Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-03-31

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All times shown according to UTC.

Time Nick Message
05:25 egonw joined #bioclipse
06:27 Gpox joined #bioclipse
06:28 Gpox joined #bioclipse
06:54 CIA-58 bioclipse: goglepox * r9508 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Removed tabs and trailing spaces
07:15 egonw joined #bioclipse
07:15 olass joined #bioclipse
07:35 rojasm joined #bioclipse
07:42 olass moin
07:42 zarah hello olass, you fantastic person you
07:42 olass @botsnack
07:42 zarah ;)
07:48 jonalv joined #bioclipse
08:14 masak joined #bioclipse
08:54 egonw brb
09:08 egonw joined #bioclipse
09:09 CIA-58 bioclipse: jonalv * r9509 /bioclipse2/trunk/plugins/net.bioclipse​.jmol/src/net/bioclipse/jmol/business/ (IJmolManager.java JmolManager.java): Added method jmol.print that should write to the jmol console for masak++ to implement.
09:09 masak bah, premature karma. :P
09:12 jonalv masak: yep feel the pressure...
09:13 masak aye. they call me Mr Newton for this very reason.
09:13 masak or was it Mr Pascal?
09:13 egonw I think we typically call you Mr Carl
09:14 egonw but I forget my name sometimes too
09:16 masak egonw: very funny... :)
09:16 egonw ha, you should have seen my comment
09:16 egonw [11:16:15] <egonw> that was clearly a bot
09:16 masak I see it.
09:17 masak reading the logs.
09:17 egonw masak++
09:17 masak :P
09:17 egonw now, please stop distracting me
09:17 masak egonw: OK, WE WON'T DISTRACT THE CHEMIST ANY MORE.
09:30 masak jonalv: here you go.
09:31 masak r9510.
09:31 CIA-58 bioclipse: carl_masak * r9510 /bioclipse2/trunk/plugins/net.bioclipse.jmol/sr​c/net/bioclipse/jmol/business/JmolManager.java: [JmolManager] implemented print-to-console
10:03 * masak wins a small battle in the war against BioclipseException
10:03 maclean joined #bioclipse
10:03 masak maclean: OH HAI
10:03 egonw hi maclean
10:04 maclean hi
10:04 zarah oh hai maclean
10:05 CIA-58 bioclipse: ospjuth * r9511 /bioclipse2/trunk/plugins/net.bioc​lipse.chemoinformatics/plugin.xml: Added submenus for Generate 2D, Generate 3D, and Generate Conformers.
10:06 olass hi maclean
10:06 CIA-58 bioclipse: ospjuth * r9512 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui/plugin.xml: Made cdk.ui use new submenus for create/recreate 2D/3D actions.
10:06 maclean hello
10:06 zarah ni hao maclean
10:06 maclean yes, yes, hello zarah, also.
10:07 CIA-58 bioclipse: ospjuth * r9513 /bioclipse2/trunk/plugins/net.bioclipse​.balloon.business/icons/balloon16.gif: Added an icon for balloon.
10:08 CIA-58 bioclipse: ospjuth * r9514 /bioclipse2/trunk/plugins/net​.bioclipse.balloon.business/ (5 files in 3 dirs): Renamed gen3Dhandler, added genConformerHandler, use new balloon icon and new submenus for generate 3D/Conformations.
10:08 CIA-58 bioclipse: carl_masak * r9515 /bioclipse2/trunk/plugins/net.bioclipse.sc​ripting.ui/src/net/bioclipse/scripting/ui/ (business/JsConsoleManager.java views/JsConsoleView.java):
10:08 CIA-58 bioclipse: [JsConsoleView] put exception-extracting code in method
10:08 CIA-58 bioclipse: Removed the duplicated code in JsConsoleManager, making it call the new method.
10:11 maclean olass : is the balloon conformer-generation stuff ready to try out?
10:11 * maclean is curious
10:11 olass well, not 100%
10:11 olass well, no, I'd say
10:11 olass it works on mac
10:11 olass for generating 3D
10:11 maclean lucky for me
10:11 olass you can try it
10:11 maclean ok
10:12 olass right-click a mol with 2D -> generate 3D > Balloon
10:12 maclean I was just looking at the website
10:12 olass that creates an new file
10:12 masak lunch &
10:12 olass masak: why the & ?
10:12 jonalv lunch&
10:12 maclean backgrounds the job
10:12 olass why eat in the background?
10:13 * jonalv goes for sushi, mmmm
10:43 maclean hmmm
10:44 maclean olass: I downloaded the balloon feature (and its plugins), and set it up to use the feature, but I don't get a 'Balloon' sub-menu under 'generate 3D'
10:44 maclean I can generate 3D, but I guess it's using cdk?
10:45 olass have you updated everything?
10:45 egonw nope
10:45 egonw oh
10:45 olass egonw: nope?
10:45 egonw maclean: balloon is not using the CDK
10:45 egonw but maybe the 'generated 3D' you used is...
10:45 maclean olass: no, I haven't - will do
10:45 maclean egonw : I know
10:45 olass egonw: you really beg to be disturbed today? ;)
10:46 egonw yes, please, so that I can complain about it again
10:46 olass lol
10:46 maclean :)
10:46 egonw now, shut up please :)
10:47 olass maclean: please report if it works
10:48 maclean okay
10:48 maclean updating would be so much nicer if I didn't have to guess which plugins have changed :/
10:50 egonw mmm...
