Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-24

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All times shown according to UTC.

Time Nick Message
07:03 egonw joined #bioclipse
07:06 Julio joined #bioclipse
07:08 Julio left #bioclipse
07:36 CIA-52 bioclipse: egonw * r7387 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: Added missing parameter info
07:36 CIA-52 bioclipse: egonw * r7388 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: More parameter info fixes
07:38 olass joined #bioclipse
07:38 egonw hi olass
07:38 egonw olass: there are some problems left...
07:38 egonw but export seems to work
07:38 olass oh
07:38 egonw jmol.run("minimize") does
07:38 olass saw that you worked late
07:38 egonw yes
07:38 olass atom typing?
07:39 egonw no longer throws an error
07:39 egonw but have to verify details
07:39 olass great
07:39 egonw 3d coord generation is broken
07:39 egonw some HOSE code problem
07:39 egonw trying to work that out...
07:39 egonw please 'svn up' and see how the system holds for you
07:39 egonw note, that I just moved to a src plugin
07:40 egonw because having the .class files in the plugin did not work for me
07:40 egonw no idea how I should work that out
07:40 egonw doing a plugin from Plug-ins gives me a jar :(
07:40 egonw so, that would be back to square one
07:43 Gpox joined #bioclipse
07:43 egonw Gpox: I've working on the cdk plugins
07:43 egonw Gpox: and were not able to work out how to have the .class in the plugin
07:43 egonw in that way, they were not visible outside the plugin :(
07:43 egonw so, now I just have src in the plugin
07:44 egonw which sort of works
07:44 egonw I think
07:44 egonw Gpox: so, please try compiling from the command line
07:44 egonw and let me know about problems you run into
07:44 egonw or other wicked tihngs you find
08:04 rojasm joined #bioclipse
08:09 egonw hi rojasm
08:14 rojasm hi egonw
08:15 edrin joined #bioclipse
08:25 * egonw is installing the Git plugin for Eclipse
08:25 egonw hi edrin
08:25 egonw edrin: we had/ve major problems with the cheminfo feature
08:25 egonw and had no time for working on xws
08:31 edrin hi egonw
08:31 edrin oh, I am sorry to hear that
08:31 edrin will you /could you solve the cheminfo problems?
08:32 CIA-52 bioclipse: egonw * r7389 /bioclipse2/trunk/plugins/net.bioclipse.xom/ (5 files in 2 dirs): Added missing license (closes #16)
08:32 egonw yeah, working on that
08:32 thomasku joined #bioclipse
08:47 jonalv joined #bioclipse
08:49 jonalv hi
08:49 zarah hi jonalv
08:53 egonw weird
08:53 jonalv egonw: It is sad that there is no link back to the bug in the mails though... :(
08:53 egonw well, there is
08:53 egonw ./cgi-bin/bla
08:53 egonw I think I fixed this
08:53 egonw which is when I discovered I do not get any email ... :)
08:54 egonw might you please file a new bug report?
08:54 egonw because email to farmbio seems to work
08:54 egonw then you can tell me if the email now has a full URL
08:58 egonw ah...
08:58 egonw ok, I now understand
08:58 egonw one does not get email if s?he modified the bug h[im|er]self
08:59 jonalv so I can leave it now?
08:59 jonalv oh
08:59 jonalv I guess no then... :)
08:59 egonw no, it works now
08:59 egonw please disregard my question
09:00 egonw yeah, Bugzilla is not that bad :)
09:00 egonw jonalv: btw... the git backup for Pelezilla is online :)
09:00 jonalv nice :)
09:00 egonw and updated every hour :)
09:00 egonw and...
09:00 egonw it does not make commits anymore if nothing has changed
09:01 egonw mysqldump does, by default, add a line 'dump completed on $DATE'...
09:01 egonw so, git would have to commit something every time... but no longer :)
09:01 egonw (grep -v "Dump completed" :)
09:01 jonalv hehe
09:01 jonalv sounds good
09:01 egonw try to do that with ProprietarySuperProduct X
09:03 jonalv hehe
09:05 egonw now, only if I got graphviz to work properly...
09:05 egonw really like to see some graphics in bugzilla :)
09:06 jonalv yea that would be so cool
09:06 jonalv :)
09:09 egonw btw, not sure if you noted, but uploaded UFF.txt-fixed Jmol.jar
09:09 egonw minimize works now
09:10 jonalv egonw: yea I got a mail about you closing that bug... :)
09:10 egonw good :)
09:10 egonw there are email prefs...
09:11 jonalv I think I have heard some people saying that the reporter should close the bug though...
