Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-03

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All times shown according to UTC.

Time Nick Message
06:54 thomas_ku joined #bioclipse
07:07 masak joined #bioclipse
08:02 Gpox joined #bioclipse
09:08 maclean joined #bioclipse
10:10 egonw joined #bioclipse
10:12 jonalv joined #bioclipse
10:15 olass joined #bioclipse
10:15 olass zarah: hold on to your hat
10:15 zarah olass: I'm just a bot, you expect me to understand that?
10:16 olass http://pele.farmbio.uu.se/cgi-bin/bugzilla/buglis​t.cgi?query_format=advanced&short_desc_type=a​llwordssubstr&short_desc=&target_mileston​e=2.0+release&long_desc_type=substring&lo​ng_desc=&bug_file_loc_type=allwordssubstr&amp​;bug_file_loc=&deadlinefrom=&deadlineto=&​amp;bug_status=NEW&bug_status=ASSIGNED&bu​g_status=REOPENED&emailassigned_to1=1&ema​iltype1=substring&email1=&emailassigned_t​o2=1&emailreporter2=1&emailcc2=1&emai​ltype2=substring&email2=&bugidtype=inc
10:16 zarah olass's link is also http://tinyurl.com/bw8ya6
10:16 egonw olass: please check: http://wiki.bioclipse.net/index.php?​title=Bioclipse_2.0_Cheminformatics
10:16 zarah egonw's link is also http://tinyurl.com/dh2pte
10:16 olass ah
10:16 olass zarah++
10:16 masak :)
10:16 masak @karma zarah
10:16 zarah zarah has a karma of 53
10:16 masak zarah++ # for having so much karma
10:16 olass egonw: great
10:17 olass I espcially like: Script Jmol in console [GREEN]
10:17 olass writing out the color is beautiful
10:17 olass :-)
10:17 egonw well, it used jmol.script("")
10:17 olass haha
10:17 egonw or jmol.run()
10:17 egonw but you can do anything with it...
10:18 olass minimizing things in jmol in bioclipse is a nic escreencast
10:19 egonw gist+bioclipse+manager:jmol
10:20 egonw @gist manager:jmol
10:20 masak egonw: is that a request? :)
10:20 egonw mmm... I feel a zarah RFE coming up...
10:20 masak egonw: please tell me the URL that that should translate to.
10:21 egonw "@gist manager:jmol" -> delicious.com/tags/bioclipse+gist+manager:jmol
10:21 masak egonw: consider it done.
10:21 egonw but nicer even like @bug... if it would parse the output and extract the gist numbers with link
10:21 masak um.
10:21 egonw e.g. http://delicious.com/tag/b​ioclipse+gist+manager:jmol
10:21 masak consider that the version after that.
10:21 zarah egonw's link is also http://tinyurl.com/d8kpbn
10:21 egonw (btw, bugfix: tag not tags in URL
10:22 masak oki.
10:22 egonw zarah would parse that page, and recognize the URL: http://gist.github.com/18315
10:22 egonw as http://gist.github.com/<GIST-ID>
10:22 masak egonw: so 'bioclipse' and 'gist' are part of every search?
10:23 egonw at #bioclipse certainly
10:23 masak egonw: and in other channels?
10:23 egonw not used elsewhere, afaik
10:23 masak but what if?
10:24 egonw <CHANNEL{1,}>+"gist" ?
10:24 masak awright.
10:24 egonw #cdk -> cdk+gist
10:24 masak I can do that.
10:24 jonalv @pz m321
10:24 zarah http://tinyurl.com/dgme6t
10:24 egonw #jmol -> jmol+gist
10:24 masak egonw: I geddit.
10:24 egonw #metware -> metware+gist
10:24 masak ok, ok! :)
10:24 egonw #taverna -> taverna+gist
10:25 egonw hahaha...
10:25 masak shut up! :P
10:25 masak zarah: shut up!