10:50 egonw Ola...
10:51 egonw each update could feature an update page, highlighting the updates
10:51 maclean or we could use buckminster?
10:51 egonw like installing some Eclipse features will force showing the workspace font page again...
10:52 egonw maclean: please explain
10:52 maclean I think that's what it's for
10:52 egonw URL?
10:52 maclean http://www.eclipse.org/buckminster/
10:52 zarah maclean's link is also http://tinyurl.com/2zy27g
10:53 maclean anyway, I'm distracting you - back to work!
10:53 olass buckminser would be nice
10:53 olass just no time :(
10:59 maclean hmm. after updating the cdk.jchempaint plugins, I no longer get the 'generate 3D' in the right-click context menu. great.
11:02 maclean it's probably due to partial updates, though.
11:02 maclean yay! it was
11:03 maclean olass : it does work.
11:03 olass good
11:06 maclean I wonder what happens if you give it a polypeptide :)
11:07 egonw or crambin
11:13 maclean hmm. I don't get balloon in the menu for files created by jchempaint.
11:13 maclean oh, no it's for .cml files.
11:15 olass balloon only accepts sdf and mol
11:16 olass for any other format it needs conversion and a tmep file
11:16 olass temp
11:16 maclean of course, yes.
11:16 olass this is not yet available
11:16 olass I might do it some day
11:16 olass but really, this is balloon as is
11:16 maclean fair enough
11:17 edrin joined #bioclipse
11:17 edrin hi
11:17 zarah privet edrin
11:21 CIA-58 bioclipse: ospjuth * r9516 /bioclipse2/trunk/plugins/net​.bioclipse.balloon.business/ (5 files in 4 dirs): Implemented conformer generation with a simple ugly dialog.
11:25 maclean oh, and olass : I get a null pointer exception if I try to generate 3d on a file in /Virtual.
11:26 olass hmm
11:26 olass thought I fixed that
11:26 edrin hm
11:26 olass please update andt try to generate conformers
11:26 edrin i thought there is no virtual anymore
11:26 maclean am doing :)
11:26 olass edrin: there is
11:26 olass however schedules for removal
11:26 olass however scheduled for removal
11:27 edrin ok
11:27 olass will be replaced by a file-based temp dir
11:27 olass in time
11:27 olass post 2.0
11:27 maclean heh. it does work, but you get an sdf file, which shows as multiple 2D 'conformations' :)
11:27 olass yes
11:28 olass what is wrong with this?
11:28 olass oh
11:28 olass 2D
11:28 olass yes
11:28 olass there is a bug
11:28 maclean well it does give the energies
11:28 olass jmol should be able to read these files
11:28 olass rename to .mol
11:28 olass then it opens in jmol
11:28 maclean ah ok
11:29 olass works?
11:29 maclean except that rename doesnt work :(
11:29 olass sigh
11:29 olass press F2
11:29 maclean ahh
11:29 olass rename is a known bug
11:29 masak maclean: I have a ticket for that.
11:29 olass :(
11:29 masak maclean: will look into it when time permits.
11:29 maclean ok. sorry, didn't know
11:29 olass how could you :)
11:30 maclean renaming it works -=> opens in Jmol
11:31 edrin olass: what is the release plain for bc2?
11:31 olass we need a status meeting for that
11:31 olass I am home ill today :(
11:31 olass was hoping to have that sorted out today
11:32 olass but will probably be tomorrow or thursday
11:32 olass depending on my status
11:32 * maclean is also home, ill
11:32 olass 2 lost souls
11:32 jonalv olass: I guess we could do a skype conferense today if you feel up for that...
11:32 olass let's aim for tomorrow
11:33 olass I see no urge for it today
11:34 edrin sure
11:34 maclean the jmol outline could really do with a 'collapse all' button.
11:35 jonalv maclean: what would that do?
11:35 jonalv oh for the tree?
11:35 jonalv yea...
11:35 maclean yup
11:35 jonalv patches welcome :)
11:35 maclean when you have multiple models, for example
11:35 maclean :0
11:36 jonalv The way the outline handles multiple models could be better as welll
11:36 maclean s/:O/:)/
11:36 maclean oh?
11:36 CIA-58 bioclipse: ospjuth * r9517 /bioclipse2/trunk/plugins/n​et.bioclipse.balloon.linux/ (2 files in 2 dirs): Implemented balloon for linux. No way to test it however, will need help debugging this.
11:36 jonalv That was the reason I started fiddling around with Jmol but I have not gotten there yet...
11:37 maclean what would it look like?
11:37 jonalv Checkboxes for changing what is visible
11:37 olass like pymol?
11:37 CIA-58 bioclipse: ospjuth * r9518 /bioclipse2/trunk/plugins/n​et.bioclipse.balloon.win32/ (2 files in 2 dirs): Implemented balloon for windows. No way to test it however, will need help debugging this.
11:37 maclean ah, okay, that would be cool
11:38 * jonalv has not looked at Pymol yet :)
11:38 egonw jonalv++
11:38 egonw nice idea
11:38 olass jonalv: please do asap
11:38 maclean I love pymol, but some of its gui stuff is a bit icky
11:38 jonalv egonw, olass: I am not there yet and I don't think it's as easy as it looks...
11:38 olass ack
11:38 maclean lots of fiddly menus
11:39 jonalv I doubt Jmol has a VisibleChangedListener for example...
