Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-12-05

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All times shown according to UTC.

Time Nick Message
07:40 egonw joined #bioclipse
08:11 Gpox joined #bioclipse
08:24 edrin joined #bioclipse
08:26 edrin hi
08:26 zarah hi edrin
08:26 edrin hi egonw
08:27 egonw hi edrin
09:15 shk3 joined #bioclipse
09:22 jonalv joined #bioclipse
09:59 jonalv Gpox: I realised that I really need to be able to select and dnd things from the moleculeseditor... :(
10:06 Gpox is that multi row select?
10:08 jonalv uhm
10:08 jonalv yea probably
10:08 jonalv is that more complicated?
10:10 Gpox it is if you are codeing it yourself
10:10 jonalv mhm
10:24 CIA-32 bioclipse: jonalv * r7971 /bioclipse2/trunk/plugins/​net.bioclipse.structuredb/ (6 files in 3 dirs): [structuredb] renamed AnnotationUIModel to Label
10:33 jonalv edrin: ping
10:34 edrin hi jonalv
10:34 jonalv edrin: I saw that you where talking about webservices
10:34 jonalv edrin: are you working on that?
10:34 edrin yes
10:34 jonalv edrin: what have you done?
10:34 jonalv and what is left to do?
10:35 edrin so far i only fixed the webservices plugin to work again
10:35 jonalv are you using: net.bioclipse.services?
10:36 edrin i think shk3: added some webservice manager for retrieving pdb files... but it was outdated
10:36 edrin jonalv: no
10:36 jonalv edrin: intresting :)
10:36 edrin the plugin i named net.bioclipse.webservices
10:36 jonalv okey
10:37 edrin the plugin i once wrote for bc1 but shk3 copied it to bioclipse2 dir
10:37 jonalv I think the is that net.bioclipse.services will contain gui for using services
10:37 jonalv not just webservices though
10:38 edrin i know what you mean
10:38 jonalv If you get some things with webservies to work perhaps we should add those to the services view?
10:38 edrin olas mentioned that you plan to write a GUI for for discovering webservices
10:38 jonalv (and remove all the placeholding...)
10:38 edrin yes, sure
10:39 edrin well, we must discuss how this GUI can be used...
10:39 jonalv because structuredb currently recides in that view but it feels a little strange if it is the only thing in the servies view...
10:40 edrin for example the current net.bioclipse.webservices has a wizard for WSDbfetch web service. thus you can download any EBI/EMBL database entry...
10:40 jonalv most of the other stuff is just placehoilders
10:40 jonalv that should be in this view :)
10:40 jonalv Perhaps it already is?
10:40 edrin no
10:41 edrin do you have the web service plugin checked out?
10:41 jonalv would you try to add it?
10:41 jonalv yea I have everything checked out but I haven't run it
10:41 jonalv perhaps I should try running it? :)
10:42 edrin can you run bc2 with this plugin? then go to the new button and then "Others" there is an entry with Ws Web Service...
10:43 jonalv doing that now
10:43 jonalv this feels strange
10:43 edrin why?
10:43 jonalv why am I creating a new project for this?
10:44 edrin it's the eclipse way to generate resources... why project?
10:44 jonalv so new is not project?
10:44 jonalv intresting
10:44 jonalv where did my file end up?
10:45 jonalv it told me that it couldn't save the file as a BioResource...
10:45 edrin it is in the Virtual folder
10:46 jonalv ah
10:46 jonalv so it could save it then...
10:46 jonalv strange...
10:46 edrin what did you download?
10:46 edrin what file?
10:46 jonalv 1JR8 :)
10:47 edrin ok
10:47 jonalv it worked very well actually
10:47 edrin :)
10:47 jonalv but it is not using the services view at all
10:48 edrin no
10:48 edrin well, it just retrieves files...
10:48 jonalv edrin: what's a Connection Profile? It that your stuff too?
10:49 edrin jonalv: (personally,) my idea with the service view is/was that it gives a resource where to get services from and use them in javascript scripts...