10:25 zarah masak: :)
10:26 egonw Oh, btw, I saw this bus add in Cambridge: http://tinyurl.com/bioclipsebus
10:27 masak *lol*
10:27 jonalv awesome
10:28 masak http://tinyurl.com/icanhazbioclipse
10:29 jonalv +1
10:29 egonw :)
10:29 laca69 joined #bioclipse
10:30 egonw hi laca69
10:30 laca69 Hi egon
10:30 jonalv o&
10:30 laca69 Are you there Ola?
10:30 jonalv o/
10:30 olass yup
10:34 CIA-55 bioclipse: carl_masak * r8560 /bot/trunk/zarah.pl: [zarah] has a new @gist command
10:34 masak zarah: reboot, dear.
10:34 zarah joined #bioclipse
10:34 masak @gist manager:jmol
10:34 masak oops.
10:35 * masak debugs
10:35 masak ...which means I'll have to kill her again in the same way, unfortunately.
10:35 egonw she'll has enough karma... she'll lives...
10:35 masak :)
10:35 zarah joined #bioclipse
10:36 masak @gist manager:jmol
10:36 masak oh.
10:36 masak I see.
10:36 * masak has been writing too much Perl 6 lately
10:37 CIA-55 bioclipse: carl_masak * r8561 /bot/trunk/zarah.pl: [zarah] fixed Perl 6 braino
10:37 zarah joined #bioclipse
10:37 masak @gist manager:jmol
10:38 masak ...and remember to update on pele...
10:38 zarah joined #bioclipse
10:38 masak you see, this is all really easy, in theory.
10:38 masak @gist manager:jmol
10:38 zarah http://tinyurl.com/d8kpbn
10:38 masak it's working!
10:39 egonw @gist manager:cdk
10:39 zarah http://tinyurl.com/6xhm3r
10:39 maclean huzzah!
10:39 masak in the next version, we'll be seeing links directly to the gist pastes.
10:39 egonw thanx
10:39 masak np
10:39 egonw maclean: now back to 2.0 :)
10:39 egonw masak: now back to 2.0 :)
10:39 masak aye.
10:39 egonw maclean: sorry, wrong 'ma-TAB'
10:39 egonw :)
10:39 shk3 joined #bioclipse
10:40 egonw shk3, maclean: how's the snow? did you make it back to Cambridge?
10:40 maclean Cambridge has, unfortunately been destroyed by an excess of snow.
10:41 egonw http://benmarsh.co.uk/snow/
10:41 egonw ah well... it was just a bunch of old buildings anyway
10:41 maclean Genuine newspaper headline today : "It was a day to remember"
10:41 maclean !!
10:42 masak *lol*
10:42 egonw they mean: 'a media hype to remember' right?
10:42 shk3 "
10:42 shk3 The campus is open as usual today (Tuesday 3rd February). Staff should
10:42 shk3 try to attend if it is safely and reasonably possible to do so
10:42 shk3 "
10:42 shk3 genuine email message from security
10:43 egonw :)
10:45 maclean egonw : so, any thoughts on my renderer patch/branch?
10:49 olass joined #bioclipse
10:49 stain joined #bioclipse
11:03 shk3 olass: did you read my comment on the cheat sheet problem?
11:04 olass shk3: yes
11:04 olass no idea about it
11:05 olass need to run off for lunch
11:05 olass ttl
11:05 shk3 does it work for you?
11:05 shk3 from welcome screen?
11:05 egonw I think he had one commit with a link...
11:07 shk3 hm
12:35 egonw back
12:35 jonalv joined #bioclipse
12:36 olass back
12:39 laca joined #bioclipse
12:39 masak back
12:39 zarah back
12:39 masak :)
12:40 masak you're a smart girl, zarah.
12:40 maclean joined #bioclipse
12:40 zarah masak: Not so loud, dear. I don't want my boyfriend to hear.
12:46 sneumann joined #bioclipse
12:49 jonalv okey
12:49 jonalv I have a question
12:50 jonalv how should a molecule be printed on the console?
12:50 masak left-to-right.
12:50 masak :P
12:50 jonalv cdk.fromSMILES("CCCC")
12:50 jonalv CDKMolecule:null
12:50 egonw null?
12:50 masak null?
12:50 jonalv where null would be the name...