11:39 maclean but checkboxes = yes
11:42 jonalv we need to make the move to git soon!
11:42 olass post 2.0
11:43 olass jonalv: you can always request things from the jmol community
11:43 jonalv olass: yea I guess there might be something like that...
11:43 jonalv @pz
11:43 zarah jonalv: Pelezilla is at http://bugs.bioclipse.net
11:43 masak zarah++
11:44 jonalv @pz bioclipse 2 is not released yet
11:44 zarah http://pele.farmbio.uu.se/cgi-​bin/bugzilla/show_bug.cgi?id=2
11:45 jonalv huh that is not it
11:45 jonalv zarah--
11:45 jonalv @pz bioclipse not released
11:45 zarah [590] Choose direction when adding an... http://tinyurl.com/dh6kcq
11:45 zarah [73] Bioclipse 2.0.0 final is not yet... http://tinyurl.com/6phlff
11:45 zarah Entire list at http://tinyurl.com/cfnm2k
11:56 masak http://superuseless.blogspot.com/2​009/03/walk-through-walls-ish.html
11:56 zarah masak's link is also http://tinyurl.com/d9zwwm
11:57 jonalv egonw: pling
12:01 jonalv egonw: ping
12:27 egonw pong
12:33 jonalv egonw: will only molecuels with more than 0 polymers give the Jmol outline not using atoms?
12:38 egonw dunno, ask ola
12:40 jonalv egonw: I will work according to that theori for now... It's the best solution I have...
12:40 jonalv masak: yeayea...
12:40 * masak didn't say anything
12:44 CIA-58 bioclipse: egonw * r9519 /bioclipse2/trunk/features/ (7 files in 2 dirs): Renamed folder to match feature name
12:53 egonw jonalv: it helps if you put questions to jmol-devel into context...
12:53 egonw what you like to acchieve...
12:53 jonalv egonw: uhm, I thought I had...
12:53 egonw in that way Bob has a clue what you are getting at, which would make it easier for him to give a good userful answer
12:54 egonw well, you could say something about teh Outline...
12:54 jonalv egonw: I have
12:54 egonw but not in your last email...
12:54 egonw OK, fair
12:54 jonalv I have bbeen nagging about the outline  amillion times now. Haven\t I?
12:55 jonalv oh I see
13:01 egonw fika time?
13:23 egonw ok, that was 30 mins too late
13:28 CIA-58 bioclipse: jonalv * r9520 /bioclipse2/trunk/plugins/ (9 files in 4 dirs): (log message trimmed)
13:28 CIA-58 bioclipse: Major work on Jmol. I hope I haven't broken anything...
13:28 CIA-58 bioclipse: * added debug lines and made selection in jmol update in outline. Only for one atom so far though.
13:28 CIA-58 bioclipse: * removed old unused methods and added logger calls to all the rest of the methods. And removed the erroneus outline update that made it impossible to select multiple atoms from Jmol.
13:28 CIA-58 bioclipse: * Selects on small molecules where only atoms are selected seems to be working now.
13:28 CIA-58 bioclipse: * Made the selection listener only kick in when there is exactly one chain. Might not be the right way to do it but it seems to works for all the example data at least...
13:28 CIA-58 bioclipse: More testing is called for.
13:33 egonw jonalv: blog with screenshot?
13:34 jonalv egonw: it's not done. It's just a mid step where I felt I dared to commit...
13:34 jonalv but yea perhaps...
13:34 egonw on your personal blog
13:34 jonalv egonw: I only have one which is about ORMs and Hibernate... :)
13:35 egonw so?
13:35 egonw anyone is actually reading that blog who will not like you blogging about Jmol?
13:35 jonalv egonw: you think I should start a general personal blog?
13:35 egonw yes
13:35 jonalv egonw: only I would not like that... :)
13:35 jonalv using that blog that is...
13:36 egonw then start a new one
13:36 egonw I have 6 or so :)
13:36 jonalv I guess I could start up one and blog about this...
13:36 egonw let me know the URL
13:36 egonw and I add you to planet.bioclipse.net
13:36 jonalv yes, I just need a name I think...
13:39 egonw "I just need a name I think"
13:39 egonw sounds good to me
13:39 egonw jonalv++
13:39 jonalv egonw: good idea, egonw++
13:40 edrin ola: what is the reference for hivrtpred ?
13:40 edrin oh
13:40 edrin he is not here
13:47 olass joined #bioclipse
13:50 masak now he is.
13:50 olass so I am
13:51 masak olass: welcome back.
13:51 olass @thank masak
13:51 zarah masak: olass says thank you
13:51 masak zarah: you're welcome.
13:51 zarah masak: excuse me?
13:51 olass @thank zarah for thanking masak
13:51 zarah olass: you're welcome.
13:51 masak zarah: you're a smart girl.
13:51 zarah masak: Then how come I'm stuck in this vat, with no body? Over.
13:52 jonalv masak++
13:53 masak :)
13:53 masak zarah++
14:03 egonw how do I vote for a bug again?!?!
14:09 jonalv egonw: I thought the link was on the bug on bugzilla...
14:10 egonw it is now
14:10 jonalv egonw: how do I add a blog to planet.bioclipse.net?
14:10 egonw voting was not yet enabled for web stuff
14:10 egonw file a bug report
14:15 olass jonalv: why a blog?