10:50 edrin jonalv: dont think so
10:50 edrin i am for lunch
10:50 edrin back in 30 min
10:50 jonalv edrin: oki
10:50 jonalv I will leave for lunch soon too
11:00 * jonalv lunch
12:10 * jonalv is back
12:21 gilleain joined #bioclipse
12:22 gilleain good noon.
12:24 jonalv gilleain: hi
12:24 gilleain hi
12:24 zarah hi gilleain
12:24 jonalv all good?
12:25 gilleain yeah, I just had a cunning plan to speed up scrolling in jcp. it sortof makes a difference.
12:25 jonalv okey
12:25 jonalv good :)
12:25 gilleain and you?
12:25 jonalv I am trying to figure out what to spend the rest of this day on
12:25 jonalv so far I don't really know...
12:26 gilleain something that will be fun to program, I would recommend.
12:26 gilleain new code, perhaps
12:26 jonalv like what?
12:26 gilleain I don't know, but fresh new code is always fun, before you hit the point where it is difficult to get things done :)
12:27 jonalv I think I am at that point...
12:27 gilleain oh :(
12:32 jonalv I am gonna have a look at the problem to have all javascript commandos run as jobs
12:33 jonalv structuredb.subStructureSearch( "db", molecule.fromSmiles("C=C=C=O") ); takes ages and it really needs a progressmonitor... :)
12:33 gilleain hmm, sounds good.
12:33 gilleain I'm just backlogging : 1JR8, eh? That sounds like a large structure, somehow.
12:33 jonalv yea :)
12:34 jonalv it was a pdb file... :)
12:34 gilleain hmmm. no, just a thiol oxidase, I must be thinking of something else.
12:38 gilleain really large are things like proteasomes, with chains A-Z,1-2 (or 26 chains, I suppose).
12:38 gilleain or virus structures, of course
12:45 jonalv okey
12:46 egonw jonalv: that's actually where that vflib patch comes in
12:46 jonalv egonw: uhm what where?
12:46 egonw substructure search
12:47 jonalv what's the vflib patch?
12:48 jonalv egonw: you sort of lost me...
12:48 egonw different algorithm for substructure search
12:48 egonw much faster than the current algorithm
12:48 jonalv oh nice
13:03 CIA-32 bioclipse: jonalv * r7972 /bioclipse2/branches/jonalv-RunJSCommandsAsJobs/: Created branch for trying to get all js commandos to be run as jobs with the posibility to connect to the progressmonitor
13:11 gilleain joined #bioclipse
13:13 edrin jonalv: regarding the services view
13:13 edrin what is it supposed to do?
13:14 jonalv edrin: collect all services...
13:14 edrin sure
13:14 jonalv browse services
13:14 edrin and then?
13:14 edrin what can it do with it?
13:15 jonalv you drag something and drop it on the view and the service is run
13:15 jonalv for example
13:15 edrin no, this wont work
13:15 jonalv edrin: please explain
13:15 jonalv I think it's olas idea from the beginning...
13:16 jonalv I am just contnuing what he started...
13:16 edrin services are not always taking *any* string
13:16 edrin the input must be compatible with the service
13:17 edrin (service's function)
13:17 egonw ah... edrin, the view is supposed to check that
13:17 jonalv yea but why is that a problem?
13:17 jonalv yea
13:17 edrin ah ok
13:17 egonw it will ensure that nothing bad is really send of to a service...
13:17 edrin ok
13:18 edrin and how is the result collected? is there a listview that collects/lists the results?
13:19 egonw don't exactly remember what Ola had in mind for that...
13:19 egonw I guess virtual project folders
13:19 jonalv results should be opened in an editor or stored in the virtual
13:20 jonalv it not the result takes ages to get and the job has been moved to background in which case it will just tell you that it ios finnisehed and then when you click it will it open ineditor
13:21 edrin i think it would be great if the webservice's function would be reflected in a "manager's" API. thus one could write javascripts against it.
13:22 edrin for example one could drag a function from the service view to the javascript editor....
13:22 edrin hm
13:23 jonalv oh nice idea
13:23 edrin regarding javascript... the scripting console is not working for me since some/several weeks..