09:11 egonw in great detail you can indicate what email you want, and what not
09:11 egonw jonalv: good point
09:12 egonw http://en.wikipedia.org/wiki/Image​:Bugzilla_Lifecycle_color-aqua.svg
09:12 zarah egonw's link is also http://tinyurl.com/5d7jkd
09:12 jonalv I have been in one of those marathon meetings about Brunn but I am catching up on Bioclipse related mails now...
09:13 egonw I think some CDK might still be broken
09:13 egonw but cannot run Ola tests
09:13 egonw as they require test files that do not seem to be in the repository
09:13 egonw mmm... let's file a bug report :)
09:13 egonw ah, nice
09:14 egonw just noted that Mylyn actually shows bug dependencies :)
09:14 jonalv yup, I haven't checked how complicated dependencies you can make though...
09:20 egonw btwm feel free to reopen the bug if you disagree
09:25 egonw do we have a Bioclipse favion?
09:25 egonw do we have a Bioclipse favicon?
09:25 egonw do we have a Bioclipse favicon.ico?
09:26 * jonalv doesn't know what favion, favicon, or favicon.ico would be...
09:30 shk3 joined #bioclipse
09:31 shk3 egonw: did you look why generateCoordinates doesn't show up in the console?
09:31 egonw mom
09:31 egonw it should
09:32 egonw it has the needed @PublishedMethod annotation
09:32 masak joined #bioclipse
09:33 shk3 ah, i need to update
09:33 shk3 thanks for looking
09:41 egonw shk3: I had to redo the org.openscience.cdk plugins
09:42 egonw so do expects some bumps in the ride...
09:42 egonw please report thoe
09:42 egonw e.g. generated3dcoordinates is currently not working, see #51
09:42 gilleain joined #bioclipse
09:52 shk3 i just found the saveCML method consideres the string it gets as absolute,
09:52 shk3 whereas loadMolecule takes it relative to workspace
09:52 shk3 which one is right?
09:52 shk3 should be uniform, in any case
09:53 egonw loadMolecule
09:53 egonw see bug #31
09:53 egonw @pele 31
09:55 shk3 may i fix this?
09:55 shk3 I feel like
09:56 egonw sure
10:21 shk3 btw, confusing behaviour in console
10:21 shk3 if you right click, the selection disappears
10:21 shk3 still seems to work
10:21 shk3 but confusing
10:24 egonw http://chem-bla-ics.blogspot.com/20​08/10/git-eclipse-integration.html
10:24 zarah egonw's link is also http://tinyurl.com/5vw3y5
10:27 gilleain huh. so the git-plugin is progressing, eh?
10:32 egonw jonalv: your use case: http://www.collaborativedrug.com/pages/intro_video
10:32 zarah egonw's link is also http://tinyurl.com/67tk3c
10:33 egonw company with a good user base!
10:33 egonw never heard of them before
10:33 egonw nice polished GUI
10:33 egonw this is web based, thogh
10:45 egonw gilleain: yes, it seems so :)
10:46 shk3 ok, done so far
10:46 shk3 good code reuse, btw
10:46 shk3 wasn't that great in the old code ;-)
10:46 shk3 question:
10:46 shk3 what to do if the file already exists?
10:47 shk3 right now, it's silently overwritten
10:48 egonw fail
10:48 shk3 throw exception, you mean?
10:48 egonw check the wiki for the proper way of doing this
10:48 jonalv egonw: great movie. Thanks!
10:48 egonw or ask jonalv
10:49 jonalv (jonalv is back from lunch...)
10:49 egonw jonalv: it nicely describes what structuredb must be able to do
10:49 shk3 jonalv: what do you think?
10:49 jonalv egonw: I realised that structuredb should work toghether with Brunn as well
10:49 jonalv shk3: sry I am not sure I understood the question...
10:50 shk3 if a save method in cdk manager is called
10:50 shk3 with an existing file,
10:50 shk3 I throw an excpetion, right?
10:50 shk3 works fine at least
10:50 shk3 message of exception is printed in console
10:51 jonalv shk3: yea that works
10:51 jonalv But I can't help to get the feeling that you want to be able to just overwirtie somehow...
10:53 shk3 yes indeeed
10:53 shk3 add a boolean parameter?
10:53 shk3 force or so?
10:54 jonalv gilleain: ping
10:54 gilleain pong
10:55 jonalv gilleain: regarding the mail thread Rich progress manager
10:55 gilleain Uh-huh?
10:55 jonalv gilleain: is the method that takes the progressmonitor situated on a manager?
10:56 jonalv if so you can do the "injection" using AOP at the method call to the manager
10:56 jonalv and not swap progressmoniotr but decorate the original progressmonitor
10:56 gilleain Hmmm. It's on a job.
