_in_Bioclipse and here http://pele.farmbio.uu.se/xmpp​-services/index.php/Tutorials and report back any errors...
12:44 maclean I mean, ola has his hiv-predict stuff.
12:45 zarah edrin's link is also http://tinyurl.com/c5c7du
12:45 edrin except the 106630 gist everything should complete within ~1 minute
12:45 maclean well, sure, I'll try them, but that's not really an answer to the question...
12:46 edrin maclean: currently it's mainly a demo of XMPP Services
12:46 maclean I guess I could read the tutorials page
12:46 maclean erk! that page renders horribly in safari 4
12:47 edrin maclean: later a user I hope would do the same with it what you just suggested with the protein pictures, just not pictures but for example protein motif prediction
12:47 maclean hmmm, okay.
12:47 edrin maclean: the xmpp wiki page?
12:47 maclean this page http://pele.farmbio.uu.se/xmpp-services/index.php
12:47 zarah maclean's link is also http://tinyurl.com/dlsq5z
12:47 maclean in fact, all of them
12:49 maclean http://gilleain.tumblr.com/post/103725079
12:49 zarah maclean's link is also http://tinyurl.com/c34l6y
12:53 maclean hmm. yes, none of those 'tutorials' are really what I would call a tutorial.
12:53 maclean they don't produce some test results (like pictures, motifs, sequence alignments, etc, etc)
12:54 maclean afk
12:56 edrin maclean: they are supposed to demo a web service API
12:57 edrin olass: did you see, maclean has problems to see the wiki
12:59 olass maclean: you can't see the wiki?
12:59 * olass just created an XMPP cheat sheet
13:00 maclean does "afk" not mean anything to you guys :)
13:00 olass nope
13:00 olass we are always at the keyboard
13:00 olass ;)
13:00 egonw grmph...
13:00 egonw SF commit is really slow
13:00 maclean no, no I can _see_ it, but my browser makes it look horrible
13:01 egonw cdk 1.2.2 patches have not made bioclipse svn yet
13:01 maclean see my tumblr post above...
13:01 maclean It may be a safari-only problem, so don't worry about it.
13:03 maclean edrin : but a 'web service API' will have some downstream effect on users who are not writing web services, yes?
13:03 maclean In fact, even the web service developers might want a concrete example, I would think.
13:03 egonw maclean: of what?
13:03 egonw example code of a client or server?
13:03 egonw example code of a client or service?
13:04 maclean anything.
13:04 maclean either, both.
13:04 egonw xws4j.sf.net
13:04 egonw there is demo code there
13:04 * maclean takes a look
13:04 egonw (and I plan to write a short groovy code example for both)
13:05 maclean no, no, no. this is not a tutorial either.
13:06 maclean this is like those programming language books that have database examples with "cat" and "dog" records.
13:06 maclean I mean an /actual/ example of something that someone would /want/ to do.
13:06 egonw right
13:07 maclean Anyway, I don't mean to whinge about it.
13:08 * maclean goes back to annealing runs.
13:08 egonw bah...
13:09 egonw sf svn ridiculously slow :(
13:09 egonw commiting does not work :(
13:14 jonalv I HATE CIRCULAR DEPENDENCY CHECKING!
13:15 jonalv ALWAYS CIRCULAR DEPENDECYS, IAM GOING CRACY!
