| Time |
S |
Nick |
Message |
| 05:29 |
|
|
masak joined #bioclipse |
| 07:07 |
|
CIA-20 |
bioclipse: carl_masak * r4677 /branches/bioclipse2/core/plugins/net.bioclipse.ui/src/net/bioclipse/ui/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.ui/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/net.bioclipse.scripting/src/net/bioclipse/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.core/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.bioclipse.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/bioinformatics/plugins/net.bioclipse.biojava.business.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/bioclipse/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/bioclipse/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.recording/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 |
