Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-03-26

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Time Nick Message
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06:26 CIA-22 bioclipse: Annzi * r5179 /bioclipse2/trunk/plugins/net.bioclipse.moss/ (2 files in 2 dirs): Corrected the parameters that exclude atoms and molecules as seed and from mining since they seemed to set same parameter.
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09:58 CIA-22 bioclipse: jonalv * r5180 /bioclipse2/trunk/plugins/net.bioclipse.usermanag​er/src/net/bioclipse/dialogs/EditUserDialog.java: Fixed GUI problem. Still can't log in though...
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11:58 egonw Uppsala might be interested in hearing that Bob Hanson just release a Jmol version which comes with the UFF force field for geometry optimization...
11:58 masak ok
11:58 masak sounds good
11:58 egonw steinbeck__: the code is LGPL, so incorporation in the CDK is an option
11:59 egonw his demo Jmol script:
11:59 egonw load caffeine.xyz
11:59 egonw minimizationSteps = 80
11:59 egonw minimizationRefresh = true
12:00 egonw minimizationCriterion = 0.001
12:00 egonw select connected(2) or connected(3) or oxygen and connected(1)
12:00 egonw connect aromatic modify
12:00 egonw calculate aromatic
12:00 egonw set measurementunits pm
12:00 egonw measure {_O}[1] {_O}[2]
12:00 egonw color measure red
12:00 egonw minimize
12:01 steinbeck__ egonw: very interesting indeed
12:55 olas egonw: heard about it
12:56 olas would be really nice in CDK and Bioclipse
12:56 olas what model does it work with?
12:56 olas I guess Bob adapted it to use the Jmol model
12:56 olas and I guess someone (egonw?) will adapt it to the CDK model
12:57 olas Bioclipse can use both, depending on editor
12:57 olas but very interesting indeed!
12:59 egonw yes, it uses the Jmol data model
12:59 egonw but only for the input...
13:00 egonw as the original code uses simple double[] like things
13:21 CIA-22 bioclipse: jonalv * r5181 /bioclipse2/trunk/ (2 files in 2 dirs): CAn log in and log out now. Events are fired. I have a feeling the serialisation to file isn't working perfect though...
13:36 olas perfectly
13:37 olas perfectly yet
13:37 olas prefectly yet, but will be fixed ;-)
13:37 olas (just some suggestions for changes in the commit msg)
13:43 egonw yeah, a shame that one cannot commit fixes to commit messages :)
13:43 egonw maybe Uppsala should work on a svn/hg/git replacement
13:44 olas sound slike a good idea
13:44 olas I'll put all my focus on that
13:44 * egonw is relocating to his other WUR desk
13:44 egonw bbl
14:14 CIA-22 bioclipse: carl_masak * r5182 /bioclipse/trunk/plugins/net.bioclipse.base2/src/​net/bioclipse/base2/model/Base2ModelObject.java:
14:14 CIA-22 bioclipse: [Base2ModelObject.java]
14:14 CIA-22 bioclipse: * typo
14:39 CIA-22 bioclipse: jonalv * r5183 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): fixed some progress monitor stuff
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16:01 CIA-22 bioclipse: Annzi * r5184 /bioclipse2/trunk/plugins/net.bioclipse.moss/ (10 files in 5 dirs): Poking here and there: added help, documentation and worked with file paths but no actual(working)change were done.
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16:21 olas hi rklancer
16:22 rklancer hi
16:22 olas /me@coffee
16:22 olas hmm
16:22 * olas @ coffee
16:22 olas brb
16:28 CIA-22 bioclipse: jonalv * r5185 /bioclipse2/trunk/plugins/ (6 files in 6 dirs): The sandbox testt for the usermanager now passes
16:31 olas jonalv++
16:31 jonalv well It doesn't seem to work 100% yert though :(
16:31 jonalv I can't seem to get the file persisting to woek when running it
16:32 jonalv I keeps saying that it can't file the file and recreates it :/
16:47 CIA-22 bioclipse: ospjuth * r5186 /bioclipse2/trunk/plugins/net.bioclipse.core/s​rc/net/bioclipse/core/domain/IBioObject.java: removede deprecated getParsedResource()
16:48 CIA-22 bioclipse: ospjuth * r5187 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (4 files in 2 dirs): Some small updates for forms in QSAR plugin. Nothing useful yet.
