Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-03-30

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All times shown according to UTC.

Time Nick Message
06:51 egonw joined #bioclipse
07:04 Gpox joined #bioclipse
07:16 egonw moin
07:16 zarah oh hai egonw
07:16 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
07:16 egonw @msg
07:16 zarah egonw: 3 d 13 h 34 m 20 s ago, olass said remember 20.00 with edrin
07:16 zarah egonw: 3 d 14 h 9 m 49 s ago, masak said proof-of-concept: http://gist.github.com/86206
07:32 rojasm joined #bioclipse
07:47 rojasm joined #bioclipse
08:20 rojasm joined #bioclipse
08:22 jonalv joined #bioclipse
08:23 jonalv oh hai
08:23 zarah saluton jonalv
08:24 masak joined #bioclipse
08:43 jonalv egonw: do you know how to get Jmol to tell me what is selected?
08:44 egonw AFAIK via the listeners
08:44 egonw but it has been a while since I looked at it
08:45 jonalv egonw: no the listener only tells me that the selections have changed and that there now are x number of atoms seleted. Not which ones... :(
08:45 egonw ic
08:45 egonw mom
08:46 egonw check out:
08:46 egonw http://chemapps.stolaf.edu/jm​ol/docs/?ver=11.8#setpicking
08:47 zarah egonw's link is also http://tinyurl.com/dehfgj
08:47 egonw http://chemapps.stolaf.edu/jmol/docs/#setcallback
08:47 zarah egonw's link is also http://tinyurl.com/cp6nq2
08:47 egonw btw, set MinimizationCallback
08:47 egonw sounds interesting too
08:50 jonalv oh this seems complicated...
08:51 masak does someone understand this one? I don't. http://use.perl.org/~Ovid/journal/38621?from=rss
08:51 zarah masak's link is also http://tinyurl.com/ck6pal
08:55 jonalv egonw: I must admit that I don't understand taht setcallback. That seems to be related to JavaScript. Wher are not using JavaScript, are we?
08:55 egonw possibly...
08:56 egonw the mechanism is quite the same, I think...
08:56 egonw you register a listener...
08:56 egonw and Jmol calls it...
08:56 jonalv egonw: yea but can I really change _how_ the listener will be called?
08:56 egonw if I understood correctly, there was this Jmol interface which returned a int or so...
08:57 egonw which defined what was listened too...
08:57 egonw that should match the set *CallBack stuff
08:57 jonalv that feels a bit uhm unnecessary....
08:57 egonw no, guess not
08:57 egonw but did not want to imply that
08:57 egonw what you will want to do, is experiment with the different call back patsh
08:57 jonalv sry?
08:57 egonw and see which one does what
08:58 edrin joined #bioclipse
08:58 jonalv uhm what's a patsh?
08:58 edrin hi
08:58 zarah privet edrin
09:04 masak privet edrin
09:05 egonw jonalv: where's your blog again?
09:05 jonalv egonw: lol
09:05 jonalv hang on
09:06 jonalv egonw: http://loveorm.blogspot.com/
09:07 jonalv egonw: it's sort of dead for the moment and about a narrow subject...
09:07 egonw ummm...
09:07 egonw are you happy about that name...
09:08 egonw with an increasing Swedisch vocabulary, but still thinking English...
09:08 egonw love orm ??
09:08 egonw I'll await a blog name change
09:08 jonalv egonw: it was a project to get rid of some built up anger about Hibernate
09:09 jonalv Hibernate is an ORM you know...
09:09 jonalv I don't see the problem of the name honestly...
09:09 egonw silly associations
09:09 jonalv are you thinking snake?
09:09 egonw let's continue about something else, shall we ? :)
09:10 jonalv huh?
09:10 egonw nvm
09:10 jonalv okey now you really peaked my interest
09:10 jonalv I am afraid I won't be able to get anything done until you explain what you are thinking...
09:10 jonalv :)
09:13 masak jonalv: http://dictionary.reference.com/browse/pique
09:13 zarah masak's link is also http://tinyurl.com/c5jpxy
09:13 jonalv masak: now that's just cheating at Scrabble
09:14 masak http://eggcorns.lascribe.net/​forum/viewtopic.php?pid=8518
09:14 zarah masak's link is also http://tinyurl.com/cywa7x
09:15 masak peak/peek/pique. :)
09:26 olass joined #bioclipse
09:26 olass moin
09:26 zarah saluton olass
09:27 * olass is not feeling well today
09:27 jonalv olass: that sounds bad. What's up?
09:27 egonw broken leg?
09:28 olass nah, just a headache and fever
09:28 egonw ha, too much bear
09:28 egonw beer
09:28 olass :)
09:28 olass not really
09:28 egonw how was the skiing?