10:57 gilleain Not a manager.
10:57 jonalv http://en.wikipedia.org/wiki/Decorator_pattern
10:57 zarah jonalv's link is also http://tinyurl.com/r6gcx
10:57 jonalv gilleain: why is it not on a manager? Is it not for the Bioclipse 2 project?
10:57 gilleain It is for bc2, but it's a compute job.
10:58 * jonalv is starting to get worried now
10:58 gilleain I thought you might.
10:58 jonalv what is a "compute job"?
10:58 gilleain Well there's this net.bc.compute plugin.
10:58 jonalv I have a feeling we are solving the same problem at two different locations now...
10:58 gilleain I know what you mean.
10:59 jonalv right... Let me put it like this: If you do it the Bioclipse 2 way I can help you. If you don't I can not help you... :)
11:00 gilleain Well, the net.bc.core.Job is meant for Actions, right?
11:00 shk3 can I get the help text in the manager (in @published) on the console?
11:00 jonalv shk3: help managaer.method
11:00 jonalv or man manager.method
11:01 gilleain I am doing something more than just an Action.
11:01 gilleain (I think).
11:01 jonalv gilleain: hang on (I am checking out what net.bc.core.Job is...)
11:02 jonalv gilleain: please exlpain what you ae doing :)
11:02 gilleain Okay, it breaks down like this:
11:03 gilleain A long running Job (a Seneca CASE Job) is passed to the JobManager
11:03 gilleain Which schedules and runs it.
11:03 gilleain The Seneca plugin uses the compute plugin to do wizard stuff, and menu items.
11:04 jonalv gilleain: net.bc.core.jobs contains olas old job implementiation for Bioclipse which I think should be consdiered deprecated when I get things sorted out... :)
11:04 gilleain Right.
11:04 gilleain I see.
11:04 shk3 great
11:04 jonalv Okey I envisions things like this
11:04 jonalv Something calls the manager method calculateLongCalculation
11:04 jonalv probably a job
11:05 jonalv no sry
11:05 jonalv probably a gui action
11:05 jonalv zarah: slap jonalv
11:05 * zarah karate-chops jonalv into two equally sized halves
11:05 jonalv that method is annotated with @Job annotation
11:06 gilleain Okey. So can I ask : why are we not using Eclipse's Job management mechanism? So that we can use AOP?
11:06 jonalv thus a job is created and sheduled which calls that method inside the job
11:06 jonalv gilleain: we are using Eclipse's job api under the hood
11:06 gilleain Ahh.
11:06 gilleain Cool.
11:07 gilleain So I can use your suggestion of decorating the ProgressMonitor.
11:07 gilleain Also; you don't see any difference between long-running Jobs and short 'Actions'?
11:08 jonalv there is a variant of the @Job annotated mdethod that also takes a progressmonitor (that's not the one that actually got called) and the monitor can be decorated using AOP
11:08 gilleain Great.
11:08 jonalv I only differentiate between @jobs which are runned asyncronilsy and can not return and standard mangaer methods that can return
11:08 gilleain And they are blocking, right?
11:09 jonalv the jobs are sheduled and run in completely different thread
11:09 gilleain Anyway, I'll leave further questions until I have tried it out, to get it working. Thanks, jonalv++
11:10 jonalv gilleain: for now I think they should block the entire workspace so that only one job can run simultaneosly but that could probably be specified for each manager method perhaps using annotations too
11:10 jonalv gilleain: but, this is not fully functional...
11:10 gilleain Ah, okay.
11:10 gilleain I can wait for that - I just want to see it running! :)
11:11 gilleain (my new ProgressMonitor, that is)
11:11 jonalv I started to implement it for structuredb and it was sort of working for importing molecules from sdf before I started the big structuredb refactoring
11:11 gilleain Yes, I saw some of that stuff when I was searching for the string "Progress" in all plugins.
11:12 jonalv My plan was to get his working when structuredb needed it...
11:13 jonalv but egonw was asking about it too and I also know olas needs it so perhaps I will have to do something about it when I get back from my vacation in two weeks from now...
11:15 * jonalv is gonna try out the cdk.save functions now since shk3 has marked the bug as fixed... :)
11:16 gilleain Have a good vacation, by the way!
11:17 jonalv yea that I plan. I will not shoe up on #Bioclipse but I might answer mails.... :)
11:18 egonw at what time are you going offline?
11:19 jonalv egonw: soonish... :)
11:19 masak jonalv: haveagoodvacation!
11:19 jonalv masak: hi fancy seeing you in here :)
11:20 masak indeed.
11:20 masak today's the day.