13:24 jonalv masak++ is (slowly) working on a new javascript console
13:24 edrin jonalv: i think this is highly required... because using services in scripts is nearly the same power then using in taverna workflow...
13:24 jonalv yea
13:24 edrin and in fact, i would use these
13:25 jonalv :)
13:50 jonalv does anyone know if subprogressmonitors can be visualised in some nice way?
13:51 egonw no, don't think so...
13:51 egonw would be really, really welcome...
13:51 jonalv perhaps I could start two works then..
13:51 jonalv jobs that is
13:51 gilleain I think there is such a thing as a ProgressGroup
13:52 jonalv gilleain: cool
13:52 jonalv gilleain: where did you pick that up?
13:52 gilleain I dug through a lot of stuff about progress monitors when trying to make a custom one.
13:52 egonw but that's still just plain text, right?
13:52 jonalv where can I read about it?
13:52 gilleain Ummm. mom
13:53 gilleain egonw : don't think so.
13:54 gilleain there were some tutorials, but I didn't bookmark them for some reason. I'm crap at bookmarking.
13:55 egonw funny... I was just the other day suggesting someone how important it is to keep a lab notebook (electronic, or otherwise :)
13:56 jonalv right, I must start doing that somehow.. :)
13:56 egonw gilleain: I can very much recommend delicious.com
13:56 egonw and citeulike.org for papers
13:57 gilleain bah! you'll have me twittering next :)
13:57 egonw nah... that's not something I would recommend to anyone...
13:57 egonw unless I hated him/her
13:57 egonw friendfeed.com is much nicer
13:57 gilleain I have a high tech notebook that uses a graphite drawing interface, on a compressed cellulose surface
13:58 egonw yes... as said: (electronic, or otherwise :)
13:58 egonw it's just a matter of actually using it...
13:58 egonw bookmarking via old fashing electronics is only a slightest bit faster
13:59 egonw so no worries about that
13:59 gilleain Well, the particular paper-based archive is at home, so I'll mail you jonalv if I have any insights…
14:00 egonw ha... yes, another disadvantage of delicious.com... it's always around :)
14:00 gilleain oh, and the conclusion I came to about custom progress-monitors was simple : you can't do it :(
14:00 jonalv What I want to do is run a javascript as a job
14:00 jonalv I won\t know how many ticks tha javascript will ned though
14:00 jonalv but each manager call can be a subjob
14:01 jonalv and I might know how many ticks those take so it would be nice to report that...
14:01 gilleain http://www.eclipse.org/articles/Art​icle-Progress-Monitors/article.html
14:01 zarah gilleain's link is also http://tinyurl.com/6pyuhb
14:02 gilleain that tutorial emphasised that if you don't know how long the job will take, you should use the IProgressMonitor.UNKNOWN
14:02 egonw we should really get in contact with some core eclipse developer and ask about this...
14:02 gilleain "So, first and foremost: do not guess on the number of work items. It’s a simple binary answer: either you know exactly how many things that will be processed…or you don’t know."
14:02 jonalv I know I have read that one...
14:02 gilleain Okey.
14:02 jonalv nothing in it about groups though right?
14:03 gilleain no, that's true.
14:03 gilleain but when deep-diving into the eclipse core, I noticed these ProgressGroups things.
14:04 gilleain What I think they are is like when you have multiple bars in one progressmoitor window
14:04 gilleain subtasks, yes?
14:04 jonalv that's sort of what I want yea
14:05 jonalv only the top one will nbe IProgressMonitor.UNKNOWN...
14:05 jonalv <jonalv> structuredb.subStructureSearch( "db", molecule.fromSmiles("C=C=C=O") ); takes
14:05 jonalv ages and it really needs a progressmonitor... :)                       [13:33]
14:05 jonalv <gilleain> hmm, sounds good.
14:05 jonalv <gilleain> I'm just backlogging : 1JR8, eh? That sounds like a large structure,
14:05 jonalv somehow.