12:51 egonw default to hash if CDKConstatns.TITLE == null
12:51 jonalv egonw: hash?
12:51 masak .hashcode
12:52 jonalv why would I want to print a hashcode?
12:52 egonw looks better than null?
12:52 jonalv might as well print the BioObject id...
12:52 egonw maybe chem formula then?
12:52 jonalv but that one is 36 chars...
12:52 jonalv egonw: yea that would be a variant. can I get that one somehow?
12:52 egonw inchikey?
12:52 Gpox maclean: How do i render a molecule that fit to a rectangle in the new Renderer?
12:53 maclean Gpox : do you mean fitToScreen?
12:53 jonalv egonw: is a inchikey humanly readabkle?
12:53 egonw yes
12:53 maclean if so, there is a RenderModel.fitToScreen(boolean) method
12:53 egonw it's a string of 27 hexademical chars
12:53 jonalv (jonalv needs to study chemoinformatics)
12:54 jonalv egonw: and inchi is a part of cdk?
12:54 jonalv cdk generates inchi?
12:54 maclean (and by 'screen' I really mean whatever drawing boundbox is passed in the paint methods)
12:54 egonw @gist manager:inchi
12:54 zarah http://tinyurl.com/bqjdeh
12:54 jonalv the core cdk we have in bc?
12:55 jonalv egonw: is the inchi manager contributed by cdk.business?
12:55 egonw no
12:55 jonalv (zarah++)
12:55 egonw so, that's not an option I guess
12:55 jonalv exactly
12:55 egonw molecular formula might be interesting...
12:55 egonw IMolecularFormula
12:56 egonw MolecularFormulaManipulator
12:56 jonalv molecularformula feels like what you want to use if you don't have a name...
12:56 egonw that one might be useful
12:57 egonw MolecularFormulaManipulator.getString() seems appropriate
12:57 egonw should I make that visible from the CDKManager?
12:57 egonw if so, please file a bug report
12:57 egonw I think that would make sense
12:57 jonalv egonw: I can't fing that method...
12:57 jonalv |find
12:57 egonw please file a bug report
12:57 egonw I'll do it asap
12:58 egonw meaning, just after the bug fix I am doing now
12:58 jonalv could you teach me how to do it really fast? :)
12:58 jonalv or I will just file a bug report...
12:58 egonw drop by
13:02 shk3 olass: coming back to the cheat sheet stuff
13:02 shk3 did you try from the welcome screen in the downlaod?
13:03 CIA-55 bioclipse: jonalv * r8562 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKMolecule.java: added toString method to CDKMolecule
13:06 maclean hmmm. I take it that it is not possible to open a dialog from a manager method?
13:07 Gpox maclean: thanks that worked, but is it really be a state? i want to do this once when i open an editor but after that it should not change as i want to scroll and stuff
13:07 Gpox maybe have that method public
13:07 maclean what method?
13:08 Gpox calculateZoom
13:08 maclean ahh
13:08 maclean mom
13:09 Gpox calculateBounds can be static and should possible be public too
13:09 maclean er...
13:09 maclean no for both of those, I think
13:10 maclean it is either fitToScreen or not
13:10 maclean well, okay, they could be static
13:11 maclean scrolling is handled
13:12 Gpox how?
13:12 maclean It's not so nice, but what you have to do is have a boolean that records whether it is a new chem-model or not
13:12 edrin joined #bioclipse
13:12 edrin hi
13:13 zarah ni hao edrin
13:13 maclean then, on the first call, it's "paint(obj, new SWTDrawVisitor(GC), bounds, true)"
13:13 masak ni hao edrin
13:13 edrin olass: btw. the webservices plugin should work fine now
13:13 maclean and on subsequent calls, it's false.
13:14 Gpox yeah it just feels wrong doing it in the paint method
13:14 maclean oh, and you call repaint(Visitor) when nothing has changed (ie : scrolling)
13:15 Gpox ok i will try that
13:16 Gpox the generator list should probably be java.util.List instead of ArrayList
13:17 maclean sure
13:19 masak I'm running Bioclipse with the net.bioclipse.sampledata_feature. how do I import the sample data?