11:20 jonalv http://www.youtube.com/watch?v=xMm7gqowAO4
11:20 zarah jonalv's link is also http://tinyurl.com/yqtdcp
11:21 jonalv :)
11:21 masak jonalv: was that entirely necessary?
11:21 jonalv masak: LOL
11:22 egonw wow...
11:22 egonw what a noise
11:22 gilleain hmm, that doesn't mix well with the wu-tang.
11:22 gilleain but the visuals are nice...
11:22 egonw with roxette is OK
11:22 masak it doesn't mix well with my lunch.
11:22 egonw which reminds me to hit the next button
11:22 gilleain masak: :)
11:23 shk3 do we have manger methods for gui stuff,
11:23 shk3 like opening a file
11:23 shk3 or a molecule in jcp?
11:23 egonw ui.open
11:25 gilleain It might be a bit soon, but it would be nice to have a place to store bioclipse scripts.
11:25 gilleain On the wiki, perhaps, like :
11:25 jonalv uhm what's wrong with cdk.saveMDLMolfile( (cdk.fromSmiles("CCC"), "/Virtual/test.mdl" )?
11:25 gilleain http://pymolwiki.org/index.​php/Category:Script_Library
11:25 zarah gilleain's link is also http://tinyurl.com/5zecp3
11:25 shk3 looks ok
11:25 shk3 no
11:25 shk3 one ( too much
11:26 jonalv gilleain: egonw is using some git thing for that...
11:26 jonalv shk3: thanks
11:26 egonw gist
11:26 shk3 without the ( works great
11:26 gilleain egonw using git for something! shock! :)
11:26 egonw gits.github.com
11:26 egonw gist.github.com
11:27 gilleain ohh.
11:27 gilleain Now I remember you posting links to things on there.
11:27 shk3 when I try help something the prompt doesn't show up
11:27 shk3 and console seems blocked
11:27 egonw http://delicious.com/search?p=gist+bioclipse
11:28 zarah egonw's link is also http://tinyurl.com/5dan3n
11:28 gilleain Hmm. So indexed-by-search. S'okay.
11:29 shk3 can somebody confirm or reject my observation about the help?
11:29 egonw better link:
11:29 egonw http://delicious.com/tag/bioclipse+gist
11:29 zarah egonw's link is also http://tinyurl.com/5gqjet
11:30 jonalv shk3: Are you really running latest version from svn?
11:30 shk3 think so
11:30 shk3 but I should perhaps update everything
11:30 shk3 hope that doesn't break something...
11:30 jonalv shk3: yea because I think masak fixed soemthing like this...
11:31 masak I did.
11:31 shk3 ah ok
11:31 shk3 updating
11:32 masak the console isn't really a console... it's an abstraction on top of a normal text widget
11:32 masak sometimes that abstraction breaks.
11:32 masak I'm sure there are better ways to write a console. there's a vt100 project for Eclipse that I'd like to peruse further.
11:34 gilleain I hate to mention it, but I see that on windows we still have the newline problem...
11:34 gilleain Would it be helpful if I tried to fix this myself?
11:34 egonw did someone do this Bioclipse.NEW_LINE static String already?
11:35 gilleain Or am I likely to break things :)
11:35 CIA-52 bioclipse: egonw * r7393 /bioclipse2/trunk/plugins/ (18 files in 14 dirs): Smiles -> SMILES (closes #53)
11:35 gilleain Also, paths.
11:35 jonalv egonw: I am pretty sure that Bioclipse.NEW_LINE is one totally the wrong abstraction level. There must be an Eclispe solution or even better a java solution for this...
11:36 egonw no, Java only has this getProperty
11:36 egonw which you can set to the static Bioclipse.NEW_LINE when the class is initialized
11:37 egonw or whatever root class any class in any plugin has always access too
11:37 gilleain System.getProperty("line.separator"), specfically.
11:38 CIA-52 bioclipse: egonw * r7394 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): JMol -> Jmol
11:39 gilleain and "path.separator", is also relevant. At least mac doesn't use "::" anymore...
11:39 Juli2 joined #bioclipse
11:39 egonw hi Juli2
11:41 Juli2 left #bioclipse
11:42 egonw i've seen several jul*'s online now...
11:43 egonw I fear it might be a spam bot
11:46 jonalv egonw: the ip is Leiden University sounds familiar...
11:50 masak how come it left so quickly?
11:54 egonw ah...
11:55 egonw rojasm: didn't you have a new student?
11:56 jonalv Well I am heading out now. You all try to cope without me now and don't do anything I wouldn't do! ;)
11:56 masak jonalv: !
11:56 masak haveagoodvacation!