16:48 CIA-22 bioclipse: ospjuth * r5188 /bioclipse2/trunk/plugins/net.bioclipse.services/ (5 files in 4 dirs): Renamed extension point and adapted all uses for this.
16:51 CIA-22 bioclipse: ospjuth * r5189 /bioclipse2/trunk/plugins/net.bio​clipse.cdk/META-INF/MANIFEST.MF: Removed JCP from export in manifest as it obviously is not included in the current net.bioclipse.cdk version.
16:53 CIA-22 bioclipse: ospjuth * r5190 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/ (.classpath plugin.xml): Excluded all JCP-related stuff from build and commented out JCPEditor from plugin.xml. cdk.ui now compiles.
17:05 rklancer question to anyone:
17:05 rklancer do you have your compilers set somehow to ignore @Overrides?
17:05 olas hmm
17:05 olas let me check
17:05 rklancer right now I see 32 "must override a superclass method" errors in my problems view
17:06 olas that is settable, yes
17:06 rklancer just in 3 projects I'm not using but...
17:06 rklancer olas, how? didn't see it in Preferences -> Java -> Compiler
17:07 olas on page Error/Warniongs
17:07 rklancer hmm...
17:07 olas section: Name shadowing and conflicts
17:08 olas hmm
17:08 olas maybe not, did not finish the reading...
17:08 olas section: Annotations
17:08 olas I have Ignore set
17:09 rklancer i don't have anything set to "error" under Annotations
17:09 rklancer the only option that even mentions @overrides is "Missing '@override' annotation'
17:09 olas prefs -> java > compiler > Errors/Warnings > Annotations
17:09 rklancer but that's kind of the opposite of what I'm looking for
17:09 rklancer :)
17:09 olas yes
17:10 olas right..
17:10 olas dunno then
17:10 rklancer huh
17:10 rklancer maybe everybody has the errors
17:10 rklancer guess I could ask in #eclipse if i was desperate
17:10 rklancer but it's not a problem for me now
17:10 jonalv but don't those methods overide methofds or what?
17:10 olas where do you get errors?
17:10 rklancer ah
17:10 rklancer let's see
17:10 olas I have none in bc currently...
17:11 rklancer since I'm not familiar with the code in the plugins in question I may be missing something I'm ignorant of ... I'll check ...
17:11 olas let me know
17:11 olas the plugins
17:11 olas so, can I remove net.bc.logging now?
17:11 olas you have fixed all deps for that?
17:11 rklancer e.g., "The method accountExists(String) of type UserManager must override a superclass methodnet.bioclipse.usermanager/src/net/biocl​ipse/usermanager/businessUserManager.javaline 29"
17:12 olas jonalv: are you listening?
17:12 * jonalv is not using it so he guess it works without it yea :)
17:12 rklancer yeah, I removed all deps to net.bc.logging
17:12 olas ok
17:13 rklancer as far as I know... wonder if grant sparks is still interested in working on automatic builds...
17:13 rklancer so I could get an email if I broke something on the canonical build :)
17:13 jonalv rklancer: But it does override that method from the interface
17:13 rklancer hmm
17:14 jonalv I know that masak has the same åproblames that you do. He use to remove those override annotations
17:14 jonalv They are autognereataed by Eclipse btw..
17:15 rklancer hmm.
17:15 jonalv and they are quite usefull
17:16 rklancer i wonder if it's an eclipse weirdness
17:16 rklancer on each of these errors I have two markers:
17:16 olas rklancer: please email grantsparks on bioclipse-devel
17:17 olas I mean, cc bioclipse-devel
17:17 rklancer olas, good idea, I've been meaning to
17:17 CIA-22 bioclipse: ospjuth * r5191 /bioclipse2/trunk/plugins/net.bioclipse.biomoby/: Initial import from 1.2.0.