14:05 jonalv <jonalv> yea :)
14:05 jonalv <jonalv> it was a pdb file... :)                                                [13:34]
14:05 jonalv <gilleain> hmmm. no, just a thiol oxidase, I must be thinking of something else.
14:06 jonalv <gilleain> really large are things like proteasomes, with chains A-Z,1-2 (or 26
14:06 jonalv chains, I suppose).                                                  [13:38]
14:06 jonalv <gilleain> or virus structures, of course
14:06 jonalv <jonalv> okey                                                                   [13:45]
14:06 gilleain wtf?
14:06 jonalv <egonw> jonalv: that's actually where that vflib patch comes in                 [13:46]
14:06 jonalv <jonalv> egonw: uhm what where?
14:06 jonalv <egonw> substructure search
14:06 jonalv <jonalv> what's the vflib patch?                                                [13:47]
14:06 jonalv <jonalv> egonw: you sort of lost me...                                          [13:48]
14:06 jonalv <egonw> different algorithm for substructure search
14:06 jonalv <egonw> much faster than the current algorithm
14:06 jonalv <jonalv> oh nice
14:06 gilleain time travel witchcraft!
14:06 jonalv <CIA-32> bioclipse: jonalv * r7972 /bioclipse2/branches/jonalv-RunJSCommandsAsJobs/:
14:06 jonalv Created branch for trying to get all js commandos to be run as jobs with the
14:06 jonalv posibility to connect to the progressmonitor                           [14:03]
14:06 jonalv *** gilleain (n=maclean@guest500.wtgc.org) has quit:                            [14:06]
14:06 egonw jonalv: ??
14:06 jonalv *** gilleain (n=maclean@guest500.wtgc.org) has joined channel #bioclipse        [14:11]
14:06 jonalv <edrin> jonalv: regarding the services view                                     [14:13]
14:06 jonalv <edrin> what is it supposed to do?
14:06 jonalv <jonalv> edrin: collect all services...                                         [14:14]
14:07 jonalv <edrin> sure
14:07 jonalv <jonalv> browse services
14:07 jonalv <edrin> and then?
14:07 jonalv <edrin> what can it do with it?
14:07 jonalv <jonalv> you drag something and drop it on the view and the service is run      [14:15]
14:07 jonalv <jonalv> for example
14:07 jonalv <edrin> no, this wont work
14:07 jonalv <jonalv> edrin: please explain
14:07 jonalv <jonalv> I think it's olas idea from the beginning...
14:07 jonalv <jonalv> I am just contnuing what he started...                                 [14:16]
14:07 jonalv <edrin> services are not always taking *any* string
14:07 jonalv <edrin> the input must be compatible with the service
14:07 jonalv <edrin> (service's function)                                                    [14:17]
14:07 jonalv <jonalv> yea but why is that a problem?
14:07 edrin ehm?
14:07 jonalv <egonw> ah... edrin, the view is supposed to check that
14:07 jonalv <jonalv> yea
14:07 jonalv <edrin> ah ok
14:07 jonalv <egonw> it will ensure that nothing bad is really send of to a service...
14:07 jonalv <edrin> ok
14:07 jonalv <edrin> and how is the result collected? is there a listview that collects/lists the
14:07 gilleain AARGH!
14:08 jonalv results?                                                                [14:18]
14:08 jonalv <egonw> don't exactly remember what Ola had in mind for that...                 [14:19]
14:08 jonalv <egonw> I guess virtual project folders
14:08 jonalv <jonalv> results should be opened in an editor or stored in the virtual
14:08 jonalv <jonalv> it not the result takes ages to get and the job has been moved to background
14:08 jonalv in which case it will just tell you that it ios finnisehed and then when you
14:08 jonalv click it will it open ineditor                                         [14:20]
14:08 jonalv <edrin> i think it would be great if the webservice's function would be reflected in a
14:08 jonalv "manager's" API. thus one could write javascripts against it.           [14:21]
14:08 jonalv <edrin> for example one could drag a function from the service view to the javascript
14:08 jonalv editor....                                                              [14:22]
14:08 jonalv <edrin> hm
14:08 jonalv <jonalv> oh nice idea                                                           [14:23]
14:08 jonalv <edrin> regarding javascript... the scripting console is not working for me since
14:08 jonalv some/several weeks..