13:17 CIA-40 bioclipse: egonw * r10069 /bioclipse2/trunk/cdk-externals/trunk/ (147 files in 82 dirs): Uploaded CDK 1.2.2 (fixes #975)
13:17 zarah bug #975 | http://tinyurl.com/c46ctg
13:17 CIA-40 bioclipse: egonw * r10070 /bioclipse2/trunk/cdk-externals/trunk/org.open​science.cdk.standard/src/org/openscience/cdk/ (event/ICDKChangeListener.java geometry/GeometryTools.java):
13:17 CIA-40 bioclipse: Patching GeometryTools and ICDKChangeEvent from jchempaint-primary
13:17 CIA-40 bioclipse: Was git-svn-id:
13:17 CIA-40 bioclipse:  https://bioclipse.svn.sourceforge.net/s​vnroot/bioclipse/bioclipse2/trunk@9295 fcb5ba71-d80d-0410-8237-ba3920747fcc
13:18 CIA-40 bioclipse: Author: goglepox <goglepox@fcb5ba71-d80d-0410-8237-ba3920747fcc>
13:18 CIA-40 bioclipse: egonw * r10071 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.standard/src/org/opens​cience/cdk/geometry/GeometryTools.java: Applied jchempaint-primary commit 14507
13:18 CIA-40 bioclipse: egonw * r10072 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.standard/src/org/opens​cience/cdk/geometry/GeometryTools.java: Applied jchempaint-primary commit 14534
13:19 CIA-40 bioclipse: egonw * r10073 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.standard/src/org/opens​cience/cdk/geometry/GeometryTools.java: Applied jchempaint-primary commit 14542
13:19 CIA-40 bioclipse: egonw * r10074 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.standard/src/org/opens​cience/cdk/geometry/GeometryTools.java: Applied jchempaint-primary commit 14507
13:19 egonw he he... finally...
13:30 egonw olass: miscalculated
13:30 egonw the PubChem data is 55GB
13:31 olass ok
13:31 egonw pele is still fine, though
13:31 olass good
13:32 * olass has been wondering why PZ has been slow lately
13:32 egonw mmm
13:32 * egonw is using just one processor
13:33 egonw and memory is still OK too
13:34 egonw ah, no... memory is about used all
13:34 egonw not not swapping much though
13:36 egonw olass: ping
13:37 olass @pong
13:37 egonw there is ICDKMolecule.getFingerprint
13:37 jonalv ALWAYS CIRCULAR DEPENDECYS, IAM GOING CRAzY!
13:37 jonalv AAAAAAAAAAHAHHHHAAHAHAHAHAHHA CIRCULAR DEPS
13:37 jonalv :(
13:38 maclean jonalv : to resolve the circular dependencies, you must first resolve the circular dependencies.
13:40 masak argh, metacircular dependencies!
13:41 olass oval dependencies?
13:42 maclean oval ones sound much nicer
13:47 masak spiral dependencies...
13:51 jonalv egonw: thankyou :)
13:51 egonw jonalv: that's what postdocs are for
13:51 egonw help PhD students :)
13:51 jonalv :)
13:52 CIA-40 bioclipse: carl_masak * r10075 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
13:52 CIA-40 bioclipse: [JsConsoleView] added back @SuppressWarnings
13:52 CIA-40 bioclipse: Was lost after the move in r10068.
13:52 CIA-40 bioclipse: carl_masak * r10076 /bioclipse2/trunk/plugins/net.bioclips​e.balloon.business/src/net/bioclipse/b​alloon/business/IBalloonManager.java:
13:52 CIA-40 bioclipse: [IBalloonManager] added @PublishedClass ann
13:52 CIA-40 bioclipse: Without this, the tab completion hook adding parentheses won't find the
13:52 CIA-40 bioclipse: method declarations, and thus won't add parentheses. Also, the help/man
13:52 CIA-40 bioclipse: information and the automatic doc harvester are likely to be affected by
13:52 CIA-40 bioclipse: a missing @PublishedClass annotation.
13:54 rajarshi joined #bioclipse
13:55 egonw hi rajarshi
13:55 egonw olass: is ICDKMolecule.getFingerprint() enough?
13:56 olass looks good
13:59 egonw ok, won't spend time on cdk.getFingerprint then
14:11 olass ack
14:12 shk3 do we have documentation what the manager comments should look like?
14:12 shk3 http://wiki.bioclipse.net/index.​php?title=How_to_make_a_manager tell about params having paramter descriptions
14:12 zarah shk3's link is also http://tinyurl.com/dypvah
14:19 rojasm joined #bioclipse
14:21 egonw shk3: I was just looking at calculateTanimoto()
14:21 egonw I have some comments on it...