13:19 egonw File -> New -> Data
13:19 Gpox maclean: i got two other requests. RendererModel.set/getDefaultBondColor and that the fontmanager is updated when RendererModel.setFont(...) is called
13:19 maclean Yes, that sounds good
13:20 Gpox there is a getBoundsColor
13:20 jonalv egonw: so the hydrogens must be implicit for that method to work. Does that mean that I hacve to clone the atomcontainer and remove all hydrogens from the clone before giving the method the clone?
13:20 maclean oh, and I see that you use AWT Fonts, not SWT fonts - is that because the rendermodel stores an AWT font
13:21 egonw jonalv: that should not be needed
13:21 jonalv egonw: why not?
13:21 egonw jonalv: give me a few minutes, and I'll drop by
13:21 egonw because it would be stupid
13:21 maclean because I was thinking that maybe the model should just store the name and point size of the font
13:21 Gpox maclean: i convert it to a SWT font
13:21 jonalv but the javadoc says...
13:21 Gpox and style
13:22 maclean Italic atom names? :)
13:22 Gpox Bold
13:22 egonw Uppsala-team fike-time
13:22 egonw fika-tme
13:22 egonw fika-time
13:23 egonw maclean: comic font type
13:23 egonw much more fun
13:23 maclean hah
13:23 masak egonw: I have File and New, but no Data.
13:23 jonalv fika :)
13:24 Gpox i wonder if getBoundsColor is used in the Bond generator if it refers to the color of the bonds
13:24 Gpox afk fika
13:24 egonw masak: I'll show you later
13:24 * masak doesn't like fikas
13:24 CIA-55 bioclipse: egonw * r8563 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/ (5 files in 3 dirs): Added a FromSMILES wizard (fixes #367)
13:24 zarah bug #367 | http://tinyurl.com/d4zmdu
13:24 maclean please, what is fika?
13:25 masak maclean: a silly invention by which lunch is no longer the only interruption of the workday.
13:25 maclean oh, takk.
13:25 masak http://en.wikipedia.org/wiki/Fika
13:25 zarah masak's link is also http://tinyurl.com/e7thj
13:26 * masak doesn't drink coffee, tea, warm water, chocolate or anything else which might motivate a fika
13:27 maclean Cold water? Beer? Vodka?
13:27 masak cold water, perhaps. when I'm thirsty, which I'm not.
13:28 masak I had water an hour ago.
13:28 masak bah, those humans and their social customs.
13:31 maclean :)
13:45 masak http://bldgblog.blogspot.com/2009/01/air-born.html
13:45 zarah masak's link is also http://tinyurl.com/8yj2pp
14:14 jonalv egonw: that method actually returns C and not CH4. I think we will want the hydrogens or do we?
14:14 egonw yes
14:14 masak egonw: ah, found Data. turns out I needed to add the n.b.data plugin, not just the n.b.sampledata_feature.
14:19 egonw olass: please add n.b.data to the sampledata_feature
14:19 egonw or to bioclipse_feature
14:20 egonw olass: should I file a bug report so that you don't forget?
14:36 olass egonw: no need, it will go in net.bc-feature
14:36 olass so will always be present
14:36 olass email coming out soon (I hope)
14:37 edrin olass: btw. the webservices plugin should work fine now
14:37 olass edrin: good
14:37 olass file a bug for me to test
14:37 olass I keep forgetting things
14:37 edrin @pz
14:37 zarah edrin: Pelezilla is at http://bugs.bioclipse.net
14:48 jonalv @pz jmol
14:48 zarah [358] Jmol mode for JavaScript console   http://tinyurl.com/b3z6s2
14:48 zarah [36] Create jmol-console                 http://tinyurl.com/58lt4w
14:48 zarah [48] Jmol selections                     http://tinyurl.com/6h3vnn
14:48 zarah [66] JmolManager should be fully cove... http://tinyurl.com/bnta2p
14:48 zarah [106] missing manager unit test for m... http://tinyurl.com/5s4wyd
14:48 zarah Entire list (14) at http://tinyurl.com/cog2gu
14:53 edrin left #bioclipse
15:07 masak @botsnack
15:07 zarah ;)
15:09 jonalv @botbeer
15:09 zarah ;)
15:10 CIA-55 bioclipse: jonalv * r8564 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Created method cdk.molecularFormula
15:10 CIA-55 bioclipse: jonalv * r8565 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): use molecularformula in CDKMolecule.toString if no name exists
15:14 jonalv is aliban@gmx.net == edrin?