14:15 jonalv olass: blame egonw
14:15 jonalv :)
14:15 olass jonalv: no you stand up for yourself
14:16 jonalv olass: but egonw is my big idol you know ;)
14:16 olass :(
14:16 olass there goes even more of jonalv's time...
14:16 olass jonalv: what is the purpose of the new blog?
14:17 jonalv olass: document what I do with Bioclipse...
14:17 olass your science?
14:17 olass ok
14:17 egonw discuss his work and get feedback tips, etc, so that he can be more productive
14:17 olass right
14:17 masak what's the purpose of a new-born baby?
14:17 jonalv olass: perhaps I can document the manager stuff in a blog post? :)
14:18 olass jonalv: why not on the wiki?
14:18 olass why a blog?
14:18 jonalv olass: because the wiki is old and ugly
14:18 jonalv *lol*
14:18 olass seriously
14:18 jonalv no that was a reson I made up afterwards...
14:18 masak olass: it's seriously old and ugly.
14:18 olass why not on the wiki?
14:18 jonalv but it is old and ugly...
14:19 masak olass: a wiki does not lend itself to comments as does a blog.
14:19 olass masak: a wiki lends itself to community edition, so does not a blog
14:20 masak olass: I agree. so it's a question of the result you want.
14:20 olass yes
14:20 masak comunity editing or comments.
14:20 olass seriously, we can't go and distribute our docs like this
14:21 olass I really dislike it
14:21 egonw ha, ola wants a git-backed blog so that people can fork what he blogged
14:21 olass egonw: eat dirt
14:21 jonalv olass: well masak has been twittering here for about a weeek. I wanna try these new technologies too... :)
14:21 masak it's true.
14:21 masak tweet!
14:21 olass jonalv: as long as it makes you more productive
14:21 masak :)
14:21 egonw masak: nick?
14:21 masak egonw: carlmasak
14:22 * olass hates twitter
14:22 jonalv olass: are you feeling that I am not productive?
14:22 olass jonalv: how are you feeling yourself?
14:22 masak olass: http://www.boingboing.net/2009/​03/16/supernews-twouble-wi.html
14:22 zarah masak's link is also http://tinyurl.com/dxny4y
14:22 jonalv olass: tired and like I have jsut begun to get back to Bioclipse work after that course...
14:22 masak can we stop talking about feeling ourselves?
14:22 olass masak: why?
14:22 masak olass: never mind. :P
14:23 jonalv lol
14:24 * olass is not against social networking, but sometimes it just takes your eys off what's important
14:24 olass just more distractions
14:25 masak olass: aye. I agree.
14:26 masak olass: that's why I don't do Facebook or MySpace.
14:26 olass I look into facebook once a week or so for 3 mins
14:26 egonw there is social networking and social networking
14:26 olass that's enough
14:27 * jonalv does not do facebook either...
14:27 egonw like scientific conferences can be like sleeping during the lectures, and drinking in the bar with the people of your own department
14:28 egonw likewise (but the other way around), you can actually use social media to do scientific collaboration
14:28 egonw olass: not sure what you do on facebook, but please pick your category
14:28 olass yes, but too much collaboration means you never get anything done
14:28 egonw I'm sure jonalv's blog will be in the second
14:29 olass yes
14:29 olass I'm sure
14:29 egonw deö
14:29 olass ?
14:29 egonw depends on what you collaborate on
14:29 egonw (typo)
14:29 egonw if you collaborate on 100 different things yes
14:29 egonw if you collaborate on one thing with 100 others, no
14:30 egonw social media are a means of communication
14:30 egonw and has little to do with productivity
14:30 egonw just like a mobile phone
14:30 egonw you have to know how to use it
14:30 olass egonw: it's the time that is the problem, not the media
14:31 olass whatever you use, it takes time
14:31 egonw it's the balance that is the problem
14:31 olass yes
14:31 egonw you have to make sure you get more done in the same time
14:33 * olass is working on opening cusom editors from scripting
14:33 olass masak: what should I use as newline in the console?
14:34 masak olass: "\n"
14:34 olass I want to display a multiline string
14:34 olass ok
14:36 olass jonalv: what does the annotation @GuiAction do?
14:36 masak olass: I think I can answer that.
14:36 olass ok
14:36 olass please
14:37 masak it hides away the complexity of creating an async call.
14:37 masak with Spring.
14:37 masak and also perhaps some of the thread/exception problems we had in relation to this.
14:39 jonalv yes the primary use is that it fixes the error handling but it also hides away the async call
14:40 masak jonalv++
14:40 olass so when to use it?
14:41 masak olass: when you previously would have needed an asyncExec call.
14:41 olass ok
14:41 olass is the threading of js sorted out now?
14:41 olass I have not heard any discussions lately
14:42 * olass likes this
14:42 olass but I have a feeling that some things were postponed to post 2.0
14:42 masak I think it's sorted out.
14:42 olass ok
14:42 masak olass: aye, the multiple-envs thing is postponed.
14:43 masak don't know how big that'll be.
14:43 olass ok
15:01 olass masak: a question
15:01 masak shoot.
15:01 olass if I want output to teh console, shoudl I print it or retrn a String?
15:01 masak print it.
15:01 olass returning a String does not seem to work
15:02 olass is that so?
15:02 masak returning a string is deprecated.
15:02 olass ok
15:02 masak I'm pondering whether to actually change the return type of that method to void....
15:02 masak ...or just document it as deprecated.
15:15 olass egonw: can we discuss bug #776?