09:28 olass very nice!
09:29 olass got 30 cm snow on friday
09:29 olass awesome with so much new snow
09:29 olass but
09:29 olass met my brothers one year old son, he gave us all this disease
09:29 olass kids...
09:30 olass managed to get out of bed at least
09:33 edrin heh
09:40 olass edrin: saw your email abot bioschemata. Will tend to it soon. No rush I guess..
09:40 edrin sure
09:40 edrin no rush
09:41 edrin just in case ppl wonder
09:41 olass sure
10:34 jonalv food
11:07 edrin olass: we solved the CML issue
11:07 edrin did egonw mention this?
11:07 edrin at least we found the problem
11:07 egonw and a workaround
11:07 egonw yes, I mentioned it
11:07 edrin yep
11:07 edrin good :)
12:11 egonw_ joined #bioclipse
12:46 olass joined #bioclipse
13:09 masak http://ktown.kde.org/~zrusin/g​it/git-cheat-sheet-medium.png
13:09 zarah masak's link is also http://tinyurl.com/3xdyys
13:59 CIA-58 bioclipse: goglepox * r9501 /bioclipse2/trunk/plugins/net.bioclipse.core/src/​net/bioclipse/core/ResourcePathTransformer.java: Escape spaces when converting to uri.
13:59 olass Gpox++
14:48 olass egonw_: around?
14:49 egonw_ sort of...
14:49 egonw_ trying to do VR app stuff
14:49 egonw_ reading up on Bayesian statistics...
14:50 olass ok
14:50 olass it's powerful stuff
14:50 egonw_ if you get the prior probs right
14:50 egonw_ but that's what the proposal is about :)
14:50 olass that is the thing
14:51 olass yup
14:51 egonw_ and I'm having a bad day
14:51 olass why so?
14:51 egonw_ not sure
14:51 egonw_ desoriented by the daylight savings maybe
14:51 egonw_ I think this, but Y happens
14:51 olass anyway, I was gonna ask you why we cannot open SDF files with 3D coords in Jmol
14:51 egonw_ or I say Z, but A is actually true
14:52 egonw_ focus trouble...
14:52 olass do you mind if I add it?
14:52 egonw_ olass: yeah, that's an interesting solution...
14:52 egonw_ no, sounds fine
14:52 olass ok
14:52 olass it works
14:52 egonw_ that will make use of jmol.cdk, right?
14:52 olass no
14:52 olass jmol can read sdf
14:52 olass one mol per model
14:53 egonw_ ah, so it will use IJmolModel
14:53 olass found out accidentally by renaming a sdf to mol, then it opened in jmol just fine
14:53 olass ok, adding it now
14:53 olass hmm
14:53 olass it's there already..
14:54 olass ok this needs some debugging I guess
14:54 egonw_ file a bug report
14:54 egonw_ I think it would make sense to have good user visible feedback o nthe number of models...
14:54 olass it is in the outline
14:54 egonw_ either via the Outline (though not of the things contains many, many models)...
14:55 egonw_ or via a text 'multimodel' in the Jmol display
14:55 olass would be good I guess
14:55 olass like "generated" in JCP
14:55 olass will file a bug for jonalv
14:55 egonw_ he will like that
14:56 jonalv huh?
14:56 jonalv sry?
14:56 masak bbq?
14:56 masak omg!
14:56 egonw masak: yes, sounds nice... your place?
14:56 * jonalv was deeply down in olass code for selecting JmolGroups. (whatever that is)
14:56 masak egonw: too early still, but later in the year, sure.
14:56 egonw orm med grattin?
14:56 jonalv I have a classcastexception... :(
14:59 jonalv olass: is it okey if I give that bug to Gpox?
15:00 olass which one?
15:00 olass label?
15:00 olass no
15:00 * jonalv has no idea how to write on top of jmol...
15:00 olass jmol has a command "echo"
15:00 olass you can set location of it etc
15:00 jonalv olass: okey...
15:00 jonalv I will take it then...
15:10 jonalv olass: how do I know whether we are doing proteins or molecules?
15:10 olass no idea
15:10 olass ask on jmol list?
15:11 jonalv olass: no you wrote it. You should know. Jmol people don't know
15:11 jonalv it's related to the password
15:11 jonalv hag
15:11 jonalv outline
15:11 olass I got a string
15:11 CIA-58 bioclipse: goglepox * r9502 /bioclipse2/trunk/plugins/net.bioclipse.core/src/​net/bioclipse/core/ResourcePathTransformer.java: Changed to URI mulit args constructor that handles escaping
15:11 olass parsed it
15:11 jonalv olass: do you remember where?