11:56 jonalv :)
11:57 jonalv quit 'poof'
11:57 masak not quite.
12:04 rojasm egonw
12:04 rojasm not exactly!
12:04 rojasm There are a new phD
12:04 rojasm for Bioinformatics
12:04 gilleain joined #bioclipse
12:05 gilleain left #bioclipse
12:05 gilleain joined #bioclipse
12:05 rojasm that is Julio who is contracted by TNO. But he sits here
12:06 egonw ha, ok, I was close :)
12:07 egonw jonalv++ for checking the ip
12:24 edrin egonw: question: if I have an agar plate, and I add some (20 microliter of 20 ml) hydrophobic sesquiterpenalcohol to it, do you think the diffusion of a chemical gradient (soluble in water) can be altered ?
12:24 masak hm, I like the JMol -> Jmol change
12:24 egonw no idea
12:24 masak but I actually preder Smiles to SMILES
12:25 egonw yeah, some kick on TAB fixes ...
12:27 edrin you see here: http://ec.asm.org/cgi/content/full/7/10/1661/F10
12:27 edrin something like this i want to do. i wanted the not grown area to become larger when adding this alcohol. however the are became smaller ...
12:27 zarah edrin's link is also http://tinyurl.com/66nwwa
12:28 edrin on this E strip there is a chemical in. and it creates a gradient ...
12:32 egonw really, no clue
12:33 edrin ok
13:05 CIA-52 bioclipse: shk3 * r7395 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): added a structure match
13:08 masak zarah: restart, please
13:10 zarah joined #bioclipse
13:10 egonw masak: feature request:
13:10 egonw @pelezilla
13:10 egonw taking one argument
13:10 egonw and just send it of to:
13:11 egonw http://pele.farmbio.uu.se/cgi-bin/b​ugzilla/buglist.cgi?quicksearch=bla
13:11 zarah egonw's link is also http://tinyurl.com/5kkjjq
13:11 masak egonw: will do
13:11 masak easiest way is to just paste the URL to the channel, as you just did
13:12 masak possibly in the form of a tinyurl
13:12 egonw yeah, was actually thinking of a bit more advanced
13:12 masak the more fancy way would be to scrape the page and return a list of the matching bugs
13:12 egonw was just looking at how to get buglist.cgi spit XML
13:12 masak XML would help, yes
13:13 masak but even HTML scraping is entirely within the bounds of possible things within Perl
13:13 gilleain what's this :? http://pele.farmbio.uu.se/cgi-​bin/bugzilla/show_bug.cgi?id=1
13:13 zarah gilleain's link is also http://tinyurl.com/55k8wf
13:13 masak egonw: how do you envision the result list spat out by zara?
13:13 masak s/zara/zarah/
13:13 egonw http://pele.farmbio.uu.se/cgi-bin/bugzilla/bugli​st.cgi?query_format=specific&content=SMILES
13:13 zarah egonw's link is also http://tinyurl.com/64zhp7
13:13 egonw yes, list of bugs
13:13 masak gilleain: it's a ticket without an observable
13:13 egonw top two/three or so
13:14 masak egonw: yes, but how exactly? just the names?
13:14 masak urls? descriptions?
13:14 egonw http://pele.farmbio.uu.se/cgi-bin/bugzilla​/buglist.cgi?content=SMILES&ctype=atom
13:14 zarah egonw's link is also http://tinyurl.com/6d6xrp
13:14 masak egonw: dz
13:14 egonw that's XML enough, I'd say :)
13:15 masak it sure is
13:15 shk3 we don't have a possibility to open something which is not a file right now, do we?
13:15 masak egonw: I suppose a list of ticket titles and tinyurls would be most helpful.
13:15 egonw shk3: we were talking about that yesterday...
13:16 egonw no, not now, but planned
13:16 egonw masak: yes
13:16 shk3 I think that's needed for many features
13:16 egonw shk3: /Virtual/ ?
13:16 egonw that should work
13:16 shk3 yes, that's a workaround
13:17 egonw Gpox: around?
13:17 Gpox yes
13:17 egonw oh, you are :)
13:17 egonw Gpox: please test compiling from the command line with the current trunk
13:18 egonw I'll set up a JCPPerspective branch now...
13:18 egonw and commit some patches there...
13:18 egonw to have a CDK1.2 only JChemPaint environment
13:18 egonw for BC2
13:18 egonw shk3: you will work on an applet version?
13:19 egonw Gpox: but, while I have bc.cdk.jchempaint in the Feature, the JChemPaintEditor does not show up as 'Other' editor... :(
13:21 Gpox thats odd
13:21 egonw yeah, don't see any errors...