14:08 egonw edrin: can you become op and kick jonalv?
14:08 jonalv <jonalv> masak++ is (slowly) working on a new javascript console                [14:24]
14:08 jonalv <edrin> jonalv: i think this is highly required... because using services in scripts
14:08 edrin ok
14:08 jonalv is nearly the same power then using in taverna workflow...
14:08 jonalv <jonalv> yea
14:08 jonalv <edrin> and in fact, i would use these
14:09 jonalv <jonalv> :)                                                                     [14:25]
14:09 jonalv <jonalv> does anyone know if subprogressmonitors can be visualised in some nice way?
14:09 jonalv [14:50]
14:09 jonalv <egonw> no, don't think so...                                                   [14:51]
14:09 egonw edrin: and while busy... please give me op rights too?
14:09 jonalv <egonw> would be really, really welcome...
14:09 jonalv <jonalv> perhaps I could start two works then..
14:09 jonalv <jonalv> jobs that is
14:09 jonalv <gilleain> I think there is such a thing as a ProgressGroup
14:09 jonalv <jonalv> gilleain: cool                                                         [14:52]
14:09 jonalv <jonalv> gilleain: where did you pick that up?
14:09 edrin will take some time
14:09 jonalv <gilleain> I dug through a lot of stuff about progress monitors when trying to make a
14:09 edrin from jabber
14:09 jonalv custom one.
14:09 jonalv <egonw> but that's still just plain text, right?
14:09 jonalv <jonalv> where can I read about it?
14:09 jonalv <gilleain> Ummm. mom
14:09 jonalv <gilleain> egonw : don't think so.                                              [14:53]
14:09 jonalv <gilleain> there were some tutorials, but I didn't bookmark them for some reason. I'm
14:09 jonalv crap at bookmarking.                                                 [14:54]
14:09 jonalv <egonw> funny... I was just the other day suggesting someone how important it is to
14:09 jonalv keep a lab notebook (electronic, or otherwise :)                        [14:55]
14:10 jonalv <jonalv> right, I must start doing that somehow.. :)                            [14:56]
14:10 jonalv <egonw> gilleain: I can very much recommend delicious.com
14:10 jonalv <egonw> and citeulike.org for papers
14:10 jonalv <gilleain> bah! you'll have me twittering next :)                               [14:57]
14:10 jonalv <egonw> nah... that's not something I would recommend to anyone...
14:10 jonalv <egonw> unless I hated him/her
14:10 was kicked by edrin: edrin
14:10 gilleain \o/
14:10 edrin and all this - over jabber :)
14:10 egonw edrin: tack :)
14:11 gilleain muti-tack
14:13 jonalv joined #bioclipse
14:14 egonw ha jonalv
14:14 egonw what happened?
14:14 jonalv egonw: you tell me
14:14 jonalv egonw: you kicked me... :(
14:14 egonw well, you pasted these lines:
14:14 egonw (hahahaha)
14:15 egonw yes, we kicked you, because you were flooding the channel with about 30 mins of chatting :)
14:15 jonalv huh?
14:15 jonalv I didn't mean to do that...
14:16 egonw http://colabti.org/irclogger/irclogg​er_log/bioclipse?date=2008-12-05,Fri
14:16 zarah egonw's link is also http://tinyurl.com/6r3wkv
14:16 jonalv I wonder how that happend...
14:16 egonw you started at 14:05
14:16 gilleain ending at 14:10
14:17 * egonw is trying to get drawing molecules from an empty widget going...
14:17 jonalv strange things...
14:17 jonalv anyway, seems like job groups is something else...
14:18 gilleain egonw: oh, really?
14:18 gilleain I'm trying to fix a bug with adding benzene to an empty canvas
14:18 egonw :)
14:19 egonw that sounds like the same bug...
14:19 egonw it's in adding the first atom...
14:19 gilleain also, I made a small program yesterday that connects a molecule editor to an nmr spectrum viewer
14:19 egonw ah... the SpecMol editor!