15:11 olass if it contained [ARG] then I interpreted this as a protein
15:11 olass mom, will look it up
15:12 olass StatusListener line 52
15:12 olass if (strInfo.contains("[")){
15:13 jonalv olass: no I mean when you create the outline
15:14 olass jonalv: please explain more what you want me to anser
15:14 olass you mean that chains can be in mol or proteins?
15:14 maclean joined #bioclipse
15:14 olass outline only displays what's in the model
15:15 jonalv olass: The outline can either show atoms or grousps of atoms. How can I from within the JmolPanel find out which is the case?
15:15 olass outline only displays what's in the model
15:15 jonalv okey so I need to look at the model then I take it?
15:15 jonalv how would I do that?
15:16 olass sorry, I don't understand what you mean here at all
15:16 jonalv I have fixed the selection behavior for molecules.
15:16 jonalv When I open a protein it crhases though
15:16 jonalv so I want to only run my code when I open a molecule
15:17 jonalv how do I check what is opened?
15:17 olass jmol does not distinguish between this
15:17 jonalv our editor does
15:17 olass jonalv: what I did is in the StatusListener
15:17 jonalv olass: no
15:17 olass not?
15:18 jonalv you have made much more than just the statuslistener...
15:18 olass ok...
15:18 jonalv :)
15:18 olass this was some time ago...
15:18 jonalv hehe okey. It's just that I have no idea about how outlines works
15:18 jonalv so I don't even know where to look
15:19 olass what do you want to look for?
15:19 olass and from where?
15:19 jonalv whether we are showing atoms in the oultine
15:19 jonalv from the jmolpanel, where I add the listeners
15:19 olass listen to the IStructuredSelection that is fired when user licks on stuff
15:20 jonalv yes that is what I am doing
15:20 olass if it's an atom, we have atoms
15:20 olass if chain/monomer: we have protein
15:20 olass maybe not always true
15:20 jonalv but my implementation of that listener only works for atoms not for groups of atoms
15:20 jonalv olass: it only contains a Bitset
15:20 olass jonalv: that is a new design I have never used
15:20 jonalv oh
15:20 jonalv yea possibly
15:21 jonalv |probably
15:21 olass but I know that jmol supports two types of selections
15:21 olass atomselection
15:21 olass and groupselection
15:21 olass you need to ask on jmol ML for this
15:21 jonalv mhm and I have fixed the atomselection
15:21 jonalv but they can't help me
15:21 olass have you tried?
15:21 jonalv they don't make a difference between the two states
15:21 jonalv only we do
15:22 olass what do you mean?
15:22 jonalv I don't even know how to ask them
15:22 jonalv we are not doing it that way
15:22 jonalv yet
15:22 olass define "that way"
15:22 olass bitset?
15:22 jonalv using the Jmol set picking select chain
15:23 jonalv when we select things in jmol we still select atoms
15:23 jonalv which is why things crash when I listen to it and try to update the oultine
15:23 jonalv so I ahve to not lsiten when the outline is not showing atoms
15:24 jonalv olass: do you understand what I am saying?
15:24 olass sort of but not 100
15:24 olass maybe talk more tomorrow at bmc
15:24 * jonalv must leave and fetch his bike reak soon now™
15:24 jonalv olass: so you are planning to come here tomorrow and make us all sick? :)
15:25 olass haha
15:25 olass will stay home if I'm not healthy
15:25 masak so, possibly no status meeting?
15:26 jonalv olass: do you know where you build up the model used by the outline?
15:26 olass not in memory
15:26 olass mom
15:26 masak grandpa!
15:27 olass JmolContentOutlinePage.findInModelSet?
15:29 jonalv hm I guess it\s where that model set is built up I am looking for...
15:30 jonalv gtg
15:30 olass jonalv: hold on
15:30 masak olass: he left already.
15:30 olass where?
15:31 masak to collect his bike from Mr Bike Repairman.
15:31 olass will he be back here?
15:31 masak aye.
15:31 olass ok
15:31 masak in half an hour or so.
15:31 olass jonalv: it seems the jmol objects create their own children
15:31 olass hence the JmolModelSet has a method createChildren()
15:32 olass and so has JmolModel etc
15:32 olass Maybe not an ideal design, but that's how I guilt it
15:32 olass guilt=built
15:32 olass @tell jonalv please backlog #bioclipse
15:32 zarah Consider it noted.
15:37 masak @tell jonalv backlog here: http://irclog.perlgeek.de/bi​oclipse/2009-03-30#i_1026125 :)
15:37 zarah masak's link is also http://tinyurl.com/dlscmu
15:37 zarah Consider it noted.