15:17 jonalv olass, egonw, shk3, zarah?
15:17 jonalv masak?
15:17 masak jonalv?
15:17 jonalv masak: is aliban@gmx.net == edrin?
15:17 masak no, that's his email address.
15:17 jonalv masak: so you are sure that that is his emailadress?
15:17 masak jonalv: no.
15:18 masak but that's what I usually use when emailing him.
15:18 jonalv masak: why do you say so then?
15:18 masak jonalv: I don't know. because you asked?
15:18 jonalv masak: if I want to assign a bug to edrin should I assign it to that guy?
15:18 masak yes.
15:18 shk3 its edrin
15:18 jonalv masak: was that so hard?
15:19 masak jonalv: Abbott and Costello, almost.
15:20 * maclean is on first
15:37 maclean does anyone know if the jmol.cdk plugin is obsolete?
15:38 egonw doesn't that contain the JmolView for 3D display of ICDKMolecule's?
15:39 maclean oh
15:39 maclean so...that's different from the jmolview for 3D display of...other molecules?
15:40 egonw yes
15:40 egonw the JmolEditor uses Jmol's IO and Jmol's data model
15:40 maclean oh
15:42 CIA-55 bioclipse: jonalv * r8566 /bioclipse2/trunk/plugins/net.bioclipse.core/src/​net/bioclipse/core/ResourcePathTransformer.java: [ResourcePathTransformer] Made instance volatile and changed some indentation. I am closing bug #305 for now.
15:42 zarah bug #305 | http://tinyurl.com/dg5m57
15:42 jonalv zarah++
15:42 jonalv @botbeer
15:42 zarah ;)
15:48 * egonw is heading home
15:48 egonw bye
15:51 masak olass: I just saw #297.
15:51 olass @pz 297
15:51 zarah http://tinyurl.com/cx7zcj
15:51 masak do I attempt that before or after #352? they have the same priority.
15:51 olass @pz 352
15:51 zarah http://tinyurl.com/dfsbp8
15:51 masak :)
15:52 masak oops, nvm. it was Gpox's ticket. :)
15:52 olass 297 is assigned to arvid...?
15:52 masak aye, just saw that.
15:52 olass def 352 anyways
15:52 olass 297 is lower prio :-)
15:52 masak ah, I was just cc:ed FMI.
15:55 * masak changes his saved search so it won't bother him with not-his tickets
16:50 masak left #bioclipse
17:02 edrin joined #bioclipse
17:04 shk3 olass?
17:05 shk3 ah, gone
17:16 edrin left #bioclipse
17:26 CIA-55 bioclipse: gilleain * r8567 /bioclipse2/trunk/plugins/net.bioc​lipse.jmol/src/net/bioclipse/jmol/ (4 files in 3 dirs):
17:26 CIA-55 bioclipse: - Image export handling ('snapshot') now done by a Published manager method.
17:26 CIA-55 bioclipse: - Load implemented.
18:10 CIA-55 bioclipse: gilleain * r8568 /bioclipse2/trunk/plugins/net.bioclipse.jmol/s​rc/net/bioclipse/jmol/editors/JmolEditor.java: Minor formatting changes.
18:12 CIA-55 bioclipse: gilleain * r8569 /bioclipse2/trunk/plugins/net.bioclipse.jmol/​src/net/bioclipse/jmol/views/JmolPanel.java: Removed the 'Frank' - the "Jmol" text that is in the lower right corner. Fixes bug #336 (note : is this okay with the jmol people?)
18:12 zarah bug #336 | http://tinyurl.com/alske7
18:50 jonalv joined #bioclipse

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