14:19 gilleain so that when you add atoms/bonds/rings, it creates a new spectrum
14:19 egonw excellent!
14:19 gilleain yeah, I suspect it's just like specmol :)
14:19 egonw that's very neat
14:20 egonw oh, just received a ping that Sam released a new JNI-InChI wrapper...
14:21 egonw with inchikey support
14:21 egonw and! support for macs!
14:21 gilleain \o/
14:24 egonw gilleain: I did some checking yesterday...
14:24 gilleain yas?
14:25 egonw jcp.addTom("C", Point2d) does the right thing...
14:25 egonw easily checked from the JS console :)
14:25 gilleain addTom?
14:25 gilleain = addToModel?
14:25 egonw jcp.addAtom("C", Point2d) does the right thing...
14:25 gilleain oh, addAtom, d'oh.
14:26 egonw js> jcp.zap()
14:26 egonw js> jcp.getModel().getAtomContainer()
14:26 egonw Molecule(18955858, AtomContainer(18955858))
14:26 egonw js> jcp.addAtom("C", jcp.newPoint2d(0,0))
14:26 egonw js> jcp.getModel().getAtomContainer()
14:26 egonw Molecule(18955858, AtomContainer(18955858, #A:1, Atom(13778707, S:C, 2D:[(0.0,
14:26 egonw 0.0)], AtomType(13778707, FC:0, NC:0, EV:0, Isotope(13778707, Element(13778707,
14:26 egonw S:C))))))
14:26 egonw so, it does add the atom
14:26 egonw and the coordinate
14:26 egonw however, the DrawBlaModule
14:26 gilleain but it doesn't display?
14:26 egonw does add an atom, but without coordinates...
14:26 egonw yes, it does show it...
14:27 egonw at 0,0 screen coordinates
14:27 egonw but it does show it :)
14:27 gilleain ah.
14:27 gilleain DrawBla is arvid's, I think.
14:27 gilleain But I can tak a look
14:27 egonw Gpox: ping...
14:28 gilleain No, wait, there is no DrawAtom module.
14:30 egonw there is AddAtomModule
14:30 egonw but don't spot an error there :(
14:31 gilleain no, it seems to be using (ultimately) the Atom(Point2d) constructor
14:31 egonw wihch should be fine...
14:31 egonw I can only imagine that there is no affine transformation when there are no atoms?
14:31 egonw so, it creates a null Point2d?
14:32 gilleain JCP does it right.
14:32 egonw actually... just found another nice artefact...
14:32 egonw I already have this first atom at 0,0
14:32 gilleain because my IntermediateRenderer does it right
14:32 egonw then I add a second using the draw mode
14:32 gilleain thanks to shk3++
14:32 egonw and it actually gives NaN, NaN coord :)
14:32 gilleain uh-oh
14:32 egonw gilleain: show off
14:32 gilleain well, stefan is a demanding customer :)
14:33 egonw shk3++
14:33 shk3 well, I know from old jcp where the tricky parts are
14:34 gilleain unfortunately, at the moment it means that for a cdk-client developer to use the renderer correctly they need to understand the internals
14:34 gilleain which would be me
14:35 gilleain (and presumably arvid, as he understands many of the problems)
14:35 gilleain I need to do things like add setFitToScreen(boolean) to the RendererModel
14:37 gilleain as for how to draw correctly, egonw, I don't know if this helps:
14:37 gilleain http://gilleain.tumblr.com/post/62593110
14:37 zarah gilleain's link is also http://tinyurl.com/5feedq
14:38 egonw a shame that this does not include the y-axis invert
14:38 gilleain indeed.
14:38 gilleain Arvid reminds me of that every now and then, and I forget again, sorry.
14:39 egonw :)
14:40 gilleain it's pretty important, I know, as the SDG implicitly assumes the correct coordinate system
14:40 gilleain so, generated molecules may not look right.
