| Time |
Nick |
Message |
| 05:24 |
CIA-40 |
bioclipse: egonw * r10061 /bioclipse2/trunk/plugins/net.bioclipse.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-services/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.php?title=How_to_make_a_manager#The_.40PublishedClass_and_.40PublishedMethod_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.scripting/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.bioclipse.cdk.business/src/net/bioclipse/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/2009/04/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.bioclipse.core.tests/src/net/bioclipse/core/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.scripting/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-services/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.openscience.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/svnroot/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/org.openscience.cdk.standard/src/org/openscience/cdk/geometry/GeometryTools.java: Applied jchempaint-primary commit 14507 |
| 13:18 |
CIA-40 |
bioclipse: egonw * r10072 /bioclipse2/trunk/cdk-externals/trunk/org.openscience.cdk.standard/src/org/openscience/cdk/geometry/GeometryTools.java: Applied jchempaint-primary commit 14534 |
| 13:19 |
CIA-40 |
bioclipse: egonw * r10073 /bioclipse2/trunk/cdk-externals/trunk/org.openscience.cdk.standard/src/org/openscience/cdk/geometry/GeometryTools.java: Applied jchempaint-primary commit 14542 |
| 13:19 |
CIA-40 |
bioclipse: egonw * r10074 /bioclipse2/trunk/cdk-externals/trunk/org.openscience.cdk.standard/src/org/openscience/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.bioclipse.scripting.ui/src/net/bioclipse/scripting/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.bioclipse.balloon.business/src/net/bioclipse/balloon/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.php?title=How_to_make_a_manager#The_.40PublishedClass_and_.40PublishedMethod_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.bioclipse.cdk.business/src/net/bioclipse/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.abbot.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.business/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.bioclipse.jsexecution/src/net/bioclipse/jsexecution/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.business/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.bioclipse.jsexecution/src/net/bioclipse/jsexecution/execution/ScriptExecution.java: fixed bug, that is like #1016 described for masak |
| 20:44 |
CIA-40 |
bioclipse: edrin_t * r10085 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/src/net/bioclipse/xws4j/views/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/irclogger/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irclog/out.pl?channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/ || Our Wonderful Nature http://www.spiegel.de/video/video-30120.html |