17:18 rklancer (btw, on the recruitment front, I had a nice meeting with someone who may be interested in using bioclipse and is up for a grant part of which could contribute to bc development)
17:18 CIA-22 bioclipse: jonalv * r5192 /bioclipse2/trunk/plugins/net.bioclipse.us​ermanager/src/net/bioclipse/usermanager/pr​eferences/UserManagerPreferencePage.java: added a persist command when properties have been edited
17:18 rklancer two markers:
17:19 rklancer "implements net.bioclipse...IUserManager.accountexists"
17:19 olas jonalv: this is your doing...
17:19 jonalv huh?
17:19 rklancer and "method accountexists(string) of UserManager must override a superclass method"
17:19 jonalv it works for me...
17:19 rklancer and I get two auto suggestions for the fix:
17:20 rklancer "create accountexists() in super type *IBioclipseManager*" (note)
17:20 jonalv or rather: I don't get that error :)
17:20 rklancer and "remove @Override annotation"
17:20 rklancer weird huh
17:20 CIA-22 bioclipse: ospjuth * r5193 /bioclipse2/trunk/plugins/net.bioclipse.biomoby/ (72 files in 9 dirs): Initial import from 1.2.0.
17:20 jonalv the first suggested fix is already fixed so to say...
17:20 rklancer right.
17:21 rklancer notice that that it says to create the method in IBioclipseManager ... not the immediate supertype IUserManager
17:21 rklancer wonder if it's just an eclipse bug
17:22 CIA-22 bioclipse: jonalv * r5194 /bioclipse2/trunk/plugins/net.bioc​lipse.usermanager/src/net/bioclips​e/usermanager/UserContainer.java: removed getParsedResource method
17:22 jonalv yea it's strangge
17:22 rklancer i'll search bugzilla
17:22 jonalv I know that masak has the same problem. olas: you don't?
17:26 rklancer are you using 1.6 or 1.5?
17:31 olas 1.5 for me, I think jonalv is on 1.6
17:31 olas not me
17:31 olas hmm
17:31 olas I don't have usermanager checked out
17:32 olas jonalv: I did that before you!
17:32 olas did you not update before the commit?
17:32 olas removed the deprecated?
17:32 olas see r5186
17:35 jonalv olas: look agian, I removed it from UserContainer.java
17:38 olas look again at what?
17:39 jonalv the commit log
17:39 olas oh
17:39 olas good
17:43 CIA-22 bioclipse: jonalv * r5195 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Now there is a test failing corresponding to the problems I see in the gui
17:43 rklancer aha
17:43 rklancer " With Java 5.0, @Override can only be used if your method overrides a method in a base class. With Java 6.0, @Override can also be used if your method implements a method in a base interface."
17:43 rklancer i kid you not
17:43 jonalv okey
17:44 jonalv so maybe we should bring Bioclipse into java 6 then? :)
17:44 rklancer at least according to "http://dev.eclipse.org/newslists/n​ews.eclipse.newcomer/msg19861.html"
17:44 rklancer please don't
17:44 jonalv why not?
17:44 rklancer believe it or not apple still hasn't released a final 1.6 jvm for os x
17:44 jonalv I have been running java 6 for quite some time here...
17:45 rklancer ..and apple insisted to sun that apple do all jvm development for os x
17:45 jonalv LOL and olas is truing to get me to get a mac.... :)
17:45 rklancer there is a fair amount of bile about this on the mailing lists as you can imagine
17:45 rklancer :(
17:45 * jonalv isn't that interested in a mac if he can't even use java 6
17:46 rklancer ironically it's a very nice machine otherwise
17:46 rklancer oh yeah and I like mine
17:46 jonalv olas: I thought you said that you where running java 6?
17:47 * jonalv is sort of happy with Ubuntu
17:47 jonalv But my computer is beginning to feel a bit old when running Eclipse... :)
17:47 rklancer ironically, os x and nextstep before it were helped by being pretty nice development machines
17:49 * rklancer has a pretty, 2+ ghz dual core, 3 gb ram, nicely portable laptop attached to a 24 inch widescreen monitor ... making him unsuited to develop for the majority who don't have such nice toys :)
17:49 jonalv net.bioclipse.biomoby/extjar​s/commons-logging-1.0.4.jar
17:49 jonalv that feels wrong
17:49 rklancer ooh
17:49 * rklancer doesn't have java 1.6 though
17:49 rklancer i haven't downloaded biomoby
17:49 jonalv hehe :)
17:50 jonalv It was just moved from bc1 so maybe I should give oals a chance to remove that before complaining...