14:40 egonw also important... stereo chemistry gets inverted
14:40 egonw and toxins become flavours
14:40 egonw which is ok, but
14:40 egonw flavours become toxins :)
14:41 gilleain I don't think stereo gets inverted
14:41 egonw yes, inverting the y-axis inverts the stereochemistry
14:41 gilleain because it's a symbol (filled wedge vs dashed wedge)
14:41 gilleain it's not being flipped, it's rotated in the plane
14:42 egonw they are their mirror images!
14:42 egonw no, they are not rotated
14:42 jonalv ooopss...
14:42 jonalv actually that's rather bad...
14:42 egonw y points up instead of down, as in Java
14:42 gilleain yes, yes, I know that.
14:43 gilleain I need a test case for this, it's bugging me  :-/
14:43 gilleain grr.
14:43 gilleain I should get chirality/stereo right, if anything :(
14:44 egonw ok, I think I found one bug cause
14:45 egonw great text from this song: "you tragic waste of skin" :)
14:45 gilleain the bug is in song form?
14:45 gilleain that's unusual
14:45 egonw (Placebo: song to say goodbye)
14:46 egonw Gpox: I really need your help with this...
14:46 gilleain I'm listening to Billie Holiday, myself. But what is this bug you spake of?
14:47 jonalv egonw: isn't Gpox on vacation?
14:47 egonw not yet
14:47 egonw after today
14:47 egonw that's what I understood
14:47 jonalv so one or perhaps 2 hours... :)
14:47 egonw right :)
14:48 Gpox egonw: pong
14:48 egonw please help me with this bug...
14:49 egonw I'm getting NPEs all over the place...
14:49 egonw when I do:
14:49 egonw any existint MDL file
14:49 egonw in JS console:
14:49 egonw jcp.zap()
14:49 egonw then try to add a new atom with the mouse
14:50 egonw that does not create a 2D coordinate for the new atom...
14:50 egonw verify after trying to have added the atom with:
14:50 egonw jcp.getModel().getAtomContainer()
14:52 egonw I found this problem in the code:
14:52 egonw (commit being commited)
14:52 CIA-32 bioclipse: egonw * r7973 /bioclipse2/trunk/cdk-externals/trunk/​org.openscience.cdk.render/src/org/ope​nscience/cdk/renderer/Renderer.java: Fixed a NPE caused by no affine transformation define (e.g. when there are no atoms in the model)
14:58 egonw oh... let me try something
14:58 egonw ok, found a fix
14:58 egonw but does not fix enough...
14:59 egonw at least it is a start
15:00 CIA-32 bioclipse: egonw * r7974 /bioclipse2/trunk/cdk-externals/trunk/​org.openscience.cdk.render/src/org/ope​nscience/cdk/renderer/Renderer.java: Return (0,0) upon the exception
15:02 gilleain well look, why don't I make the IntermediateRenderer work like it should, and be AWT/SWT independent? Then you can try it out, and see if it looks right...
15:02 gilleain it may have been tweaked too much to be swing-jcp compliant, of course.
15:03 egonw yes, we should head that way...
15:03 egonw but not now...
15:03 gilleain ok
15:04 egonw let's see next week...
15:04 egonw ok, got to go offline now, for Sinterklaas...
15:04 egonw bbl
15:04 edrin what is a Sinterklaas
15:05 gilleain Santa claus
15:05 gilleain in dutch
15:05 jonalv only I thought that would be around chrsitmus
15:05 edrin ok
15:06 edrin we call it Nikolaus and he is coming the 6.
15:06 jonalv intresting
15:06 jonalv Isn't it the 24:th or 25:th in most parts of the world?
15:07 edrin no
15:07 jonalv in some parts at least right?
15:10 jonalv http://en.wikipedia.org/wiki/Santa_Claus
15:10 zarah jonalv's link is also http://tinyurl.com/hkpjr
15:10 jonalv it seems a complicated topic... :)
15:11 edrin well, http://en.wikipedia.org/wi​ki/Saint_NicholasNikolaus
15:11 zarah edrin's link is also http://tinyurl.com/6mhabl
15:17 CIA-32 bioclipse: jonalv * r7975 /bioclipse2/branches/jonalv-​RunJSCommandsAsJobs/plugins/ (5 files in 4 dirs): [jonalv-branch] First step, using different structuredb instances for jsconsole and gui accomplished
15:18 * jonalv afk
15:24 gilleain afk?