14:21 egonw * can you please use 80 char line length max
14:22 egonw * please do use import org.openscience.cdk.similarity.Tanimoto
14:22 egonw * please reuse a Fingerprinter instance, instead of instantiating 2! for each comparison, instead of just 1 for the whole method
14:23 egonw * fix the ClassCast source in the method at line 2178
14:23 egonw * change the order in which the calculateTanimoto method call each other?
14:25 egonw (because I want to have the method which takes two IMolecule reuse a new method I am writing: calculateTanimoto(BitSet, BitSet)
14:25 egonw )
14:27 shk3 can you tell me what to do with the comments?
14:29 egonw fix them?
14:29 egonw well, not the commend
14:29 egonw but the code that effected them...
14:29 egonw well, not the comments
14:29 egonw but the code that effected them...
14:30 shk3 I mean: what should the comments look like?
14:30 shk3 is there an example?
14:30 shk3 changing stuff but keeping silently to yourself what it should be like is not so great
14:30 jonalv could someone give me some small code bit that has to be run in the gui thred?
14:30 olass jonalv: open an editor?
14:30 masak jonalv: ui.open(...)
14:30 egonw * can you please use 80 char line length max
14:31 egonw that is:
14:31 jonalv that is _not_ using a manager...
14:31 egonw make the lines shorter
14:31 olass shk3: are you talking about inline documentation for JSconsole help command?
14:31 olass jonalv: yes
14:31 shk3 yes
14:31 olass Messagebox.openInfo(blabla)
14:31 egonw oh, not about my comments?
14:31 jonalv olass: okey hit me, please
14:31 shk3 the javadoc of the manager interfaces
14:31 masak @slap jonalv
14:31 egonw javadoc or PublishedMethod?
14:31 * zarah loves jonalv, so no slapping
14:31 olass lol
14:32 shk3 params should not have params in it
14:32 shk3 I understood
14:32 olass jonalv: is what shk3 asks for not listed in the wiki manager page?
14:32 shk3 not in http://wiki.bioclipse.net/index.​php?title=How_to_make_a_manager
14:32 zarah shk3's link is also http://tinyurl.com/dypvah
14:32 egonw it should not have param *descriptions*
14:32 egonw just the Java type + name
14:32 shk3 aha
14:32 shk3 and where should descriptions go?
14:32 shk3 or no descriptions?
14:33 egonw in they summary part
14:33 egonw of PublishedMethod
14:33 olass ashk3: http://wiki.bioclipse.net/index.ph​p?title=How_to_make_a_manager#The_.40PublishedClass_and_.40P​ublishedMethod_annotations
14:33 zarah olass's link is also http://tinyurl.com/dypvah
14:33 olass it shows the params
14:33 jonalv olass: MessageBoc has no openInfo method...
14:33 olass and methodSummary
14:34 shk3 and the description is sort of implicit?
14:34 egonw no, the param description should be in the summary field of PublishedMethod
14:35 shk3 well
14:35 shk3 looking at the examples:
14:35 shk3 @PublishedMethod(params = "IMolecule mol, boolean overwrite",
14:35 shk3 methodSummary = "saves mol to a file, if previously read from file. " +
14:35 shk3 "Overwrite determines if existing file shall be overwritten.")
14:35 shk3 the description of the mol parameter is
14:35 shk3 the "saves mol to a file"?
14:36 egonw ah, ok, yes, in that sense it is implicit in the *summary*
14:36 egonw but not implicit in the params field content
14:37 CIA-40 bioclipse: ospjuth * r10077 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (5 files in 3 dirs): Added a tutorial cheatsheet for XMPP + IO Data. Solves #1014.
14:37 CIA-40 bioclipse: shk3 * r10078 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: updated javadoc
14:38 jonalv hm can it be that the tests are run using the gui thread when running plugin tests?
14:40 olass jonalv: that could be
14:40 olass not sure
14:40 olass google for it?
14:40 zarah olass: http://www.takeourword.com/
14:41 olass zarah: thanks for the tip
14:41 zarah for: olass says thank you
14:41 olass lol
14:41 olass masak: zarah is weird today...
14:41 masak olass: we're all weird today.
14:41 jonalv olass: how would you google for that?