15:15 egonw sure
15:15 egonw please
15:16 olass if you right-click an SDF which has 3D coordinates, and select "open with", do you see Jmol as an aternative?
15:17 olass I agree that SDFEditor should be default for this fle, but it should also be possible to open in Jmol (since jmol supports this)
15:17 egonw right
15:17 egonw yes, that's fine...
15:17 egonw that's what I replied
15:17 egonw it's now just under Other...
15:17 egonw but you want it linked as secundairy editor... right?
15:18 egonw that should be easy
15:18 olass well
15:18 egonw or am I missing something?
15:18 olass no
15:18 olass it's just that the contenttype is already there
15:18 egonw so?
15:18 olass so I fear the contenttype is incorrect
15:18 egonw how so?
15:18 olass well, jmol does not show up as a secondary editor
15:18 egonw you don't want to link the Jmol editor to this content type?
15:18 olass yes
15:19 egonw why not?
15:19 olass well, it already is linked
15:20 egonw where?
15:20 egonw I don't see it in the plugin.xmo
15:20 egonw I don't see it in the plugin.xml
15:20 olass in plugin.xml of the jmol plugin
15:20 egonw only links to PDB
15:20 olass not?
15:20 egonw mdlMOlefile3D
15:20 olass hmmm
15:20 olass ok, please add it
15:20 egonw and cml.singleMolecule3D
15:20 olass maybe I was mistaken
15:32 rajarshi joined #bioclipse
15:35 egonw hi rajarshi!
15:35 masak hi rajarshi!
15:36 jonalv hi rajarshi!
15:36 zarah hi rajarshi!
15:36 olass masak: why should not the method open( String filePath ) be called?
15:37 masak olass: is there a comment that says that?
15:37 olass the implementation says:         throw new IllegalStateException("This method should not be called");
15:37 olass but it is still published
15:37 masak olass: I talked with jonalv about that one last week.
15:37 olass and?
15:37 masak basically it's a Liskov failure.
15:37 olass who is he?
15:37 masak "she"
15:38 olass she
15:38 masak she described how inheritance should work.
15:38 masak and sometimes it, well, doesn't.
15:38 masak this is such a case.
15:38 masak http://en.wikipedia.org/wiki/​Liskov_substitution_principle
15:38 zarah masak's link is also http://tinyurl.com/34kjhn
15:39 masak basically, if B inherits from A, B should be able to do all that A can do.
15:39 masak and a B can be used as an A in all situations.
15:39 masak pretty easy to swallow, really.
15:39 masak but it doesn't always hold. :/
15:39 masak (in practice.)
15:39 olass masak: why should the method not be called?
15:40 masak olass: are you in a position where you'd like to call it? :)
15:40 olass yes
15:40 masak olass: may I then refer you to jonalv, who implemented that method?
15:41 olass are you saying he implemented the method? It just throws an exception!
15:41 olass I can try to fix it
15:41 masak please talk to jonalv first...
15:41 masak I'm sure he had his reasons.
15:41 olass where is jonalv?
15:41 olass off writing bogs?
15:41 olass blogs?
15:41 maclean throwing an exception is a kind of implementation :)
15:41 * jonalv enters
15:41 jonalv I have Jonas here...
15:41 olass say hi from me
15:42 olass jonalv: quick question
15:42 olass public void open( String filePath ) {
15:42 jonalv we are trying to get Brunn working on his computer...
15:42 olass throw new IllegalStateException("This method should not be called");
15:42 olass why the exception?
15:42 jonalv olass: seems like that method should ne be called...
15:42 masak :)
15:42 olass jonalv: why?
15:43 jonalv olass: There is probably another method you should call instead...
15:43 olass no
15:43 olass there isn't
15:43 jonalv which manager is this?
15:43 olass UIManager
15:43 masak I can just feel how we're being maximally productive right now.
15:43 olass I will implement this now
15:43 jonalv are you using the Spring built object?
15:43 jonalv olass: no please don't
15:43 olass why not?
15:43 masak jonalv: that's what I said.
15:43 jonalv olass: that method looks like that for a good reason
15:43 olass give me a reason
15:43 olass else I do it
15:43 masak give him a reason!
15:44 masak jonalv: give him the reason. :)
15:44 jonalv olass: I don't have time to exaplin this now. Could you file a bug for me instead?
15:44 olass I need this now
15:44 jonalv I need to help Jonas...
15:44 jonalv What are you trying to do?
15:44 olass jonalv: I'll blog about it and link a gist that you can download via git, is that ok?
15:45 jonalv olass: :)
15:45 jonalv olass: I am not blogin I am helping Jonbas getting Brunn to satart...
15:45 olass then you can comment next week vis subversion, link that to pelezilla and I get the answer after christmas
15:45 olass ok?
15:45 olass whateve
15:45 * olass is implementing it now
15:45 maclean sometimes there's a genuine reason to have an unimplemented method like that, olass
15:46 olass revert it if you like
15:46 olass yes
15:46 olass I fully agree
15:46 olass but I think I deserve an explanation
15:46 jonalv olass: please just tell me what you are doing
15:46 jonalv olass: you have found a bug in my code
15:46 olass I want to open a file from console by supplying its path
15:46 jonalv olass: please don\t fic it in the wrong way
15:47 jonalv olass: other things _WILL_ break
15:47 olass ??
15:47 masak ¿¿
15:47 olass jonalv: so if I file a bug, will you solve this?