17:50 rklancer well I wouldn't "complain" per se
17:50 rklancer just get to work :)
17:51 jonalv Oh I can't do more than one thing at a time.... :)
17:51 rklancer haha
17:52 CIA-22 bioclipse: jonalv * r5196 /bioclipse2/trunk/plugins/net.​bioclipse.usermanager.tests/: added data file to ignore
17:52 olas will update all biomoby from their SVN soon
17:52 olas I will not mess with biomobys deps
17:52 rklancer hmm
17:53 jonalv Actually I am sort of heading homewards soon. It's almost 7 here :)
17:53 rklancer well a friend just texted me to get coffee, so maybe I won't be "getting to work" :)
17:53 jonalv olas: Then I hope biomobys deps will not mess with us :)
17:54 CIA-22 bioclipse: ospjuth * r5197 /bioclipse2/trunk/plugins/​net.bioclipse.biomoby.ui/: Initial import from 1.2.0 with a lot of changes to make it compile.
17:54 olas LOL
17:54 olas I will go to the store and get something to eat and then continue
17:55 olas need to get some work done
17:55 jonalv you really working latre tonight? :)
17:55 olas yup
17:55 CIA-22 bioclipse: ospjuth * r5198 /bioclipse2/trunk/plugins/​net.bioclipse.biomoby.ui/ (67 files in 15 dirs): Initial import from 1.2.0 with a lot of changes to make it compile.
17:55 olas left early yesterday
17:56 jonalv Well I am heading home now anyway
17:57 olas bike to hörnan?
17:57 jonalv yup
17:57 jonalv so come and join me if you want :)
17:59 rklancer olas, yesterday I found myself working on logging again (despite my best intentions to do something else now)
18:00 rklancer ...and I found myself wanting to make a new plugin
18:00 rklancer (actually, I did)
18:01 rklancer and I called it .. "net.bioclipse.logger". It's different than net.bioclipse.logging ... wholly new ... does that square with you?
18:06 rklancer olas, sorry, heading out...if you have a comment email
18:07 rklancer also, for the public record: http://dev.eclipse.org/newslists/n​ews.eclipse.newcomer/msg19354.html
18:08 rklancer for java 1.5 compliance, we shouldn't annotate methods with @override unless they override methods in a super*class* (i.e., interface methods do not count ... and see http://blogs.sun.com/ahe/entry/override_snafu)
19:10 CIA-22 bioclipse: ospjuth * r5199 /bioclipse2/trunk/plugins/ (25 files in 13 dirs): Major refactoring for biomoby in Bioclipse2.
19:13 CIA-22 bioclipse: ospjuth * r5200 /bioclipse2/trunk/plugins/ (8 files in 6 dirs): Finished refactoring of model from ui plugin.
19:16 CIA-22 bioclipse: ospjuth * r5201 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Added import of log4j in maniifest.
19:18 CIA-22 bioclipse: ospjuth * r5202 /bioclipse2/trunk/plugins/ne​t.bioclipse.biomoby.tests/: Initial import of tests plugin for biomoby.
19:18 CIA-22 bioclipse: ospjuth * r5203 /bioclipse2/trunk/plugins/n​et.bioclipse.biomoby.tests/ (12 files in 8 dirs): Initial import of tests plugin for biomoby.
19:20 CIA-22 bioclipse: ospjuth * r5204 /bioclipse2/trunk/plugins/ (14 files in 4 dirs): Refactored existing tests to test plugin.
19:23 CIA-22 bioclipse: ospjuth * r5205 /bioclipse2/trunk/plugins/n​et.bioclipse.biomoby.tests/ (2 files in 2 dirs): Added stub for testing biomoby central.
19:46 CIA-22 bioclipse: ospjuth * r5206 /bioclipse2/trunk/plugins/net.bioclipse.biomoby​.tests/src/net/bioclipse/biomoby/tests/central/ (3 files): Started on tests for Biomoby central.
19:46 olas bye
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