13:22 egonw doing something wrong...
13:22 masak zarah: reboot, dear
13:22 zarah joined #bioclipse
13:23 masak @pelezilla SMILES
13:23 zarah masak: http://pele.farmbio.uu.se/cgi-bin/b​ugzilla/buglist.cgi?content=SMILES
13:23 masak that's the easy version :)
13:23 egonw hehehe
13:23 masak the advanced version will have to come later, when I have the tuits
13:23 egonw sure, no rush
13:23 masak it's a breeze to develop zarah, that's what makes it so fun
13:23 masak you're a smart girl, zarah
13:24 zarah masak: Flattery will get you anywhere.
13:24 egonw :)
13:24 shk3 egonw: would work on the applet
13:25 shk3 I think it is important to have it share things with the swing version as much as possible
13:25 egonw well, that's what the whole design is about :)
13:25 CIA-52 bioclipse: egonw * r7399 /bioclipse2/branches/jchempaintPerspective/: Branch for a JChemPaint Perspective, using the new experimental JCP 3.0 code.
13:25 masak haha, at another channel someone said "change 37 GBP to NZD" and a bot answered "I'm bored of you doing this, fuck off and use xe.com yourself"
13:25 gilleain :)
13:26 gilleain Rebellious bots++
13:26 masak (bots with attitude)++
13:26 shk3 so the code for the swing stuff is in the org.os.cdk.jcp project?
13:26 shk3 TestEditor is the jcp app?
13:26 egonw yes
13:27 shk3 so I should create a package there?
13:28 shk3 shouldn't we rename testeditor, btw?
13:29 egonw yes, please go ahead
13:29 * egonw is really getting the hang of git and git-svn development :)
13:31 CIA-52 bioclipse: egonw * r7400 /bioclipse2/branches/jchempaintPerspective/pl​ugins/net.bioclipse.cdk.jchempaint.business/ (18 files in 8 dirs): Copied template for adding the JChemPaint manager
13:31 CIA-52 bioclipse: egonw * r7401 /bioclipse2/branches/jchempaintPerspective/pl​ugins/net.bioclipse.cdk.jchempaint.business/ (15 files in 8 dirs): Tuned example code for JCP manager
13:31 CIA-52 bioclipse: egonw * r7402 /bioclipse2/branches/jchempaintPerspective/plugin​s/net.bioclipse.cdk.jchempaint.business/src/net/b​ioclipse/cdk/jchempaint/business/Activator.java: Fixed plugin ID
13:31 CIA-52 bioclipse: egonw * r7404 /bioclipse2/branches/jchempaintPerspective/ (5 files in 4 dirs): Now actually implemented a method
13:31 CIA-52 bioclipse: egonw * r7403 /bioclipse2/branches/jchempaintPerspect​ive/plugins/net.bioclipse.cdk.jchempain​t.business/src/net/bioclipse/cdk/jchemp​aint/business/JChemPaintManager.java: Use the 'jcp' namespace
13:31 CIA-52 bioclipse: egonw * r7405 /bioclipse2/branches/jchempaintPerspective/pl​ugins/net.bioclipse.cdk.jchempaint.business/ (2 files in 2 dirs): Found the proper way of providing user feedback.
13:31 CIA-52 bioclipse: egonw * r7406 /bioclipse2/branches/jchempaintPerspective/​features/net.bioclipse.jchempaint_feature/ (. .project build.properties feature.properties feature.xml): Added a JChemPaint feature, without CDK1.0 stuff, to have a clean environment in BC2 to work JCP3
13:33 shk3 egonw: I am just talking to gillieaiaeen
13:33 shk3 it seems the renderer is not yet ready
13:33 egonw umm... no
13:33 egonw did I say that?
13:33 shk3 I doubt if we can work on the app without that being sort of stable
13:33 shk3 we found trunk still have nilsouts stuff
13:34 egonw trunk of what?
13:34 shk3 cdk
13:34 egonw yeah, the new stuff is in branches
13:34 egonw gilleain can tell you which
13:35 shk3 hm, so i would check out the branch and work on org.os.cdk.jcp project using that?
13:35 egonw yes
13:35 gilleain well, the closest I have is (mine) :
13:35 gilleain http://gilleain.blogspot.com/2008/10/​font-management-and-glyphvectors.html
13:35 zarah gilleain's link is also http://tinyurl.com/5uqr9c
13:36 gilleain Or Gpox's:
13:36 gilleain http://gilleain.blogspot.com/2008/10/​font-management-and-glyphvectors.html
13:36 zarah gilleain's link is also http://tinyurl.com/5uqr9c
13:36 egonw umm ??