15:47 jonalv olass: yes
15:47 jonalv olass: if I can
15:47 olass today?
15:48 * olass is implementing open("my/path", "jcp")
15:48 masak it's 17:45!
15:48 olass :)
15:48 olass ok, tomorrow
15:48 maclean the night is young
15:49 olass maclean: you are such a poet
15:49 masak by the way, do we get overtime on this job?
15:49 maclean heh. not really.
15:49 masak didn't think so.
15:49 olass hah
15:49 olass I wish...
15:49 masak ergo, tomorrow.
15:49 * olass would be millionaire...
15:49 * masak haggles for jonalv in his absence
15:50 olass :)
15:50 olass grr
15:50 masak rawr!
15:50 olass I was just in the middle of coding this up
15:50 olass now I'm stuck with a partially working new UIManager
15:50 olass *grmpf*
15:50 olass *morr*
15:50 masak good thing you're working in a branch.
15:50 olass right...
15:50 masak right? :)
15:51 olass I'm working in the branch HEAD
15:51 olass everything is a branch, right?
15:51 masak olass: not in svn.
15:52 olass damnit
15:52 masak olass: and HEAD is the name of a revision, not a branch.
15:52 olass ok ok
15:52 masak maybe not in CVS, though.
15:52 * olass will file a bug for jonalv
15:52 jonalv olass: okey Jonas is leaving now. I am all yours.
15:52 olass :)
15:52 olass ok
15:53 jonalv olass: How can I recreate your problem on my computer?
15:53 olass then I need to commit
15:53 olass and... it's really not a problem
15:53 olass I am implementing open("path/to/mool.mol", "jcp")
15:53 jonalv olass: this is why we need git. Being able to work two people on the same branch...
15:53 olass opening a file in a designated editor
15:54 olass jonalv: I hear you
15:54 jonalv ah, I thought we had that method...
15:54 olass no
15:54 olass (not that I've found at least...)
15:54 olass we have open( final IBioObject bioObject, final String editor)
15:54 olass this is not what I want
15:54 jonalv aha
15:55 olass jonalv: can I commit?
15:55 jonalv olass: sure I will have a look at it. But I do wonder what you where trying to do...
15:56 olass you still donät understand?
15:56 olass open a file in an editor!
15:56 olass from console
15:56 olass are you with me now?
15:56 olass public void open( String filePath, String editor )
15:57 jonalv olass: but we had ui.open
15:57 olass yes?
15:57 jonalv olass: didn't that work?
15:57 olass no
15:57 olass it chosed the wrong editor
15:57 jonalv oh I thought it did...
15:57 jonalv hang on...
15:57 olass I wanted to open in jmol, it opened in JCP
15:58 jonalv aha
15:58 olass are you with me?
15:58 jonalv and then you got the exception?
15:58 jonalv did you get the exception?
15:58 olass ?
15:58 jonalv saying that that method should not be called?
15:58 olass I have never got any exception
15:58 olass jonalv: please, you're killing me
15:59 jonalv olass: likewise
15:59 olass THE METHOD DOES NOT EXIST!
15:59 masak calm down, both of you.
15:59 olass *argh*
15:59 masak olass: especially you. :)
15:59 jonalv olass: off course it exists, it's just the new world order
15:59 olass ??
15:59 masak ¿¿
16:00 jonalv olass: could you give me a couple of minutes to look into this? Jonas just left
16:00 olass sure
16:00 * jonalv is not so good at doing more than one thing at a time
16:00 jonalv it's not so easy for a bear with a very small brain
16:00 masak jonalv++ # single-tasking
16:01 masak food &
16:01 jonalv olass: the method you are looking for is: net.bioclipse.ui.business.UIManager.open(IFile file)
16:02 jonalv olass: that's where the file is opened
16:02 olass to me it seems it takes an IFile, not a (String path, String editorID)
16:02 jonalv The one using a String is never called, the string is translated to an IFile and the method taking an IFIle is called
16:02 olass and he ditorID?
16:03 olass and the editorID?
16:03 jonalv olass: oh the editorid? No there is no such method I think
16:03 olass how does spring inser that?
16:03 jonalv that method seems to be the method choosing which editor should open the file
16:03 olass < jonalv> olass: off course it exists, it's just the new world order
16:03 jonalv I guess it just opens the file with the same editor that would be used if you doubleclick on it...
16:03 olass I know
16:04 olass that is what I have been trying to say all the time
16:04 olass and that is not what I want
16:04 jonalv ah then we where missunderstanding eachother
16:04 olass clearly
16:04 olass and
16:04 olass many times
16:04 olass over and over again
16:04 olass well
16:04 jonalv it is not so easy for a bear with a very small brain...
16:04 olass bear?
16:04 jonalv yes
16:04 olass like a brown bear?
16:05 olass or grizzly?
16:05 jonalv like Winnie the Puh
16:05 olass ah
16:05 olass ok
16:05 olass commit coming up
16:05 jonalv but write the new method just like the old one, using the new World order :)
16:06 jonalv ...or I could do that... :)
16:06 olass wait for the commit
16:06 jonalv oki
16:07 olass then please do as you like
16:07 olass and jonalv...
16:07 jonalv olass: yes?...
16:07 CIA-58 bioclipse: ospjuth * r9521 /bioclipse2/trunk/plugins/​net.bioclipse.ui.business/ (6 files in 4 dirs): Added an extension point for defining editor shortnames and open from UIManager. FIXME for jonalv placed.
