Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-14

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All times shown according to UTC.

Time Nick Message
05:35 olas joined #bioclipse
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07:33 olas egonw: coffee
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08:48 CIA-30 bioclipse: shk3 * r7295 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): 2d/3d generation works at least for mol files
08:48 masak joined #bioclipse
08:49 shk3 hi all
08:49 zarah hi shk3
08:49 shk3 hi olas
08:49 shk3 I have a question
08:51 olas shk3: shoot
08:51 shk3 when/if a mol file is opened in jcp and I then try a coordinate generation,
08:52 shk3 there is a problem
08:52 shk3 the selection then is no loner of type IFile, but CDK10Molecule
08:52 shk3 so a line like this:
08:52 shk3 mol = Activator.getDefault().getCDKManager().loa​dMolecule((IFile)ssel.getFirstElement());
08:52 shk3 gives a classcastexception
08:52 shk3 is this a known behaviour?
08:53 shk3 I thought the resources in navigator would be independent of editors
08:53 shk3 and parsing and so on
08:54 jonalv joined #bioclipse
08:54 jonalv zarah: hi
08:54 zarah hello jonalv :)
08:55 shk3 hi jonalv
08:55 shk3 i am looking at the coordinate generation
08:55 shk3 works at least for mol files
08:56 shk3 but I came across a problem
08:56 jonalv I have been thinking about that
08:56 shk3 which seems to have taken olas by surprise
08:56 jonalv It can take a while right?
08:56 shk3 don't think so
08:56 shk3 just need to look at cml
08:56 shk3 but I think we need another content type there
08:57 shk3 right now, there is 2d and 3d, but we also need 2dand3d
08:57 jonalv Because if it takes a while we should run it in a job and to run things in a job they need to be void things...
08:57 olas shk3: I see your point
08:57 shk3 ah, you mean the generation
08:57 shk3 for 3d, yes
08:57 olas maybe we should add that contentType?
08:58 olas on the other hand
08:58 olas what do you need it for?
08:59 olas usually you can operate on multipl content types
08:59 shk3 well, jonalv wants to have different wording for menu items
08:59 shk3 create and recreate coordinates
08:59 olas sounds reasonable
08:59 shk3 such a file would need recreate2d and recreate3d
08:59 olas so?
08:59 shk3 right now, 2d has recreate 2d and create 3d
08:59 shk3 and 3d has recreate 3d and create 2d
08:59 olas sounds good
09:00 olas but?
09:00 shk3 no but
09:00 olas so why do you need more contenttypes?
09:00 shk3 since menu wording is bound to content type, i need another one
09:00 shk3 or can I change the wording somewhere else?
09:00 olas can you not use a core expression?
09:01 shk3 what is a core expression?
09:01 olas mom
09:01 olas http://wiki.eclipse.org/Command_Core_Expressions
09:01 zarah olas's link is also http://tinyurl.com/4y98b4
09:01 olas you can combine stuff with <and>, <or> etc
09:02 olas 2d AND 3d should be possible
09:02 olas to create
09:02 olas like that
09:02 olas have a go and see if it works
09:02 olas I think it will
09:04 masak joined #bioclipse
09:05 shk3 can a file have several content types?
09:06 egonw joined #bioclipse
09:06 masak egonw, olas: sushi?
09:07 * olas has a box
09:07 masak olas: how unfortunate
09:08 olas yes...
09:08 masak egonw?
09:08 olas egonw sushi? You must be joking :-)
09:09 masak I have no data about egonw, so I'm not joking :)
09:09 egonw olas: why?
09:09 shk3 olas: sorry, don't understand this
09:10 olas egonw: you like sushi?
09:10 shk3 I can <and> combine.
09:10 shk3 ok.
09:10 olas I thought you didn't...
09:10 shk3 thanks
09:10 olas maybe I am mistaken
09:10 shk3 but for this to work, a file would need to have several content types
09:10 shk3 2d and 3d
09:10 shk3 not sure if this is possible
09:11 olas a file?
09:11 olas ok then do a new contenttype
09:11 olas I'm fine with that
09:11 shk3 well yes, the context menu is for a file
09:11 olas but do it for all moleculefiles
09:12 shk3 well, a mol file cannot be both
09:14 jonalv zarah: masak is practising on you...
09:14 zarah jonalv: eh... wha'?
09:15 jonalv zarah: yes indeed...
09:15 zarah jonalv: I see.
09:15 masak zarah: don't mind him.
09:15 zarah masak: are you talking to *me*?
09:15 masak zarah: I'm just doing som git practice.
09:15 zarah masak: are you making fun of me?
09:15 masak zarah: no.
09:15 zarah masak: I see.
09:20 CIA-30 bioclipse: jonalv * r7296 /bioclipse2/trunk/plugins/net.bioclipse​.core/src/net/bioclipse/core/business/ (CreateJobAdvice.java ICreateJobAdvice.java): Deleted duplicated (I don't know how that happend) classes
09:27 shk3 olas: what do you think about the class cast problem?