13:36 gilleain (or, rather, Gpox's visitor architecture)
13:36 gilleain Oh, wait.
13:36 gilleain That's the same link, isn't it.
13:36 gilleain sorry:
13:37 gilleain http://gilleain.blogspot.com/2008/10/shadows.html
13:37 zarah gilleain's link is also http://tinyurl.com/68nwrd
14:00 shk3 egonw: is the date for a jcp meeting in uppsala fixed?
14:00 egonw yes
14:00 shk3 when?
14:02 shk3 I mean: what's the date?
14:03 egonw 20-21
14:03 egonw will email it around
14:04 egonw expecting we start 20th early
14:04 egonw nov
14:04 shk3 ok
14:05 shk3 I still get the impression it's better to wait with starting the application
14:05 shk3 perhaps the meeting would be best for finalizing the renderer etc. and merge it to trunk
14:05 shk3 then start writing apps?
14:05 egonw the idea is to actually see if the design holds when making an application
14:06 egonw don
14:06 egonw don't worry about nice GUIs
14:06 egonw just embedded as applet
14:06 egonw so that we can test of mouse events get picked up
14:06 egonw and renderings get properly updated
14:06 gilleain uh-huh.
14:07 gilleain so, it would be code to test the mouse-relay/wiimote stuff?
14:07 shk3 but that assumes the renderer to exists
14:07 egonw not sure if Wii runs applets...
14:07 gilleain :)
14:07 egonw but hooking up a Wii mote with my laptop is possible too...
14:08 egonw will think about how to create 'mouse' events...
14:08 egonw in Java, that is
14:10 egonw http://code.google.com/p/wiiusej/
14:10 zarah egonw's link is also http://tinyurl.com/5fnbf8
14:10 egonw mmmm... I found myself something to do :)
14:11 egonw http://www.youtube.com/watch?v=mgTwWzhTVEY
14:11 zarah egonw's link is also http://tinyurl.com/5pcfvl
14:12 gilleain some thing ELSE to do...
14:14 shk3 so you (egonw) think i should go ahead building an applet?
14:14 egonw I think that would be good for the progress, yes
14:14 egonw I won't think what you *should* do...
14:14 egonw but I'd certainly welcome if you would
14:15 egonw +it
14:19 gilleain Okay, so shk3 and I have agreed on a plan.
14:19 egonw a cunning one?
14:19 gilleain yes
14:19 gilleain I will make an interface
14:19 egonw go on
14:19 gilleain for generating intermediate rendering objects from chemobjects
14:20 gilleain so that, if things change, the applet will still work.
14:20 gilleain the basic flow would be :
14:20 egonw make sure to synchronize with Gpox
14:20 gilleain sure
14:20 egonw Gpox: still around?
14:20 Gpox yes
14:20 egonw I'll actually go for some running in about 10 minutes
14:21 gilleain Hey, Gpox, how's it going?
14:22 Gpox egonw: I found a problem with the cdk plugins
14:23 egonw ok, tell me (or file a bug report)
14:23 Gpox if i change  "Bundle-Classpath: jar/jniinchi-0.4.jar"  to "Bundle-ClassPath: jar/jniinchi-0.4.jar" it works
14:23 egonw crap
14:24 egonw that should say:
14:24 egonw Require-Bundle: net.sf.jniinchi
14:24 egonw or is this for the net.sf.jniinchi plugin?
14:24 egonw btw, I don't see any difference
14:25 Gpox p vs. P in ClassPath
14:25 Gpox it is the plugins in cdk-external
14:25 Gpox it took a while for me to spot it
14:26 egonw ah, indeed ...
14:26 egonw ok, hang on
14:27 egonw ok, that applies to all cdk-externals/*
14:28 egonw but not org.openscience.cdk.*
14:28 egonw correct?
14:29 egonw I'm fixing those
14:29 Gpox the org.openscience.cdk is source now so i compile them too
14:29 egonw yes, good... does that work?
14:29 egonw shall I commit those ClassPath fixes?
14:29 Gpox yes
14:31 Gpox and then i have to figure out how to get them into my local git branch
14:37 egonw commited
14:38 Gpox ok good, time to learn some more git
14:38 egonw what is your set up?
14:38 egonw remember that 'git rebase' and 'git svn rebase' are your friends...
14:40 Gpox yeah I got a branch for my building edits and use rebase to keep those on top
14:41 egonw good :)
14:47 egonw OK, found a bug in org.openscience.cdk.core
14:47 egonw the isotope.xml was not copied correctly...
14:47 egonw :(
14:52 egonw OK, time to log out
14:52 egonw bye all!