16:07 olass if you don't document the new world order soon I fear I have no other choice but to give you all my bugs
16:08 olass because working this way is really a waste of time for me
16:08 jonalv olass: I will blog about it
16:08 olass sounds good
16:08 olass then I can copy the blog to the wiki
16:08 olass because there's where the doc should be
16:08 jonalv well then I can say how things work and how I would like things to work
16:08 olass sounds good
16:09 jonalv because I am not happy with how things are working now
16:09 olass how about a wiki page of how things work, and then you link to that page in your blog with comments?
16:09 jonalv olass: yea sure, that works
16:09 jonalv olass: I will do this first thing tomorrow
16:09 olass well
16:10 jonalv it will probably take a day to write though...
16:10 olass !
16:10 olass jonalv: that's what I feared
16:10 olass blogs take so much longer time
16:10 olass but maybe it's worth it
16:10 olass I can settle with the wiki page and some pointers
16:11 olass you decide
16:11 jonalv olass: I mean the wikipage will take a day to write
16:11 jonalv olass: the blog post I could proabbly do much faster
16:11 olass :)
16:11 olass jonalv: did you see my fixme for you?
16:11 olass in UIMAnager?
16:11 jonalv olass:  I don't feel that the blog post has to be complete but I feel that the wiki page has to be complete and correct 3 years from now as well
16:12 olass but wiki pages can be updated
16:12 jonalv olass: looking at it
16:12 jonalv olass: is that method working as it is now?
16:13 olass no
16:13 olass it's just a stub
16:13 CIA-58 bioclipse: ospjuth * r9522 /bioclipse2/trunk/plugins/net.bioclipse.jmol/ (META-INF/MANIFEST.MF plugin.xml): Added jmol and 3d as shortnames for jmol editor using the new EP.
16:13 jonalv olass: I don't know how to open a certain IFile in a certain editor. Is there a method doing this?
16:14 olass IDE.openEditor( page, file, editorid);
16:14 jonalv oki
16:15 olass it's the new world order I cannot work with
16:15 olass else I would just use the resourcepathtransformer
16:15 jonalv olass: lol, you just implement the version taking an IFIle and don't deal with anything else
16:15 olass ?
16:16 olass I implement the version taking a Stinrg
16:16 olass not an IFile
16:16 jonalv no you wantto work with IFIles, didn't we agree that Bioclispe should work with IFIles?
16:16 olass not from console
16:16 olass from console, only paths
16:16 jonalv olass: that is the same thing
16:16 olass ?
16:16 olass path!=Ifile
16:17 jonalv the same managers are used from ui and console
16:17 olass so?
16:17 jonalv Spring translates from String to IFIle so you only implement the method taking an IFile
16:17 jonalv I thought you knew this...
16:17 olass where is this documented?
16:18 olass anyway, we take two strings
16:18 jonalv We have talked about this a million times and I think there is a mail about it.
16:18 olass will Spring translate both strings to IFile?
16:18 jonalv olass: ah now it's gettng intresting
16:18 olass the editorID too?
16:18 olass that would be bad
16:19 jonalv olass: it will translated the String at the same position as the Ifile in the method signature taking the IFIle
16:19 olass hmm
16:19 jonalv so they need to have the same order. And yes, this is definitly soemthign that I need to document
16:19 olass so it should rad: public void open( final IFile file, String editor )
16:19 jonalv yes
16:20 jonalv I am gonna try and fix this before heading home. Wish me luck! :)
16:20 olass godd luck!
16:20 olass good
16:20 olass *blah*
16:20 * olass is morring
16:21 olass things are not going well today
16:21 jonalv olass: you are sick!
16:21 olass ill
16:21 olass yes
16:21 jonalv I just couldn't resist the chance to say it that way :)
16:21 olass :)
16:22 jonalv I had a terribkle day yesterday...
16:22 olass me too
16:22 olass was even iller :)
16:23 jonalv I was not ill but nothing worked...
16:25 jonalv olass: You don't have to write to console and do return when things go wrong you can just throw a BioclipseException with the message isntead
16:25 olass ok
16:25 olass sounds better I guess
16:25 jonalv yes
16:26 jonalv I got masak to sort of like the BioclipseExceptions that way
16:26 jonalv they are treated seperately by the error reporting code in the console
16:26 jonalv Onlky the message is printed not the classname first
16:29 jonalv olass: what is the id for the jmol editor?
16:29 jonalv olass: what should I write to test the method?
16:29 olass you can now refer to it by its alias
16:29 olass jmol
16:29 jonalv hm
16:30 jonalv that did not work. I will debug and see what's going on...
16:31 jonalv olass: my aliasmap is empty
16:32 jonalv olass: am I missing a commit perhaps?
16:32 olass jmol
16:32 * jonalv updates...
16:32 olass 9522
16:32 jonalv sorry...
16:32 olass that is the only alias I have done yet
16:32 olass to test with
16:32 olass try ui.getEditors()
16:32 jonalv you snuck in a commit which I missed :)
16:33 olass hehe
16:34 jonalv okey, I get a java.lang.NumberFormatException: For input string: ""
16:34 jonalv but the editor opens now :)
16:35 olass hmm
16:35 olass please commit
16:35 jonalv it works now
16:36 olass good
16:37 CIA-58 bioclipse: jonalv * r9523 /bioclipse2/trunk/plugins/net.bioclipse.u​i.business/src/net/bioclipse/ui/business/ (IUIManager.java UIManager.java): made open(String filePath, String editor) according to the new world order
16:37 jonalv olass: please test now
16:37 olass updating
16:38 olass jonalv: did you do anything else but edit the methid? any spring stuff?