14:41 jonalv we all go a little mad sometimes
14:42 olass @google eclipse junit ui thread
14:42 zarah olass: http://osdir.com/ml/java.abbo​t.user/2005-04/msg00007.html
14:42 olass jonalv: you see?
14:42 masak @google java must die
14:42 zarah masak: http://pavangayakwad.blogspot.com/2005/03​/executables-c-and-java-too-must-die.html
14:42 masak :>
14:42 jonalv olass: reading now
14:43 jonalv it seems complicated... :(
14:44 egonw shk3: will you look at those commetns on your calculateTanimoto code, or shall I file a reminder in Pelezilla?
14:44 egonw those=my
14:46 shk3 doing it right now
14:46 egonw ok, thanx
14:48 CIA-40 bioclipse: shk3 * r10079 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: cleanup of tanimoto stuff
15:15 * olass is proud of hist last gist
15:15 egonw olass++
15:16 egonw URL?
15:16 olass coming right up
15:16 olass It's actually still just a script)
15:21 edrin left #bioclipse
15:22 olass egonw: http://gist.github.com/107008
15:22 olass egonw: it's the first useful script I have written for Bioclipse
15:22 egonw hahaha
15:22 olass first time the script does something simpler than I would have solved in Java
15:23 egonw it seems we are approaching something releasable then
15:23 olass quite some progress actually
15:23 olass indeed
15:25 olass @tell edrin please mark bugs as finished when you have solved them
15:25 zarah Consider it noted.
15:25 olass @tell edrin else they do not show up in my queries so I can confirm and close them
15:25 zarah Consider it noted.
15:34 rojasm joined #bioclipse
15:37 jonalv all my tests except the one for callback in JavaScript passes now. Next step is probaly to actuallu try and use this somethow... ...by rewertiting the gistmanager as a first step
15:46 egonw jonalv++
15:46 jonalv egonw: new branch on pele
15:46 egonw ok
15:46 egonw tomorrow
15:46 egonw sorry about that
15:47 jonalv I just wonder how many errors I have introduced today...
15:47 egonw :)
15:47 jonalv egonw: it's okey, I am giving up now as well
15:47 jonalv I think I need a nights sleep before I start trying to use this and find all the errors...
15:47 jonalv :)
15:57 ilogger2 joined #bioclipse
16:16 edrin joined #bioclipse
16:35 edrin left #bioclipse
18:14 edrin joined #bioclipse
18:15 egonw joined #bioclipse
18:30 CIA-40 bioclipse: edrin_t * r10080 /bioclipse2/trunk/plugins/net.bioclips​e.jsexecution/src/net/bioclipse/jsexec​ution/execution/ScriptExecution.java: shows the exact error exception now
18:38 CIA-40 bioclipse: egonw * r10081 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Added variants for calculating tanimoto
18:38 CIA-40 bioclipse: egonw * r10082 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Better code: calculate the fingerprint for the reference only once
19:17 CIA-40 bioclipse: egonw * r10083 /bioclipse2/trunk/plugins/ (5 files in 3 dirs): Renamed method to match the naming scheme of other save methods (fixes #1003)
19:17 zarah bug #1003 | http://tinyurl.com/c4wyr3
19:26 CIA-40 bioclipse: edrin_t * r10084 /bioclipse2/trunk/plugins/net.bioclips​e.jsexecution/src/net/bioclipse/jsexec​ution/execution/ScriptExecution.java: fixed bug, that is like #1016 described for masak
20:44 CIA-40 bioclipse: edrin_t * r10085 /bioclipse2/trunk/plugins/net.bioclip​se.xws4j/src/net/bioclipse/xws4j/view​s/servicediscovery/TreeObject.java: adapted to current xws4j
20:44 CIA-40 bioclipse: edrin_t * r10086 /bioclipse2/trunk/plugins/net​.bioclipse.xws4j/jars/xws4j/ (4 files): updated to current xws4j
20:56 CIA-40 bioclipse: edrin_t * r10087 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (.classpath META-INF/MANIFEST.MF build.properties): updated to current xws4j svn
21:48 Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/ || Our Wonderful Nature http://www.spiegel.de/video/video-30120.html

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