15:56 CIA-58 bioclipse: carl_masak * r9503 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java:
15:56 CIA-58 bioclipse: [ScriptingConsoleView] fixed #78
15:56 CIA-58 bioclipse: The method convenientLineBreak, upon finding NEWLINE in a string, broke it not
15:56 CIA-58 bioclipse: after the NEWLINE, but 1 character after its beginning. This caused errors on
15:56 CIA-58 bioclipse: Windows, where NEWLINE.equals("\r\n").
15:56 CIA-58 bioclipse: In other words, the whole bug was a case of insufficient generalization.
15:56 CIA-58 bioclipse: carl_masak * r9504 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
15:56 CIA-58 bioclipse: [JsConsoleView] various code simplifications
15:56 CIA-58 bioclipse: ...including the removal of a bug similar to #78, assuming that NEWLINE is
15:56 CIA-58 bioclipse: one character long.
16:01 jonalv oh hai
16:01 zarah saluton jonalv
16:01 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
16:01 jonalv zarah: tell me...
16:01 zarah jonalv: 28 m 37 s ago, olass said please backlog #bioclipse
16:01 zarah jonalv: 24 m 12 s ago, masak said backlog here: http://irclog.perlgeek.de/bi​oclipse/2009-03-30#i_1026125 :)
16:02 jonalv olass: But where does it start? Even though they build themself there must be a starting position...
16:03 olass createControl in JmolContentOutlinePage
16:03 olass the setInput(...)
16:03 olass line 198
16:04 jonalv hm intresting
16:27 jonalv olass: what is the criteria for doing the advanced outline?
16:27 olass what is an advanced outline?
16:27 jonalv I am guessing the number of chains is not it right?
16:27 jonalv the one not showing atoms
16:27 jonalv what would you call it?
16:27 CIA-58 bioclipse: carl_masak * r9505 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java:
16:27 CIA-58 bioclipse: [ScriptingConsoleView] fixed #566
16:27 CIA-58 bioclipse: Turns out we don't want to eat spaces as aggressively as we have done so far;
16:27 CIA-58 bioclipse: it screws up indentation. New rule is to eat only one space, and only when
16:27 CIA-58 bioclipse: it contributed to the breaking of a line. This matters so that we won't loop
16:27 CIA-58 bioclipse: infinitely; see added comment.
16:28 olass jonalv: jag gjorde en outline
16:28 olass men gör gärna två om du vill
16:28 olass hmm
16:29 olass english, right
16:29 jonalv olass: yes and it comes in two flavours
16:29 olass it does?
16:29 jonalv olass: what determines which flavour it's gonna choose?
16:29 olass [18:30] < jonalv> I am guessing the number of chains is not it right? <- could be true
16:29 jonalv yes if you open a molecule it shows atoms
16:29 jonalv olass: but can't you havea protein with one chain?
16:30 olass sry, I don't remember this
16:30 olass but sounds right
16:31 olass I'm guessing this is done in JmolModel.createChildren
16:32 olass maybe not
16:32 olass JmolChain it seems
16:32 * jonalv is not sure...
16:36 olass Well
16:36 olass if (group instanceof Monomer) {
16:36 olass seems all have group
16:36 olass and that Monomer is a special group
16:37 jonalv uhm okey, will have to look into this further tomorrow
16:37 olass jonalv: how do I use progressmonitors in managers?
16:38 jonalv olass: to do it the right way the manager need to be according to the "New World order"
16:38 olass which is?
16:38 jonalv which manager are you in?
16:38 olass BalloonManager
16:38 jonalv two Spring beans. one for the scripting and one for the gui
16:38 olass can you talk me through it?
16:38 jonalv they have different aspects for create job
16:39 jonalv I think it would be better to do that face to face
16:39 olass no manager docs?
16:39 jonalv you can look at how it's done in the cdk manager
16:39 olass *sigh*
16:39 jonalv and do it the same way
16:41 CIA-58 bioclipse: ospjuth * r9506 /bioclipse2/trunk/plugins/net.bioclipse.ba​lloon.business/src/net/bioclipse/balloon/ (business/BalloonManager.java handlers/BalloonHandler.java): Use workspace path from selection if available.
16:42 * jonalv heads to swim. cya
17:34 CIA-58 bioclipse: ospjuth * r9507 /bioclipse2/trunk/plugins/net.bioclipse.ba​lloon.business/src/net/bioclipse/balloon/ (handlers/BalloonHandler.java ui/ ui/BalloonDialog.java): Balloon runs as a Job. Also started on a BalloonDialog for setting params to Balloon.
17:36 olass bye
18:00 egonw joined #bioclipse
18:30 edrin left #bioclipse

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