16:38 jonalv olass: nope
16:38 olass ok
16:39 jonalv I added another method though
16:39 jonalv The one using an Ifle
16:39 jonalv |IFile
16:39 jonalv It would make me gald if you looked at the diff
16:39 jonalv |glad
16:41 olass jonalv: the jmol menus don't work for me
16:41 olass do they work for you?
16:41 jonalv I haven't tried them in a while
16:42 olass please do now
16:42 jonalv doing so
16:42 jonalv seems to work for me
16:42 olass hmm
16:42 jonalv which action is not working for you?
16:43 olass hmm, all
16:44 olass why are all atoms selected by default?
16:44 jonalv any exceptions or what happends?
16:44 olass DEBUG - Running jmol script: 'select none'
16:44 olass script compiler ERROR: command expected
16:44 olass ----
16:44 olass >>>> select none <<<<
16:44 olass DEBUG - Jmol said: 'pending'
16:44 olass DEBUG - JmolListener.notifyCallback( type = 10, data = [null, Jmol script terminated, script compiler ERROR: command expected
16:44 olass ----
16:44 olass >>>> select none <<<<, 1]) called
16:44 olass nopaste!
16:45 jonalv huh what the heck?
16:45 jonalv select none is a command...
16:45 olass yes
16:46 olass I typed that
16:46 olass select none
16:46 olass to get rid of all teh halos
16:46 olass and
16:46 jonalv and it didn't work?
16:46 olass clicking on an atom in jmol does not select it in outline
16:46 olass no
16:46 jonalv olass: which file are you looking at?
16:47 olass does it matter?
16:47 jonalv olass: it might...
16:47 jonalv at least I would like to ruul that out...
16:47 olass hmm
16:47 olass restart did the trick
16:47 olass hmm
16:48 jonalv scary
16:48 olass ok, I get it
16:49 olass will send you a file
16:49 jonalv k
16:49 * jonalv has a bad feeling about this...
16:49 olass hmm
16:49 olass strange
16:50 jonalv what is?
16:51 olass I think the select atomno= string shoudl be condensed
16:51 olass if possible
16:52 jonalv okey, where are you now?
16:52 olass mail sent
16:52 olass sent you a file
16:52 olass please try it
16:54 jonalv I have opened it
16:54 jonalv how is this supposed to work?
16:56 jonalv this is so borken! :)
17:02 olass jonalv: failed for you too?
17:02 olass jonalv: it worked until your latest jmol commit...
17:02 jonalv olass: hang on
17:02 jonalv olass: commit pending
17:03 jonalv a quick and dirty fix...
17:03 CIA-58 bioclipse: jonalv * r9524 /bioclipse2/trunk/plugins/net.bioclipse.jmol/s​rc/net/bioclipse/jmol/views/JmolListener.java:
17:03 CIA-58 bioclipse: Quick and ugly hack to make sdf files opened in jmol work a little bit better.
17:03 CIA-58 bioclipse: (I turned of the jmolselctionlisteners effect for one more case which I think
17:03 CIA-58 bioclipse: should include all of these forms of sdf files) (I didn't even know we wanted to
17:03 CIA-58 bioclipse: open SDF files with jmol until five minutes ago...)
17:03 jonalv brb
17:06 jonalv back
17:06 jonalv olass: does it work for you know?
17:06 jonalv |now
17:07 olass mom
17:07 olass yes
17:07 olass but selections don't
17:07 olass anyway
17:08 olass why is selection append default?
17:08 jonalv olass: nope, selections only work for small molecules
17:08 olass that should be if I hold shift and click, right?
17:08 jonalv olass: that's a Jmol feature as far as I understand
17:08 olass jonalv: this is a small mol, but many of them
17:08 olass hmmmm
17:08 jonalv olass: okey, it only works for _one_ small molecule currently
17:09 olass ok
17:09 * olass is happy it works
17:09 olass jonalv++
17:12 jonalv The problem I had yesterday was how to know how I where to turn off that listener where it did not work...
17:17 jonalv olass: may I go home now? :)
17:17 olass jonalv: thanks for today
17:18 * olass is at home already
17:18 jonalv thanks yourself!
17:18 jonalv yes... :)
17:18 olass jonalv: probably wonät make it to bmc tomorrow..
17:18 jonalv oki
17:18 jonalv np
17:18 olass don't want you all to get ill
17:18 olass but you'll be there on thursday, right?
17:19 jonalv no we don't want that either :)
17:19 olass I need to talk to you about jobs
17:19 olass in managers
17:19 * olass wants to learn spring magic
17:19 olass well, use it at least
17:19 olass :)
17:19 jonalv yes, I will be here until Bioclipse 2 is released more or lesss. THen I am going to work with Brunn for a whil;e
17:19 olass sounds like a good plan
17:20 olass see you tomorrow then
17:20 olass on IRC
17:20 jonalv yup
17:20 jonalv bye
17:20 olass bye
17:30 masak I'm here again. o/
17:58 edrin left #bioclipse
18:17 olass bye for today
18:21 masak left #bioclipse

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