09:27 edrin joined #bioclipse
09:27 edrin hi
09:27 zarah hi edrin
09:28 masak hi edrin
09:28 edrin hi masak
09:29 olas shk3: if you have a class cast problem, you should probably do instanceof before casting
09:29 shk3 hm yes, but how can the selection be a molecule?
09:30 shk3 I thought in bc2
09:30 shk3 the parsing is internal only
09:30 shk3 in an editor or so
09:30 olas please explain in more detail what you mean
09:31 shk3 [09:51] <shk3> when/if a mol file is opened in jcp and I then try a coordinate generation,
09:31 shk3 [09:52] <shk3> there is a problem
09:31 shk3 [09:52] <shk3> the selection then is no loner of type IFile, but CDK10Molecule
09:31 shk3 [09:52] <shk3> so a line like this:
09:31 shk3 [09:52] <shk3> mol = Activator.getDefault().getCDKManager().loa​dMolecule((IFile)ssel.getFirstElement());
09:31 shk3 [09:52] <shk3> gives a classcastexception
09:31 shk3 [09:52] <shk3> is this a known behaviour?
09:31 shk3 [09:53] <shk3> I thought the resources in navigator would be independent of editors
09:31 shk3 [09:53] <shk3> and parsing and so on
09:31 shk3 this looks like the editor influences the navigator content
09:31 shk3 which surprises me for bc2
09:31 olas it does not
09:32 shk3 no?
09:32 olas but do you really want to parse the file again?
09:32 shk3 I thought I need to
09:32 olas ok
09:32 shk3 I thought in bc2 I need to
09:32 olas from any BioResource you can get the underlying IResource
09:32 olas this is the intention at least
09:32 shk3 (plus I don't need a cdk10molecule, I need a cdkmolecule)
09:32 olas the last part is trivial
09:33 olas cdk.create(myCDK10olecule)
09:33 shk3 ok, so I need to check if it's a file or not
09:33 olas where cdk is CDKManager
09:33 olas yes
09:33 shk3 ok, thanks
09:33 olas no prob :-)
09:35 gilleain BioResource?
09:35 gilleain Do they still exist?
09:37 olas hmm, no
09:37 gilleain (Because they do not seem to)
09:37 olas BioObject
09:38 gilleain which does in deed have a getResource()
09:47 shk3 jonalv: the coordinate generation works
09:47 jonalv shk3: I will retry after lunch :)
09:48 shk3 with cml files, I get a "Resetting to invalid mark" sometimes
09:48 jonalv exactly
09:48 shk3 this is a problem with readerfactory
09:48 shk3 I try to figure it out
09:48 jonalv sound good
09:48 shk3 but it's no the generation as a such
09:48 shk3 so try a mol file
09:48 shk3 better
09:48 shk3 for now
09:48 * jonalv -> at lunch
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10:28 edrin egonw, olas: I sent this google docs mail invitation to u
10:56 thomasku joined #bioclipse
11:14 egonw edrin: received and accepted
11:14 edrin fine :)
11:17 * egonw is back from lunch
11:19 jonalv egonw: what was it I should write to try the subversion connection with git?
11:41 jonalv okey I give up for now. Getting git-svn on a mac seems to require too many things
12:03 egonw jonalv: that would be: git svn fetch; git svn rebase
12:21 gilleain joined #bioclipse
12:23 egonw MS in action: netbooks with XP with more than 1.5GB need a special license
12:23 egonw hahahaha
12:24 gilleain How do they justify this?
12:25 egonw do they?
12:25 egonw why should they?
12:26 gilleain Well, I mean, do they give a reason?
12:26 egonw mom
12:26 gilleain oh, http://www.fudzilla.com/index.php?option=com_c​ontent&amp;task=view&amp;id=9919&amp;Itemid=1
12:26 zarah gilleain's link is also http://tinyurl.com/46qm74
12:27 egonw the article I'm reading just not list a reason
12:27 gilleain Ah. :)
12:52 edrin hehe
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13:18 egonw olas: pin
13:18 egonw +g
13:18 egonw shouldn't we go?
14:13 rojasm1 joined #bioclipse
14:35 olas egonw: yes, we did
14:35 olas :-)
14:49 edrin coffee?
14:58 karma24 joined #bioclipse
14:58 karma24 is anyone familiar with using genecards?
15:02 edrin hello karma24: who are you?
15:02 karma24 a student
15:03 karma24 im taking a bioinformatics course
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16:05 edrin joined #bioclipse
16:05 edrin hi
16:05 zarah hi edrin
16:09 jonalv http://wiki.bioclipse.net/index.php?ti​tle=How_to_run_manager_methods_in_jobs
16:09 zarah jonalv's link is also http://tinyurl.com/3sc3vo
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16:25 olas hi edrin
16:35 edrin olas: more effort in what way?
16:36 * olas is writing :-)
16:36 edrin ah
16:37 olas ok, what do you think now?
16:38 olas must leave in 10 mins
16:39 edrin well one could support a biomoby2xws proxy?
17:10 edrin bye
17:10 edrin have a nice evening
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