14:53 gilleain bye
14:54 rojasm I try to update my bioclipse2!
14:54 rojasm and I found that net.bioclipse.xom is not a java project. Should I commit with the patch
14:55 gilleain what do you mean "not a java project"?
14:55 gilleain It's a bioclipse2 plugin...
14:56 rojasm jetzt but for me when I downloaded the .project file don't specify that it is a java project
14:57 rojasm or is it only for me?
15:00 gilleain hmmm. not for moe.
15:00 gilleain s/moe/me/
15:01 shk3 it works for me
15:01 rojasm ok! I try to replace it again with the repository
15:01 shk3 is there a difference between project types?
15:01 shk3 I thought it's just if you create a a project of a certain type,
15:01 shk3 some files get included or not.
15:02 shk3 but once it's there, it has no type (my understanding, proof me wrong).
15:02 rojasm strange now it is included  with the specifications
15:02 rojasm mmm
15:05 rojasm oder question?
15:05 rojasm do I need the /cdk-externals/trunk? is it the same like svn cdk project?
15:07 gilleain hmmm. not sure. what repository are you referring to?
15:08 gilleain oh, right now I see it
15:09 gilleain yes, you need all of cdk-externals/* AND cdk-externals/trunk/*
15:09 gilleain so, the org.jama, net.sf.jiinchi, etc are the third-party libs
15:10 shk3 can anybody tell me something about the job stuff?
15:10 shk3 I added @Job
15:10 gilleain and the trunk/org.openscience.cdk.* plugins are the cdk stuff.
15:10 shk3 to my manager method
15:10 shk3 but it seems that's not enough
15:11 shk3 there is this page: http://wiki.bioclipse.net/index.p​hp?title=Long_running_operations on the wiki
15:11 zarah shk3's link is also http://tinyurl.com/5gd3pf
15:11 shk3 do I need to do this?
15:11 shk3 in the implementation
15:11 shk3 to have it run as a job
15:12 gilleain this is what I was discussing with jonalv earlier.
15:12 gilleain unfortunately he has now gone on holiday for 2 weeks :)
15:12 shk3 and the result ;-)
15:12 shk3 ?
15:13 gilleain backlog?
15:14 gilleain all I understood was that I should be using the bioclipse way, rather than the eclipse way.
15:14 shk3 @Jobs must be void?
15:14 gilleain what the bioclipse way is, exactly, I am not yet sure.
15:14 gilleain Yes, the return type should be void.
15:14 shk3 hm, ok
15:16 gilleain http://wiki.bioclipse.net/index.php?ti​tle=How_to_run_manager_methods_in_jobs
15:16 zarah gilleain's link is also http://tinyurl.com/3sc3vo
15:16 gilleain did you see that?
15:17 shk3 no
15:18 gilleain Well, see that then.
15:18 gilleain :)
15:23 CIA-52 bioclipse: carl_masak * r7409 /bot/trunk/zarah.pl: [zarah] refined whispered command match syntax
15:42 olass joined #bioclipse
15:42 olass hi
15:42 zarah hi olass
15:43 masak hi olass
15:43 olass hi masak
15:43 olass anything happenede today?
15:43 * olass has been writing all day
15:43 edrin hi olass
15:44 edrin what did you write?
15:44 CIA-52 bioclipse: shk3 * r7410 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): also fixed the saveasmdl2
15:44 olass hi
15:44 zarah hi olass
15:44 olass helping out on a paper
15:44 olass so many things I have promised to do before my vaccations
15:46 olass must run off now
15:46 olass just wanted to check in and say hi
15:46 olass most ppl seems to have left already
15:46 olass have a nice weekend everyone
15:46 olass I might look in on sunday for some work
15:46 olass bye for now!
15:49 CIA-52 bioclipse: shk3 * r7411 /bioclipse2/trunk/plugins/net.bio​clipse.cml/src/net/bioclipse/cml/ (3 files in 2 dirs): made it a job and added a method for scripting
15:50 CIA-52 bioclipse: shk3 * r7412 /bioclipse2/trunk/plugins/net.bioclipse.cml/src/ne​t/bioclipse/cml/managers/IValidateCMLManager.java: made it a job and added a method for scripting
15:53 masak @tell egonw I made a stab at implementing the list functionality for @pelezilla, but I'm unable to install XML::LibXML on pele. maybe you could give it a try?
15:53 zarah Consider it noted.
15:53 masak botsnack
15:53 zarah ;)
15:55 masak time to head home.
15:56 masak have a nice weekend, everyone!
15:56 gilleain you too.
16:18 shk3 joined #bioclipse
17:51 rojasm joined #bioclipse
18:06 edrin left #bioclipse

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