15:25 gilleain oh, away from keyboard. I'm not fluent in irc-ese.
15:29 jonalv &me is back
15:30 jonalv mm yohurt
15:56 egonw Santa Claus != Sinterklaas
15:58 egonw you would want to read the details from: http://en.wikipedia.org/wiki/Sinterklaas
15:58 zarah egonw's link is also http://tinyurl.com/yty82s
16:04 edrin egonw: is Sinterklaas == St. Nikolaus? i guess so because it's the 6. in germany
16:04 jonalv egonw: You wanna be my code reviewer + merger for my new Bioclipse branch? :)
16:35 egonw edrin: yes
16:35 egonw edrin: yes, the 6th is his birthday
16:35 egonw we celebrate at the eve before his birthday
16:35 egonw NL is large, so that leaves him enough time to vistit belgium and germany on the 6th :)
16:37 egonw jonalv: sure
16:37 egonw email me with details
16:37 egonw or file a bug report with pz
17:36 ilbot2 joined #bioclipse
17:36 Topic for #bioclipseis now An open source workbench for chemo- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 alpha released! See http://bioclipse.blogspot.com/
18:11 CIA-32 bioclipse: jonalv * r7983 /bioclipse2/branches/jonalv-​RunJSCommandsAsJobs/plugins/ (7 files in 5 dirs): It works! Further testing is needed but then there will come a blog post!
18:11 jonalv yey great success
18:11 jonalv now afk
18:17 edrin left #bioclipse
18:39 gilleain joined #bioclipse
20:17 egonw moin
20:17 zarah hi egonw
20:35 CIA-32 bioclipse: egonw * r7984 /bioclipse2/trunk/cdk-externals/trunk/ (9 files in 5 dirs): Synchronized with CDK's jchempaint-primary branch (rev 13493)
20:51 egonw Gpox: do you happen to be around?
21:04 Gpox ah yes, forgott to turn on the computer
21:07 Gpox egonw: pong
21:07 egonw hi
21:07 zarah hi egonw
21:07 egonw I saw some of your commits...
21:07 egonw but don't think you managed to fix the draw-a-molecule-after-zap(), or did you?
21:07 egonw it's not working for me at least...
21:07 egonw and now debug stepping through the code
21:08 Gpox well it sorta worked for me
21:08 egonw really?
21:08 egonw I now do get a first atom...
21:08 egonw but at the top left of the window
21:08 egonw after which I cannot do anything with it...
21:09 egonw such as add a bond to it...
21:09 Gpox now it should make a space 2x2 centert around 0,0 when the atomcontainer is empty or only one atom
21:09 egonw not seeing that :(
21:10 egonw which patch is doing that?
21:11 Gpox ah taht is in jchempaint-primary@13493
21:11 egonw mmm
21:12 egonw that should be included in the new cdk-eclipse export I just made:
21:12 egonw [21:35:43] <CIA-32> bioclipse: egonw * r7984 /bioclipse2/trunk/cdk-externals/trunk/ (9 files in 5 dirs): Synchronized with CDK's jchempaint-primary branch (rev 13493)
21:12 egonw :(
21:14 * egonw is checking that the complete patch made it into that update...
21:18 egonw yes, seems so :(
21:18 egonw and bc2 is up to date too :(
21:22 egonw no, does not seem to work :(
21:25 egonw OK, rebooted eclipse
21:26 egonw maybe that helps
21:26 egonw damn, no :(
21:26 egonw I get these coordinates: NaN, NaN
21:29 egonw no, it's not Egon-proof yet
21:31 egonw OK, going offline now...
21:31 egonw Gpox: have a nice holiday!
21:31 egonw Next week, the 11th... hack, settlers, dinner at my place
21:32 egonw I hope you can make it...
21:32 egonw (if you rather skip the hack part of it, that's fine too, it's your holiday after all :)
21:50 edrin joined #bioclipse

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